diff --git a/.Rbuildignore b/.Rbuildignore
index 0496b081c..3f0c01c7d 100755
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -12,6 +12,7 @@
 ^codecov\.yml$
 ^cran-comments\.md$
 ^CRAN-RELEASE$
+^\.github$
 ^doc$
 ^docs$
 ^git_.*\.sh$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 000000000..8a0497696
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,124 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+#                                                                      #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
+# ==================================================================== #
+
+on:
+  push:
+    branches:
+      - premaster
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: windows-latest, r: 'oldrel'}
+          - {os: macOS-latest,   r: 'oldrel'}
+          - {os: ubuntu-16.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: windows-latest, r: 'devel'}
+          - {os: macOS-latest,   r: 'devel'}
+          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          # - {os: windows-latest, r: '3.6'}
+          # - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          # - {os: ubuntu-16.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          # - {os: ubuntu-16.04,   r: '3.3',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml
new file mode 100644
index 000000000..425e90867
--- /dev/null
+++ b/.github/workflows/codecovr.yaml
@@ -0,0 +1,68 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+#                                                                      #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
+# ==================================================================== #
+
+on:
+  push:
+    branches:
+      - premaster
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml
new file mode 100644
index 000000000..c16fa4766
--- /dev/null
+++ b/.github/workflows/lintr.yaml
@@ -0,0 +1,66 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+#                                                                      #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
+# ==================================================================== #
+
+on:
+  push:
+    branches:
+      - premaster
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("lintr")
+        shell: Rscript {0}
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
diff --git a/.gitlab-ci.R b/.gitlab-ci.R
deleted file mode 100644
index 53bf9273f..000000000
--- a/.gitlab-ci.R
+++ /dev/null
@@ -1,54 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# Antimicrobial Resistance (AMR) Analysis                              #
-#                                                                      #
-# SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
-#                                                                      #
-# LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
-#                                                                      #
-# This R package is free software; you can freely use and distribute   #
-# it for both personal and commercial purposes under the terms of the  #
-# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# the Free Software Foundation.                                        #
-#                                                                      #
-# We created this package for both routine data analysis and academic  #
-# research and it was publicly released in the hope that it will be    #
-# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
-# ==================================================================== #
-
-install_if_needed <- function(pkg, repos, quiet) {
-  package_path <- find.package(pkg, quiet = quiet)
-  if (length(package_path) == 0) {
-    message("NOTE: pkg ", pkg, " missing, installing...")
-    install.packages(pkg, repos = repos, quiet = quiet)
-  }
-}
-
-gl_update_pkg_all <- function(repos = "https://cran.rstudio.com",
-                              quiet = TRUE,
-                              install_pkgdown = FALSE,
-                              install_lintr = FALSE) {
-  # update existing
-  update.packages(ask = FALSE, repos = repos, quiet = quiet)
-
-  install_if_needed(pkg = "devtools", repos = repos, quiet = quiet)
-  if (install_pkgdown == TRUE) {
-    install_if_needed(pkg = "pkgdown", repos = repos, quiet = quiet)
-  }
-  if (install_lintr == TRUE) {
-    install_if_needed(pkg = "lintr", repos = repos, quiet = quiet)
-  }
-  install_if_needed(pkg = "cleaner", repos = repos, quiet = quiet)
-  
-  devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)
-
-  cat("INSTALLED:\n")
-  instld <- as.data.frame(installed.packages())
-  rownames(instld) <- NULL
-  print(instld[, c("Package", "Version")])
-
-  return(invisible(TRUE))
-}
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
deleted file mode 100644
index ddc701037..000000000
--- a/.gitlab-ci.yml
+++ /dev/null
@@ -1,190 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# Antimicrobial Resistance (AMR) Analysis                              #
-#                                                                      #
-# SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
-#                                                                      #
-# LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
-#                                                                      #
-# This R package is free software; you can freely use and distribute   #
-# it for both personal and commercial purposes under the terms of the  #
-# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# the Free Software Foundation.                                        #
-#                                                                      #
-# We created this package for both routine data analysis and academic  #
-# research and it was publicly released in the hope that it will be    #
-# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
-# ==================================================================== #
-
-# to do a full CRAN check with R-Hub:
-# chck <- rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name'])
-
-stages:
-  - test
-  - check
-  - lint
-  - website
-  - coverage
-  
-image: rocker/r-base
-
-before_script:
-  - apt-get update -qq  --allow-releaseinfo-change
-  # install dependencies for packages
-  - apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev > /dev/null
-  # recent pandoc
-  - wget --quiet https://github.com/jgm/pandoc/releases/download/2.9.2.1/pandoc-2.9.2.1-1-amd64.deb
-  - dpkg -i pandoc*.deb
-  - rm pandoc*.deb
-  # set R system language
-  - echo "LC_ALL=en_US.UTF-8" >> /etc/environment
-  - echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
-  - echo "LANG=en_US.UTF-8" > /etc/locale.conf
-  - locale-gen
-  # cache R packages
-  - mkdir -p installed_deps
-  - echo 'R_LIBS="installed_deps"' > .Renviron
-  - echo 'R_LIBS_USER="installed_deps"' >> .Renviron
-  - echo 'R_LIBS_SITE="installed_deps"' >> .Renviron
-  # set language
-  - echo 'LANGUAGE="en_US.utf8"' >> .Renviron
-  - echo 'LANG="en_US.utf8"' >> .Renviron
-  - echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
-
-# ---- TEST
-
-R-release_test:
-  stage: test
-  when: always
-  allow_failure: false
-  script:
-    - Rscript -e 'sessionInfo()'
-    # install missing and outdated packages
-    - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE,  install_lintr = TRUE)'
-    - Rscript -e 'devtools::test(stop_on_failure = FALSE)'
-  cache:
-    key: release
-    paths:
-      - installed_deps/
-      
-R-devel_test:
-  stage: test
-  when: always
-  image: rocker/r-devel
-  allow_failure: false
-  script:
-    - Rscriptdevel -e 'sessionInfo()'
-    # install missing and outdated packages
-    - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE,  install_lintr = TRUE)'
-    - Rscriptdevel -e 'devtools::test(stop_on_failure = FALSE)'
-  cache:
-    key: devel
-    paths:
-      - installed_deps/
-      
-# ---- CHECK
-      
-R-release:
-  stage: check
-  when: on_success
-  allow_failure: true
-  script:
-    - Rscript -e 'sessionInfo()'
-    # install missing and outdated packages
-    - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE,  install_lintr = TRUE)'
-    # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
-    - rm -rf vignettes
-    - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
-    # build package
-    - R CMD build . --no-build-vignettes --no-manual
-    - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-    - Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
-    - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
-  artifacts:
-    when: always
-    paths:
-      - '*.Rcheck/*'
-    expire_in: '1 month'
-  cache:
-    key: release
-    paths:
-      - installed_deps/
-
-R-devel:
-  stage: check
-  when: on_success
-  image: rocker/r-devel
-  allow_failure: true
-  script:
-    - Rscriptdevel -e 'sessionInfo()'
-    # install missing and outdated packages
-    - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)'
-    # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
-    - rm -rf vignettes
-    - Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
-    # build package
-    - Rdevel CMD build . --no-build-vignettes --no-manual
-    - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-    - Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
-    - Rdevel CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
-  artifacts:
-    when: always
-    paths:
-      - '*.Rcheck/*'
-    expire_in: '1 month'
-  cache:
-    key: devel
-    paths:
-      - installed_deps/
-      
-# ---- OTHER
-
-lintr:
-  stage: lint
-  allow_failure: true
-  when: always
-  only:
-    - premaster
-    - master
-  script:
-    # check all syntax with lintr
-    - Rscript -e 'lintr::lint_package(exclusions = list("R/aa_helper_functions_dplyr.R"))'
-  cache:
-    key: release
-    paths:
-      - installed_deps/
-    policy: pull # no uploading after run
-
-pages:
-  stage: website
-  allow_failure: true
-  when: always
-  only:
-    - master
-  script:
-    - mv docs public
-  artifacts:
-    paths:
-      - public
-
-codecovr:
-  stage: coverage
-  allow_failure: true
-  when: always
-  only:
-    - premaster
-    - master
-  script:
-    - apt-get install --yes git
-    # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
-    # Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages
-    - Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
-  coverage: '/Code coverage: \d+\.\d+/'
-  cache:
-    key: release
-    paths:
-      - installed_deps/
-    policy: pull # no uploading after run
diff --git a/DESCRIPTION b/DESCRIPTION
index 272b11412..252f83332 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.2.0.9025
-Date: 2020-07-03
+Version: 1.2.0.9026
+Date: 2020-07-08
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -47,10 +47,10 @@ Suggests:
     tidyr,
     utils
 VignetteBuilder: knitr,rmarkdown
-URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
-BugReports: https://gitlab.com/msberends/AMR/issues
+URL: https://msberends.github.io/AMR, https://github.com/msberends/AMR
+BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
diff --git a/NEWS.md b/NEWS.md
index 2c71df03f..6e1838911 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
-# AMR 1.2.0.9025
-## <small>Last updated: 03-Jul-2020</small>
+# AMR 1.2.0.9026
+## <small>Last updated: 08-Jul-2020</small>
 
 ### New
 * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@@ -22,7 +22,7 @@
 * Improvements for `susceptibility()` and `resistance()` and all `count_*()`, `proportion_*()` functions:
   * 95% speed improvement (!) by using other base R functions for calculation
   * Using unexisting columns wil now return an error instead of dropping them silently
-  * Using variables for column names (as well as `dplyr::all_of()`) now works again
+  * Using variables for column names (as well as selectors like `dplyr::all_of()`) now works again
 * Improvements for `as.ab()`:
   * Dramatic improvement of the algorithm behind `as.ab()`, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more
   * Added progress bar
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index 4898443b5..9751fb9f4 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 # functions from dplyr, will perhaps become poorman
@@ -77,18 +77,22 @@ check_dataset_integrity <- function() {
                                   "class", "order", "family", "genus", 
                                   "species", "subspecies", "rank",
                                   "species_id", "source", "ref", "prevalence") %in% colnames(microorganisms),
-                                na.rm = TRUE) & NROW(microorganisms) == NROW(MO_lookup)
+                                na.rm = TRUE)
     check_antibiotics <- all(c("ab", "atc", "cid", "name", "group", 
                                "atc_group1", "atc_group2", "abbreviations",
                                "synonyms", "oral_ddd", "oral_units", 
                                "iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
                              na.rm = TRUE)
   }, error = function(e)
-    stop('Please use the command \'library("AMR")\' before using this function, to load the required reference data.', call. = FALSE)
+    stop_('please use the command \'library("AMR")\' before using this function, to load the required reference data.', call = FALSE)
   )
-  if (!check_microorganisms | !check_antibiotics) {
-    stop("Data set `microorganisms` or data set `antibiotics` is overwritten by your global environment and prevents the AMR package from working correctly. Please rename your object before using this function.", call. = FALSE)
-  }
+  data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
+  data_in_globalenv <- ls(envir = globalenv())
+  overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
+  stop_if(length(overwritten) > 0,
+          "the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
+          paste0("'", overwritten, "'", collapse = ", "),
+          ".\nPlease rename your object before using this function.", call = FALSE)
   invisible(TRUE)
 }
 
@@ -198,7 +202,9 @@ stop_ifnot_installed <- function(package) {
 
 import_fn <- function(name, pkg) {
   stop_ifnot_installed(pkg)
-  get(name, envir = asNamespace(pkg))
+  tryCatch(
+    get(name, envir = asNamespace(pkg)),
+    error = function(e) stop_("an error occurred in import_fn() while using this function", call = FALSE))
 }
 
 stop_ <- function(..., call = TRUE) {
diff --git a/R/aa_helper_functions_dplyr.R b/R/aa_helper_functions_dplyr.R
index 32315def0..1c57c3983 100644
--- a/R/aa_helper_functions_dplyr.R
+++ b/R/aa_helper_functions_dplyr.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 # ------------------------------------------------
diff --git a/R/ab.R b/R/ab.R
index 624dc57cd..72364e170 100755
--- a/R/ab.R
+++ b/R/ab.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Transform to antibiotic ID
diff --git a/R/ab_class_selectors.R b/R/ab_class_selectors.R
index b60f66c67..eb6c46c8d 100644
--- a/R/ab_class_selectors.R
+++ b/R/ab_class_selectors.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Antibiotic class selectors
diff --git a/R/ab_from_text.R b/R/ab_from_text.R
index 0e0f1ed59..bb36b6a67 100644
--- a/R/ab_from_text.R
+++ b/R/ab_from_text.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Retrieve antimicrobial drug names and doses from clinical text
diff --git a/R/ab_property.R b/R/ab_property.R
index 3b04f11f7..5bec0b325 100644
--- a/R/ab_property.R
+++ b/R/ab_property.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Property of an antibiotic
diff --git a/R/age.R b/R/age.R
index f8298c9a3..953d689d7 100755
--- a/R/age.R
+++ b/R/age.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Age in years of individuals
diff --git a/R/amr.R b/R/amr.R
index d36860124..9001b3148 100644
--- a/R/amr.R
+++ b/R/amr.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' The `AMR` Package
@@ -45,7 +45,7 @@
 #' - Principal component analysis for AMR
 
 #' @section Read more on our website!:
-#' On our website <https://msberends.gitlab.io/AMR> you can find [a comprehensive tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html).
+#' On our website <https://msberends.github.io/AMR> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html).
 #' @section Contact Us:
 #' For suggestions, comments or questions, please contact us at:
 #'
@@ -59,7 +59,7 @@
 #' The Netherlands
 #'
 #' If you have found a bug, please file a new issue at: \cr
-#' <https://gitlab.com/msberends/AMR/issues>
+#' <https://github.com/msberends/AMR/issues>
 #' @name AMR
 #' @rdname AMR
 NULL
diff --git a/R/atc_online.R b/R/atc_online.R
index 735a08b23..f5133348b 100644
--- a/R/atc_online.R
+++ b/R/atc_online.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Get ATC properties from WHOCC website
diff --git a/R/availability.R b/R/availability.R
index c4e784390..091565861 100644
--- a/R/availability.R
+++ b/R/availability.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Check availability of columns
diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R
index 5647b7998..0d7aca381 100644
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Determine bug-drug combinations
diff --git a/R/catalogue_of_life.R b/R/catalogue_of_life.R
index 9fc0b5bbf..53f666bee 100755
--- a/R/catalogue_of_life.R
+++ b/R/catalogue_of_life.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' The Catalogue of Life
@@ -38,7 +38,7 @@
 #'
 #' The Catalogue of Life (<http://www.catalogueoflife.org>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
 #'
-#' The syntax used to transform the original data to a cleansed R format, can be found here: <https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R>.
+#' The syntax used to transform the original data to a cleansed R format, can be found here: <https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R>.
 #' @inheritSection AMR Read more on our website!
 #' @name catalogue_of_life
 #' @rdname catalogue_of_life
diff --git a/R/count.R b/R/count.R
index 3b4603e6e..86088ba3d 100755
--- a/R/count.R
+++ b/R/count.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Count available isolates
diff --git a/R/data.R b/R/data.R
index 07b242910..a069744b7 100755
--- a/R/data.R
+++ b/R/data.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Data sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` antimicrobials
@@ -56,13 +56,13 @@
 #' ### Direct download
 #' These data sets are available as 'flat files' for use even without R - you can find the files here:
 #' 
-#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt>
-#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt>
+#' * <https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt>
+#' * <https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt>
 #' 
 #' Files in R format (with preserved data structure) can be found here:
 #' 
-#' * <https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda>
-#' * <https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda>
+#' * <https://github.com/msberends/AMR/raw/master/data/antibiotics.rda>
+#' * <https://github.com/msberends/AMR/raw/master/data/antivirals.rda>
 #' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/>
 #'
 #' WHONET 2019 software: <http://www.whonet.org/software.html>
@@ -102,11 +102,11 @@
 #' ### Direct download
 #' This data set is available as 'flat file' for use even without R - you can find the file here:
 #' 
-#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt>
+#' * <https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt>
 #' 
 #' The file in R format (with preserved data structure) can be found here:
 #' 
-#' * <https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda>
+#' * <https://github.com/msberends/AMR/raw/master/data/microorganisms.rda>
 #' @section About the records from DSMZ (see source):
 #' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
 #'
@@ -157,7 +157,7 @@ catalogue_of_life <- list(
 
 #' Data set with `r format(nrow(example_isolates), big.mark = ",")` example isolates
 #'
-#' A data set containing `r format(nrow(example_isolates), big.mark = ",")` microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read [the tutorial on our website](https://msberends.gitlab.io/AMR/articles/AMR.html).
+#' A data set containing `r format(nrow(example_isolates), big.mark = ",")` microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read [the tutorial on our website](https://msberends.github.io/AMR/articles/AMR.html).
 #' @format A [`data.frame`] with `r format(nrow(example_isolates), big.mark = ",")` observations and `r ncol(example_isolates)` variables:
 #' - `date`\cr date of receipt at the laboratory
 #' - `hospital_id`\cr ID of the hospital, from A to D
@@ -231,6 +231,6 @@ catalogue_of_life <- list(
 #' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
 #' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
 #' - `uti`\cr A logical value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
-#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
+#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
 #' @inheritSection AMR Read more on our website!
 "rsi_translation"
diff --git a/R/deprecated.R b/R/deprecated.R
index eb6208084..d169a00e8 100755
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Deprecated functions
diff --git a/R/disk.R b/R/disk.R
index b8b403cb2..617d19eb0 100644
--- a/R/disk.R
+++ b/R/disk.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Class 'disk'
diff --git a/R/eucast_rules.R b/R/eucast_rules.R
index 403df6a45..68373aa56 100755
--- a/R/eucast_rules.R
+++ b/R/eucast_rules.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 # global variables
@@ -52,7 +52,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #' 
 #' These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use `eucast_rules(..., rules = "all")`, or set the default behaviour of the `[eucast_rules()]` function with `options(AMR.eucast_rules = "all")` (or any other valid input value(s) to the `rules` parameter).
 #'
-#' The file containing all EUCAST rules is located here: <https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
+#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
 #'
 #' @section Antibiotics:
 #' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
diff --git a/R/filter_ab_class.R b/R/filter_ab_class.R
index 972cb7566..b37ea9a09 100644
--- a/R/filter_ab_class.R
+++ b/R/filter_ab_class.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Filter isolates on result in antimicrobial class
diff --git a/R/first_isolate.R b/R/first_isolate.R
index 5901cc01c..943217a8a 100755
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Determine first (weighted) isolates
diff --git a/R/g.test.R b/R/g.test.R
index c8d2f7d55..b9f415716 100755
--- a/R/g.test.R
+++ b/R/g.test.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' *G*-test for Count Data
diff --git a/R/ggplot_pca.R b/R/ggplot_pca.R
index 9aa91a99e..4f9e7c601 100755
--- a/R/ggplot_pca.R
+++ b/R/ggplot_pca.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' PCA biplot with `ggplot2`
diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R
index 6725dda77..e6b00af86 100755
--- a/R/ggplot_rsi.R
+++ b/R/ggplot_rsi.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,12 +16,12 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' AMR plots with `ggplot2`
 #'
-#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal [ggplot2][ggplot2::ggplot()] functions.
+#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on [ggplot2][ggplot2::ggplot()] functions.
 #' @inheritSection lifecycle Maturing lifecycle
 #' @param data a [`data.frame`] with column(s) of class [`rsi`] (see [as.rsi()])
 #' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
@@ -49,13 +49,13 @@
 #'
 #' [facet_rsi()] creates 2d plots (at default based on S/I/R) using [ggplot2::facet_wrap()].
 #'
-#' [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_continuous()].
+#' [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_y_continuous()].
 #'
-#' [scale_rsi_colours()] sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using [ggplot2::scale_brewer()].
+#' [scale_rsi_colours()] sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using [ggplot2::scale_fill_manual()].
 #'
 #' [theme_rsi()] is a [ggplot2 theme][[ggplot2::theme()] with minimal distraction.
 #'
-#' [labels_rsi_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()]
+#' [labels_rsi_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()].
 #'
 #' [ggplot_rsi()] is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (`%>%`). See Examples.
 #' @rdname ggplot_rsi
diff --git a/R/globals.R b/R/globals.R
index 64e4e9c68..4adde02de 100755
--- a/R/globals.R
+++ b/R/globals.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 globalVariables(c(".",
diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R
index e9877b67a..964b15fd9 100755
--- a/R/guess_ab_col.R
+++ b/R/guess_ab_col.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Guess antibiotic column
diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R
index 93efac13e..3afd9224d 100755
--- a/R/join_microorganisms.R
+++ b/R/join_microorganisms.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Join [microorganisms] to a data set
diff --git a/R/key_antibiotics.R b/R/key_antibiotics.R
index 2c04fd441..967ed3386 100755
--- a/R/key_antibiotics.R
+++ b/R/key_antibiotics.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Key antibiotics for first *weighted* isolates
diff --git a/R/kurtosis.R b/R/kurtosis.R
index 40c2c16da..a50fadd80 100755
--- a/R/kurtosis.R
+++ b/R/kurtosis.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Kurtosis of the sample
diff --git a/R/lifecycle.R b/R/lifecycle.R
index 62c0f915e..1a8a2664a 100644
--- a/R/lifecycle.R
+++ b/R/lifecycle.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 ###############
@@ -35,7 +35,7 @@
 #' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this `AMR` package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
 #' @section Maturing lifecycle:
 #' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome [to suggest changes at our repository](https://gitlab.com/msberends/AMR/-/issues) or [write us an email (see section 'Contact Us')][AMR::AMR].
+#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome [to suggest changes at our repository](https://github.com/msberends/AMR/issues) or [write us an email (see section 'Contact Us')][AMR::AMR].
 #' @section Stable lifecycle:
 #' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
diff --git a/R/like.R b/R/like.R
index 87267d119..8b6c13de8 100755
--- a/R/like.R
+++ b/R/like.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Pattern Matching
diff --git a/R/mdro.R b/R/mdro.R
index 45520ecba..01835ad61 100755
--- a/R/mdro.R
+++ b/R/mdro.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Determine multidrug-resistant organisms (MDRO)
@@ -46,7 +46,7 @@
 #' - `guideline = "BRMO"`\cr
 #'   The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" ([link](https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH))
 #'
-#' Please suggest your own (country-specific) guidelines by letting us know: <https://gitlab.com/msberends/AMR/issues/new>.
+#' Please suggest your own (country-specific) guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>.
 #' 
 #' **Note:** Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu *et al.* in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this [mdro()] function makes sure that results from before 2016 and after 2016 are identical.
 #' @inheritSection as.rsi Interpretation of R and S/I
diff --git a/R/mic.R b/R/mic.R
index 14d95c63e..2f4939510 100755
--- a/R/mic.R
+++ b/R/mic.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Class 'mic'
diff --git a/R/mo.R b/R/mo.R
index 17b7a6795..98ac0c0eb 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Transform to microorganism ID
diff --git a/R/mo_property.R b/R/mo_property.R
index ee5fb51d4..83db22520 100755
--- a/R/mo_property.R
+++ b/R/mo_property.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Property of a microorganism
diff --git a/R/mo_source.R b/R/mo_source.R
index 8d93f3b5c..6a736b843 100644
--- a/R/mo_source.R
+++ b/R/mo_source.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' User-defined reference data set for microorganisms
diff --git a/R/p_symbol.R b/R/p_symbol.R
index b95d86a61..4254d15c1 100755
--- a/R/p_symbol.R
+++ b/R/p_symbol.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Symbol of a p-value
diff --git a/R/pca.R b/R/pca.R
index 86e17321b..9860b399e 100755
--- a/R/pca.R
+++ b/R/pca.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Principal Component Analysis (for AMR)
diff --git a/R/proportion.R b/R/proportion.R
index 5392b2d13..fac190a5c 100755
--- a/R/proportion.R
+++ b/R/proportion.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Calculate microbial resistance
diff --git a/R/resistance_predict.R b/R/resistance_predict.R
index 8022e34b1..1a7bef030 100755
--- a/R/resistance_predict.R
+++ b/R/resistance_predict.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Predict antimicrobial resistance
diff --git a/R/rsi.R b/R/rsi.R
index 6ff21c6cd..010ab632a 100755
--- a/R/rsi.R
+++ b/R/rsi.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Class 'rsi'
@@ -37,7 +37,7 @@
 #' 
 #' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline. 
 #' 
-#' The repository of this package [contains a machine readable version](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This **allows for easy implementation of these rules in laboratory information systems (LIS)**.
+#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This **allows for easy implementation of these rules in laboratory information systems (LIS)**.
 #'
 #' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
 #'
diff --git a/R/rsi_calc.R b/R/rsi_calc.R
index c92d9ba0d..dfc7acdbc 100755
--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 dots2vars <- function(...) {
diff --git a/R/rsi_df.R b/R/rsi_df.R
index e2af8191f..2dc707ece 100644
--- a/R/rsi_df.R
+++ b/R/rsi_df.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' @rdname proportion 
diff --git a/R/skewness.R b/R/skewness.R
index 455de80cd..aea1e6aa1 100755
--- a/R/skewness.R
+++ b/R/skewness.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Skewness of the sample
diff --git a/R/translate.R b/R/translate.R
index 70be53d15..f57d47045 100755
--- a/R/translate.R
+++ b/R/translate.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,18 +16,18 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' Translate strings from AMR package
 #'
 #' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
 #' @inheritSection lifecycle Stable lifecycle
-#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv>.
+#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv>.
 #'
-#' Currently supported languages are (besides English): `r paste(sort(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% unique(AMR:::translations_file$lang)), "Name"])), collapse = ", ")`. Not all these languages currently have translations available for all antimicrobial agents and colloquial microorganism names. 
+#' Currently supported languages are (besides English): `r paste(sort(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% unique(AMR:::translations_file$lang)), "Name"])), collapse = ", ")`. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names. 
 #'
-#' Please suggest your own translations [by creating a new issue on our repository](https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion).
+#' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
 #'
 #' This file will be read by all functions where a translated output can be desired, like all [mo_property()] functions ([mo_name()], [mo_gramstain()], [mo_type()], etc.).
 #'
@@ -113,9 +113,9 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
              paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
              call = FALSE)
   
-  df_trans <- df_trans %>% subset(lang == language)
+  df_trans <- subset(df_trans, lang == language)
   if (only_unknown == TRUE) {
-    df_trans <- df_trans %>% subset(pattern %like% "unknown")
+    df_trans <- subset(df_trans, pattern %like% "unknown")
   }
   
   # default case sensitive if value if 'ignore.case' is missing:
@@ -126,7 +126,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
   # check if text to look for is in one of the patterns
   any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
                                    error = function(e) {
-                                     warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
+                                     warning("Translation not possible. Please open an issue on GitLab (https://github.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
                                      return(FALSE)
                                    })
   if (NROW(df_trans) == 0 | !any_form_in_patterns) {
diff --git a/R/whocc.R b/R/whocc.R
index 6b8e2d0b8..c192064ab 100755
--- a/R/whocc.R
+++ b/R/whocc.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 #' WHOCC: WHO Collaborating Centre for Drug Statistics Methodology
diff --git a/R/zzz.R b/R/zzz.R
index fc94f4d38..528e7f3a6 100755
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 .onLoad <- function(libname, pkgname) {
diff --git a/README.md b/README.md
index d17b51112..6f6dfa6dd 100755
--- a/README.md
+++ b/README.md
@@ -3,12 +3,12 @@
 # `AMR` (for R)
 <img src="man/figures/logo.png" align="right" height="120px" />
 
-This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.gitlab.io/AMR](https://msberends.gitlab.io/AMR) to read about this package.
+This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR](https://msberends.github.io/AMR) to read about this package.
 
-*NOTE: this source code is on GitLab (https://gitlab.com/msberends/AMR) and GitHub (https://github.com/msberends/AMR).*
+*NOTE: this source code is on GitHub (https://github.com/msberends/AMR) and GitLab (https://gitlab.com/msberends/AMR).*
 
 ### How to get this package
-Please see [our website](https://msberends.gitlab.io/AMR/#get-this-package).
+Please see [our website](https://msberends.github.io/AMR/#get-this-package).
 
 ### Copyright
 
diff --git a/_pkgdown.yml b/_pkgdown.yml
index b14fec84c..abde494b1 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,11 +16,11 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 title: "AMR (for R)"
-url: "https://msberends.gitlab.io/AMR"
+url: "https://msberends.github.io/AMR"
 
 development:
   mode: "release" # improves indexing by search engines
@@ -79,8 +79,8 @@ navbar:
       href: "news/"
   right:
     - text: "Source Code"
-      icon: "fab fa-gitlab"
-      href: "https://gitlab.com/msberends/AMR"
+      icon: "fab fa-github"
+      href: "https://github.com/msberends/AMR"
     - text: "Licence"
       icon: "fa-book"
       href: "LICENSE-text.html"
diff --git a/appveyor.yml b/appveyor.yml
deleted file mode 100644
index 44b4e0169..000000000
--- a/appveyor.yml
+++ /dev/null
@@ -1,81 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# Antimicrobial Resistance (AMR) Analysis                              #
-#                                                                      #
-# SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
-#                                                                      #
-# LICENCE                                                              #
-# (c) 2018-2020 Berends MS, Luz CF et al.                              #
-#                                                                      #
-# This R package is free software; you can freely use and distribute   #
-# it for both personal and commercial purposes under the terms of the  #
-# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# the Free Software Foundation.                                        #
-#                                                                      #
-# We created this package for both routine data analysis and academic  #
-# research and it was publicly released in the hope that it will be    #
-# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
-# ==================================================================== #
-
-# Download script file from this GitLab repo
-init:
-  ps: |
-        $ErrorActionPreference = "Stop"
-        Invoke-WebRequest https://gitlab.com/msberends/AMR/raw/premaster/tests/appveyor/appveyor_tool.ps1 -OutFile "..\appveyor-tool.ps1"
-        Import-Module '..\appveyor-tool.ps1'
-
-install:
-  ps: Bootstrap
-
-cache:
-  - C:\RLibrary
-
-# Adapt as necessary starting from here
-
-environment:
-  R_ARCH: x64
-  GCC_PATH: mingw_64
-  WARNINGS_ARE_ERRORS: 1
-  PKGTYPE: both
-  USE_RTOOLS: true
-
-  matrix:
-  - R_VERSION: oldrel
-  - R_VERSION: release
-  - R_VERSION: devel
-
-matrix:
-  allow_failures:
-  - R_VERSION: "devel"
-  
-build_script:
-  # - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
-  - travis-tool.sh install_deps
-
-test_script:
-  - travis-tool.sh run_tests
-
-on_failure:
-  - 7z a failure.zip *.Rcheck\*
-  - appveyor PushArtifact failure.zip
-
-artifacts:
-  - path: '*.Rcheck\**\*.log'
-    name: Logs
-
-  - path: '*.Rcheck\**\*.out'
-    name: Logs
-
-  - path: '*.Rcheck\**\*.fail'
-    name: Logs
-
-  - path: '*.Rcheck\**\*.Rout'
-    name: Logs
-
-  - path: '\*_*.tar.gz'
-    name: Bits
-
-  - path: '\*_*.zip'
-    name: Bits
diff --git a/codecov.yml b/codecov.yml
index 765dd5a9f..6859c06eb 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 codecov:
diff --git a/cran-comments.md b/cran-comments.md
index 5652aa725..8b4439e19 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,3 +1,3 @@
 * For this specific version, nothing to mention.
 
-* Since version 0.3.0, CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.
+* Since version 0.3.0 (2018-08-14), CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.
diff --git a/data-raw/github_preview.png b/data-raw/github_preview.png
new file mode 100644
index 000000000..0feb5c9d4
Binary files /dev/null and b/data-raw/github_preview.png differ
diff --git a/data-raw/github_preview.psd b/data-raw/github_preview.psd
new file mode 100644
index 000000000..985ac64ec
Binary files /dev/null and b/data-raw/github_preview.psd differ
diff --git a/data-raw/microorganisms.txt b/data-raw/microorganisms.txt
index 32009e555..17dfbedea 100644
--- a/data-raw/microorganisms.txt
+++ b/data-raw/microorganisms.txt
@@ -736,6 +736,7 @@
 "B_ACNTB_JUNI"	"Acinetobacter junii"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Moraxellaceae"	"Acinetobacter"	"junii"	""	"species"	"Bouvet et al., 1986"	"29130b9324716febfdbce7179b01e9bd"	"CoL"	1	"13879009"
 "B_ACNTB_KOOK"	"Acinetobacter kookii"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Moraxellaceae"	"Acinetobacter"	"kookii"	""	"species"	"Choi et al., 2013"	"791314"	"DSMZ"	1	
 "B_ACNTB_LCTC"	"Acinetobacter lactucae"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Moraxellaceae"	"Acinetobacter"	"lactucae"	""	"species"	"Rooney et al., 2016"	"794598"	"DSMZ"	1	
+"B_ACNTB_LARV"	"Acinetobacter larvae"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Moraxellaceae"	"Acinetobacter"	"larvae"	""	"species"	"Liu et al., 2017"	"795207"	"DSMZ"	1	
 "B_ACNTB_LWFF"	"Acinetobacter lwoffii"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Moraxellaceae"	"Acinetobacter"	"lwoffii"	""	"species"	"Brisou et al., 1986"	"6e3b1ed9854282e9bafce3b2f7df00f9"	"CoL"	1	
 "B_ACNTB_MDST"	"Acinetobacter modestus"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Moraxellaceae"	"Acinetobacter"	"modestus"	""	"species"	"Nemec et al., 2016"	"794039"	"DSMZ"	1	
 "B_ACNTB_NCTR"	"Acinetobacter nectaris"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Moraxellaceae"	"Acinetobacter"	"nectaris"	""	"species"	"Alvarez-Perez et al., 2013"	"790645"	"DSMZ"	1	"723323008"
@@ -2430,6 +2431,7 @@
 "B_[FAM]_AEROCCCC"	"Aerococcaceae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Aerococcaceae"	""	""	""	"family"	""	"057fddc497f1546f26951ef092e02b87"	"CoL"	2	
 "B_AERCC"	"Aerococcus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Aerococcaceae"	"Aerococcus"	""	""	"genus"	""	"0fc66055ad0db611f60c4f0396421d51"	"CoL"	2	"9008009"
 "B_AERCC_CHRS"	"Aerococcus christensenii"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Aerococcaceae"	"Aerococcus"	"christensenii"	""	"species"	"Collins et al., 1999"	"2ab13ae827b3c1ddd29fe7b60049a9ac"	"CoL"	2	"409818008"
+"B_AERCC_SNGC"	"Aerococcus sanguicola"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Aerococcaceae"	"Aerococcus"	"sanguicola"	""	"species"	"Lawson et al., 2001"	"783326"	"DSMZ"	2	
 "B_AERCC_SNGN"	"Aerococcus sanguinicola"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Aerococcaceae"	"Aerococcus"	"sanguinicola"	""	"species"	"Lawson et al., 2001"	"796ff281ab493638185da69319259393"	"CoL"	2	"427222006"
 "B_AERCC_SUIS"	"Aerococcus suis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Aerococcaceae"	"Aerococcus"	"suis"	""	"species"	"Vela et al., 2007"	"17a074a54acf7f23420e046afd54c05f"	"CoL"	2	
 "B_AERCC_URIN"	"Aerococcus urinae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Aerococcaceae"	"Aerococcus"	"urinae"	""	"species"	"Aguirre et al., 1992"	"7e2ead8d8cb690684800b35f8e80dfcd"	"CoL"	2	"243230001"
@@ -8417,6 +8419,9 @@
 "B_BCTRD_GRMN"	"Bacteroides graminisolvens"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"graminisolvens"	""	"species"	"Nishiyama et al., 2009"	"0189b31b513fe80ea7ca818c9ff43192"	"CoL"	2	
 "B_BCTRD_HLCG"	"Bacteroides helcogenes"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"helcogenes"	""	"species"	"Benno et al., 1983"	"761d72b47ca1a82a5996af2572135739"	"CoL"	2	
 "B_BCTRD_INTS"	"Bacteroides intestinalis"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"intestinalis"	""	"species"	"Bakir et al., 2006"	"0bfac827879b8d5e224f7758a3d2d8f1"	"CoL"	2	"712915005"
+"B_BCTRD_KRNS"	"Bacteroides koreensis"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"koreensis"	""	"species"	"Shin et al., 2017"	"796142"	"DSMZ"	2	
+"B_BCTRD_KRBB"	"Bacteroides kribbi"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"kribbi"	""	"species"	"Shin et al., 2017"	"796143"	"DSMZ"	2	
+"B_BCTRD_LNTS"	"Bacteroides lentus"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"lentus"	""	"species"	"Eggerth, 1935"	"798327"	"DSMZ"	2	
 "B_BCTRD_LUTI"	"Bacteroides luti"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"luti"	""	"species"	"Hatamoto et al., 2014"	"791844"	"DSMZ"	2	
 "B_BCTRD_MSSL"	"Bacteroides massiliensis"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"massiliensis"	""	"species"	"Fenner et al., 2005"	"d214505a60093319e1a8e3ba61fe630f"	"CoL"	2	"708567004"
 "B_BCTRD_NORD"	"Bacteroides nordii"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"nordii"	""	"species"	"Song et al., 2005"	"7d1b475a13de2624a212b7cf1eb7e132"	"CoL"	2	
@@ -8435,6 +8440,7 @@
 "B_BCTRD_SRTR"	"Bacteroides sartorii"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"sartorii"	""	"species"	"Clavel et al., 2012"	"4f637ad6f3332fec71d795edf297f0c7"	"CoL"	2	
 "B_BCTRD_STRC"	"Bacteroides stercorirosoris"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"stercorirosoris"	""	"species"	"Kitahara et al., 2012"	"ee122c4c95090744a6bdf633fd9d5e00"	"CoL"	2	
 "B_BCTRD_RCRS"	"Bacteroides stercoris"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"stercoris"	""	"species"	"Johnson et al., 1986"	"daeebd5ec8bba7b76d45e1460db471c1"	"CoL"	2	"163009"
+"B_BCTRD_TCTM"	"Bacteroides tectum"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"tectum"	""	"species"	"Love et al., 1986"	"783467"	"DSMZ"	2	
 "B_BCTRD_THTT"	"Bacteroides thetaiotaomicron"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"thetaiotaomicron"	""	"species"	"Castellani et al., 1919"	"c4bd13e2054f15c834480d57a8577020"	"CoL"	2	"34236001"
 "B_BCTRD_UNFR"	"Bacteroides uniformis"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"uniformis"	""	"species"	"Eggerth et al., 1933"	"032345ae9e1b73dadb9b137d024b20bf"	"CoL"	2	"59604009"
 "B_BCTRD_VLGT"	"Bacteroides vulgatus"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Bacteroidaceae"	"Bacteroides"	"vulgatus"	""	"species"	"Eggerth et al., 1933"	"f973c61c6d0a4e15928dbdc436b13c0f"	"CoL"	2	"52798008"
@@ -10965,6 +10971,7 @@
 "B_CMPYL_COLI"	"Campylobacter coli"	"Bacteria"	"Proteobacteria"	"Epsilonproteobacteria"	"Campylobacterales"	"Campylobacteraceae"	"Campylobacter"	"coli"	""	"species"	"Veron et al., 1973"	"6c569c28a8b120282d777d2b1f98554e"	"CoL"	2	"40614002"
 "B_CMPYL_CNCS"	"Campylobacter concisus"	"Bacteria"	"Proteobacteria"	"Epsilonproteobacteria"	"Campylobacterales"	"Campylobacteraceae"	"Campylobacter"	"concisus"	""	"species"	"Tanner et al., 1981"	"6a7472de918950d9ea3fb4da6accbade"	"CoL"	2	"9892000"
 "B_CMPYL_CRCG"	"Campylobacter corcagiensis"	"Bacteria"	"Proteobacteria"	"Epsilonproteobacteria"	"Campylobacterales"	"Campylobacteraceae"	"Campylobacter"	"corcagiensis"	""	"species"	"Koziel et al., 2014"	"792068"	"DSMZ"	2	
+"B_CMPYL_CRYR"	"Campylobacter cryaerophila"	"Bacteria"	"Proteobacteria"	"Epsilonproteobacteria"	"Campylobacterales"	"Campylobacteraceae"	"Campylobacter"	"cryaerophila"	""	"species"	"Neill et al., 1985"	"783584"	"DSMZ"	2	
 "B_CMPYL_CNCL"	"Campylobacter cuniculorum"	"Bacteria"	"Proteobacteria"	"Epsilonproteobacteria"	"Campylobacterales"	"Campylobacteraceae"	"Campylobacter"	"cuniculorum"	""	"species"	"Zanoni et al., 2009"	"3231356e94ded6c8ed9225a8174c2247"	"CoL"	2	
 "B_CMPYL_CRVS"	"Campylobacter curvus"	"Bacteria"	"Proteobacteria"	"Epsilonproteobacteria"	"Campylobacterales"	"Campylobacteraceae"	"Campylobacter"	"curvus"	""	"species"	"Vandamme et al., 1991"	"877e011524cf683cc924bc2afa2f4f1e"	"CoL"	2	"116037008"
 "B_CMPYL_FETS"	"Campylobacter fetus"	"Bacteria"	"Proteobacteria"	"Epsilonproteobacteria"	"Campylobacterales"	"Campylobacteraceae"	"Campylobacter"	"fetus"	""	"species"	"Sebald et al., 1963"	"409ceefcdb679efc37676cadffb3e3e7"	"CoL"	2	"84210007"
@@ -15554,6 +15561,7 @@
 "B_CRYNB_AMMN"	"Corynebacterium ammoniagenes"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"ammoniagenes"	""	"species"	"Collins, 1987"	"83d6f101baca47719776d6daa091dd17"	"CoL"	2	"113607008"
 "B_CRYNB_AMYC"	"Corynebacterium amycolatum"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"amycolatum"	""	"species"	"Collins et al., 1988"	"2697fc1a982784c82efbbe6d48d1ed64"	"CoL"	2	"113611002"
 "B_CRYNB_APPN"	"Corynebacterium appendicis"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"appendicis"	""	"species"	"Yassin et al., 2002"	"a6749ae107d7955240ae4bacca4a3b53"	"CoL"	2	"423659000"
+"B_CRYNB_AQTC"	"Corynebacterium aquaticum"	"Bacteria"	"Actinobacteria"	""	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"aquaticum"	""	"species"	"Leifson, 1962"	"775153"	"DSMZ"	2	
 "B_CRYNB_AQTM"	"Corynebacterium aquatimens"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"aquatimens"	""	"species"	"Aravena-Roman et al., 2012"	"790174"	"DSMZ"	2	
 "B_CRYNB_AQUL"	"Corynebacterium aquilae"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"aquilae"	""	"species"	"Fernandez-Garayzabal et al., 2003"	"eb89e2b18e8cf702deae686db631959a"	"CoL"	2	"424012003"
 "B_CRYNB_ARGN"	"Corynebacterium argentoratense"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"argentoratense"	""	"species"	"Riegel et al., 1995"	"248437e186f079f9098b51d7eab9a104"	"CoL"	2	"417499006"
@@ -15583,6 +15591,7 @@
 "B_CRYNB_DURM"	"Corynebacterium durum"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"durum"	""	"species"	"Riegel et al., 1997"	"188914f51441fcf66e9dbdd6fa419ca5"	"CoL"	2	"413926004"
 "B_CRYNB_EFFC"	"Corynebacterium efficiens"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"efficiens"	""	"species"	"Fudou et al., 2002"	"100e54272c41242bd210c760dc3d49da"	"CoL"	2	"423379003"
 "B_CRYNB_EPDR"	"Corynebacterium epidermidicanis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"epidermidicanis"	""	"species"	"Frischmann et al., 2018"	"790130"	"DSMZ"	2	
+"B_CRYNB_FACL"	"Corynebacterium faecale"	"Bacteria"	"Actinobacteria"	""	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"faecale"	""	"species"	"Chen et al., 2016"	"794251"	"DSMZ"	2	
 "B_CRYNB_FLSN"	"Corynebacterium falsenii"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"falsenii"	""	"species"	"Sjoden et al., 1998"	"a4b0881333077324ba938902ef33b158"	"CoL"	2	"116389005"
 "B_CRYNB_FLNM"	"Corynebacterium felinum"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"felinum"	""	"species"	"Collins et al., 2001"	"633a1e897b7623235da9235464dcd67c"	"CoL"	2	"423568009"
 "B_CRYNB_FLVS"	"Corynebacterium flavescens"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"flavescens"	""	"species"	"Barksdale et al., 1979"	"2aa053a0af38954875cb97011cb29443"	"CoL"	2	"47802009"
@@ -15609,6 +15618,7 @@
 "B_CRYNB_KTSC"	"Corynebacterium kutscheri"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"kutscheri"	""	"species"	"Bergey et al., 1925"	"8ea3128da9bfa7cfc5ab4fb8c83e35fc"	"CoL"	2	"88575000"
 "B_CRYNB_LCTS"	"Corynebacterium lactis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"lactis"	""	"species"	"Wiertz et al., 2018"	"791337"	"DSMZ"	2	
 "B_CRYNB_LPPH"	"Corynebacterium lipophiloflavum"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"lipophiloflavum"	""	"species"	"Funke et al., 1997"	"da6181226ddbe16d620eb7fbd0d50b3f"	"CoL"	2	"416863001"
+"B_CRYNB_LQFC"	"Corynebacterium liquefaciens"	"Bacteria"	"Actinobacteria"	""	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"liquefaciens"	""	"species"	"Laneelle et al., 1980"	"798138"	"DSMZ"	2	
 "B_CRYNB_LOWI"	"Corynebacterium lowii"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"lowii"	""	"species"	"Bernard et al., 2016"	"794320"	"DSMZ"	2	
 "B_CRYNB_LBRC"	"Corynebacterium lubricantis"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"lubricantis"	""	"species"	"Kampfer et al., 2009"	"b1b838e48e5f986bdebfce12e92b819b"	"CoL"	2	
 "B_CRYNB_MCGN"	"Corynebacterium macginleyi"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"macginleyi"	""	"species"	"Riegel et al., 1995"	"f061871344574f355ac6ac89f02a0aaf"	"CoL"	2	"363772007"
@@ -15661,7 +15671,9 @@
 "B_CRYNB_URPY"	"Corynebacterium uropygiale"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"uropygiale"	""	"species"	"Braun et al., 2016"	"794126"	"DSMZ"	2	
 "B_CRYNB_UTRQ"	"Corynebacterium uterequi"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"uterequi"	""	"species"	"Hoyles et al., 2018"	"791215"	"DSMZ"	2	
 "B_CRYNB_VRBL"	"Corynebacterium variabile"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"variabile"	""	"species"	"Collins, 1987"	"9c6d95c70bfb58c350f5295d423094bc"	"CoL"	2	"11575001"
+"B_CRYNB_RBLS"	"Corynebacterium variabilis"	"Bacteria"	"Actinobacteria"	""	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"variabilis"	""	"species"	"Collins, 1987"	"783701"	"DSMZ"	2	
 "B_CRYNB_VTRM"	"Corynebacterium vitaeruminis"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"vitaeruminis"	""	"species"	"Laneelle et al., 1980"	"81f6de6271113a7a1d61a141786c78fe"	"CoL"	2	"116390001"
+"B_CRYNB_TRMN"	"Corynebacterium vitarumen"	"Bacteria"	"Actinobacteria"	""	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"vitarumen"	""	"species"	"Laneelle et al., 1980"	"783702"	"DSMZ"	2	
 "B_CRYNB_XRSS"	"Corynebacterium xerosis"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Corynebacteriaceae"	"Corynebacterium"	"xerosis"	""	"species"	"Lehmann et al., 1899"	"eda368b36b3b5f8557b8fc25bb3d87f6"	"CoL"	2	"27101006"
 "C_CRYNP"	"Corynophrya"	"Chromista"	"Ciliophora"	"Kinetofragminophora"	"Suctorida"	"Corynophryidae"	"Corynophrya"	""	""	"genus"	""	"30fbc7bc50db56001cfd44dcf07a5fc7"	"CoL"	3	
 "C_CRYNP_ABYS"	"Corynophrya abyssalis"	"Chromista"	"Ciliophora"	"Kinetofragminophora"	"Suctorida"	"Corynophryidae"	"Corynophrya"	"abyssalis"	""	"species"	"Bartsch et al., 2010"	"a18401393d14ee783e73e8be3c73a884"	"CoL"	3	
@@ -17842,6 +17854,7 @@
 "C_DNTST_ENPL"	"Dentostomina enoplostoma"	"Chromista"	"Foraminifera"	"Tubothalamea"	"Miliolida"	"Hauerinidae"	"Dentostomina"	"enoplostoma"	""	"species"	"DOrbigny, 1839"	"0c50c5a83074677bc408c07de08fb8aa"	"CoL"	3	
 "B_DRMBC"	"Dermabacter"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Dermabacteraceae"	"Dermabacter"	""	""	"genus"	""	"c254973d79329a9a81babca22bf7aa51"	"CoL"	2	"413976002"
 "B_DRMBC_HMNS"	"Dermabacter hominis"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Dermabacteraceae"	"Dermabacter"	"hominis"	""	"species"	"Jones et al., 1989"	"4d3ef12bee5e2d1e0093af5e6a738b0f"	"CoL"	2	"413977006"
+"B_DRMBC_JNJN"	"Dermabacter jinjuensis"	"Bacteria"	"Actinobacteria"	""	"Actinomycetales"	"Dermabacteraceae"	"Dermabacter"	"jinjuensis"	""	"species"	"Park et al., 2016"	"794255"	"DSMZ"	2	
 "B_DRMBC_VGNL"	"Dermabacter vaginalis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Actinomycetales"	"Dermabacteraceae"	"Dermabacter"	"vaginalis"	""	"species"	"Chang et al., 2016"	"794030"	"DSMZ"	2	
 "B_[FAM]_DRMBCTRC"	"Dermabacteraceae"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Dermabacteraceae"	""	""	""	"family"	""	"0f21d57e4b28d96773e1081bad008181"	"CoL"	2	
 "B_[FAM]_DERMCCCC"	"Dermacoccaceae"	"Bacteria"	"Actinobacteria"	"(unknown class)"	"Actinomycetales"	"Dermacoccaceae"	""	""	""	"family"	""	"d822dbf47675fbd561fcabd9388b58b4"	"CoL"	2	
@@ -23874,6 +23887,8 @@
 "C_FCHRA_ULRN"	"Fuscheria ulurensis"	"Chromista"	"Ciliophora"	"Gymnostomatea"	"Haptorida"	"Fuscheriidae"	"Fuscheria"	"ulurensis"	""	"species"	"Foissner et al., 2009"	"eab418d60de109c70adebdcfadd38393"	"CoL"	3	
 "C_[FAM]_FUSCHERD"	"Fuscheriidae"	"Chromista"	"Ciliophora"	"Gymnostomatea"	"Haptorida"	"Fuscheriidae"	""	""	""	"family"	""	"c142b58b7df6153f2b251f1fe35e1fcb"	"CoL"	2	
 "B_FSBCT"	"Fusibacter"	"Bacteria"	"Firmicutes"	"Clostridia"	"Clostridiales"	"(unknown family)"	"Fusibacter"	""	""	"genus"	""	"2ef1cc64021e41234ccb81337243e326"	"CoL"	2	
+"B_FSBCT_BZRT"	"Fusibacter bizertensis"	"Bacteria"	"Firmicutes"	"Clostridia"	"Clostridiales"	""	"Fusibacter"	"bizertensis"	""	"species"	"Smii et al., 2015"	"792439"	"DSMZ"	2	
+"B_FSBCT_FNTS"	"Fusibacter fontis"	"Bacteria"	"Firmicutes"	"Clostridia"	"Clostridiales"	""	"Fusibacter"	"fontis"	""	"species"	"Fadhlaoui et al., 2015"	"793321"	"DSMZ"	2	
 "B_FSBCT_PCVR"	"Fusibacter paucivorans"	"Bacteria"	"Firmicutes"	"Clostridia"	"Clostridiales"	"(unknown family)"	"Fusibacter"	"paucivorans"	""	"species"	"Ravot et al., 1999"	"e377365519fc9048e61ebe12b0acc6da"	"CoL"	2	
 "B_FSBCT_TNSN"	"Fusibacter tunisiensis"	"Bacteria"	"Firmicutes"	"Clostridia"	"Clostridiales"	"(unknown family)"	"Fusibacter"	"tunisiensis"	""	"species"	"Ben Hania et al., 2012"	"fc23fa7985bcce14cb779cfdd5e8c24a"	"CoL"	2	
 "B_FSCTN"	"Fusicatenibacter"	"Bacteria"	"Firmicutes"	"Clostridia"	"Clostridiales"	"Lachnospiraceae"	"Fusicatenibacter"	""	""	"genus"		""	"DSMZ"	2	
@@ -24127,7 +24142,9 @@
 "B_GEMLL_HMLY"	"Gemella haemolysans"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"(unknown family)"	"Gemella"	"haemolysans"	""	"species"	"Berger, 1960"	"cb12ee9348456944da1452c2ee07f711"	"CoL"	2	"37511002"
 "B_GEMLL_MRBL"	"Gemella morbillorum"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"(unknown family)"	"Gemella"	"morbillorum"	""	"species"	"Kilpper-Balz et al., 1988"	"2cf1ae502c0bf7d053d9520f7bc12d1e"	"CoL"	2	"113765006"
 "B_GEMLL_PLTC"	"Gemella palaticanis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"(unknown family)"	"Gemella"	"palaticanis"	""	"species"	"Collins et al., 1999"	"0413b4f5665e096d10b0dd2c59f07646"	"CoL"	2	
+"B_GEMLL_PRHM"	"Gemella parahaemolysans"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	""	"Gemella"	"parahaemolysans"	""	"species"	"Hung et al., 2014"	"791874"	"DSMZ"	2	
 "B_GEMLL_SNGN"	"Gemella sanguinis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"(unknown family)"	"Gemella"	"sanguinis"	""	"species"	"Collins et al., 1999"	"2c5a8f12014c650dfe5f55accde88084"	"CoL"	2	"125038007"
+"B_GEMLL_TWNN"	"Gemella taiwanensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	""	"Gemella"	"taiwanensis"	""	"species"	"Hung et al., 2014"	"791875"	"DSMZ"	2	
 "B_GMNCC"	"Geminicoccus"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"(unknown order)"	"(unknown family)"	"Geminicoccus"	""	""	"genus"	""	"3791b89a357dd7b75651125e72e5a27e"	"CoL"	2	
 "B_GMNCC_ROSS"	"Geminicoccus roseus"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"(unknown order)"	"(unknown family)"	"Geminicoccus"	"roseus"	""	"species"	"Foesel et al., 2008"	"ab4e9af2a2755d93be9d56dd1536c1e6"	"CoL"	2	
 "C_GMNLL"	"Geminiella"	"Chromista"	"Foraminifera"	"(unknown class)"	"Lagenida"	"Ellipsolagenidae"	"Geminiella"	""	""	"genus"	""	"163b7468129f33c2476fc3f18bfd8c88"	"CoL"	3	
@@ -30007,10 +30024,13 @@
 "B_LCTBC_RDNT"	"Lactobacillus rodentium"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"rodentium"	""	"species"	"Killer et al., 2014"	"791838"	"DSMZ"	2	
 "B_LCTBC_ROGS"	"Lactobacillus rogosae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"rogosae"	""	"species"	"Holdeman et al., 1974"	"1c971bb2a729c6604e6e5686fd92559f"	"CoL"	2	
 "B_LCTBC_ROSS"	"Lactobacillus rossiae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"rossiae"	""	"species"	"Corsetti et al., 2005"	"bb0621ab2aabb15f4880b9a92c698b2a"	"CoL"	2	"432194007"
+"B_LCTBC_RSSI"	"Lactobacillus rossii"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"rossii"	""	"species"	"Corsetti et al., 2005"	"784068"	"DSMZ"	2	
 "B_LCTBC_RMNS"	"Lactobacillus ruminis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"ruminis"	""	"species"	"Sharpe et al., 1973"	"227f53c5db4073601a8da25c2aa823a0"	"CoL"	2	"84370002"
 "B_LCTBC_SRMN"	"Lactobacillus saerimneri"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"saerimneri"	""	"species"	"Pedersen et al., 2004"	"48fdd7d3958b20a80de0f6aa37215fe2"	"CoL"	2	"432191004"
+"B_LCTBC_SAKE_SAKE"	"Lactobacillus sake sake"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sake"	"sake"	"species"	"Torriani et al., 1996"	"784071"	"DSMZ"	2	
 "B_LCTBC_SAKE"	"Lactobacillus sakei"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	""	"species"	"Katagiri et al., 1996"	"539147a998aca4d1b21139df1c19da17"	"CoL"	2	"39861009"
 "B_LCTBC_SAKE_CRNS"	"Lactobacillus sakei carnosus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	"carnosus"	"infraspecies"	"Torriani et al., 1996"	"dde7319e76c9247eb5ad732536eb07c8"	"CoL"	2	
+"B_LCTBC_SKEI_SAKE"	"Lactobacillus sakei sake"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	"sake"	"species"	"Torriani et al., 1996"	"798356"	"DSMZ"	2	
 "B_LCTBC_SLTL"	"Lactobacillus salitolerans"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"salitolerans"	""	"species"	"Tohno et al., 2019"	"800710"	"DSMZ"	2	
 "B_LCTBC_SLVR"	"Lactobacillus salivarius"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"salivarius"	""	"species"	"Rogosa et al., 2006"	"ac34ff01c9afe0de2ab69bfd339704b6"	"CoL"	2	"37809002"
 "B_LCTBC_SNFR"	"Lactobacillus sanfranciscensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sanfranciscensis"	""	"species"	"Weiss et al., 1984"	"4211a00b19dfc4632b868fe123b0d1b8"	"CoL"	2	"432195008"
@@ -39308,6 +39328,7 @@
 "B_NESSR_CANS"	"Neisseria canis"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"canis"	""	"species"	"Berger, 1962"	"f588178a6f811167d2a08e5d7b2a7310"	"CoL"	2	"54978009"
 "B_NESSR_CINR"	"Neisseria cinerea"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"cinerea"	""	"species"	"Murray, 1939"	"80fa1e21c2efa5f0c00ca26a5c190c1d"	"CoL"	2	"69312007"
 "B_NESSR_DENT"	"Neisseria dentiae"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"dentiae"	""	"species"	"Sneath et al., 1997"	"e6428b38ccc3818fb21e2146b9b9da01"	"CoL"	2	
+"B_NESSR_DMSN"	"Neisseria dumasiana"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"dumasiana"	""	"species"	"Wroblewski et al., 2017"	"796193"	"DSMZ"	2	
 "B_NESSR_ELNG"	"Neisseria elongata"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"elongata"	""	"species"	"Bovre et al., 1970"	"4fd583a67fe0f765137e4902de5cf11e"	"CoL"	2	"12638001"
 "B_NESSR_ELNG_GLYC"	"Neisseria elongata glycolytica"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"elongata"	"glycolytica"	"infraspecies"	"Henriksen et al., 1976"	"53eb476c001de688a708c637afc447d1"	"CoL"	2	"35693009"
 "B_NESSR_ELNG_NTRR"	"Neisseria elongata nitroreducens"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"elongata"	"nitroreducens"	"infraspecies"	"Grant et al., 1991"	"017d680b532a5e4033a40ef0dd780905"	"CoL"	2	
@@ -42653,10 +42674,12 @@
 "B_[FAM]_PANBCLLC"	"Paenibacillaceae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	""	""	""	"family"	""	"06f43a6ef8ac500d8120040e50675f88"	"CoL"	2	
 "B_PNBCL"	"Paenibacillus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	""	""	"genus"	""	"d778edb5225cb28bd7344ed5dbd083e1"	"CoL"	2	"114086007"
 "B_PNBCL_ABYS"	"Paenibacillus abyssi"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"abyssi"	""	"species"	"Huang et al., 2015"	"792663"	"DSMZ"	2	
+"B_PNBCL_ACRS"	"Paenibacillus aceris"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"aceris"	""	"species"	"Hwang et al., 2017"	"795204"	"DSMZ"	2	
 "B_PNBCL_ACET"	"Paenibacillus aceti"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"aceti"	""	"species"	"Li et al., 2016"	"794569"	"DSMZ"	2	
 "B_PNBCL_AEST"	"Paenibacillus aestuarii"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"aestuarii"	""	"species"	"Bae et al., 2010"	"2eaeee843908dc72f01599c01d1d7824"	"CoL"	2	
 "B_PNBCL_AGRX"	"Paenibacillus agarexedens"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"agarexedens"	""	"species"	"Uetanabaro et al., 2003"	"34f7325ea04df422addf6139f76227a4"	"CoL"	2	"429906007"
 "B_PNBCL_AGRD"	"Paenibacillus agaridevorans"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"agaridevorans"	""	"species"	"Uetanabaro et al., 2003"	"830aae21cbe86216066ba7af5f9c87cb"	"CoL"	2	"429907003"
+"B_PNBCL_ALBD"	"Paenibacillus albidus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"albidus"	""	"species"	"Zhuang et al., 2017"	"796151"	"DSMZ"	2	
 "B_PNBCL_ALGN"	"Paenibacillus alginolyticus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"alginolyticus"	""	"species"	"Shida et al., 1997"	"bc3b26b031ae0349cad729c4a579522e"	"CoL"	2	"114087003"
 "B_PNBCL_ALGR"	"Paenibacillus algorifonticola"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"algorifonticola"	""	"species"	"Tang et al., 2011"	"29a27c78f5d93976913c98158bea624d"	"CoL"	2	
 "B_PNBCL_ALKL"	"Paenibacillus alkaliterrae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"alkaliterrae"	""	"species"	"Yoon et al., 2005"	"819caeb31dafeee45c8b67e01809e774"	"CoL"	2	
@@ -42705,6 +42728,7 @@
 "B_PNBCL_DNDR"	"Paenibacillus dendritiformis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"dendritiformis"	""	"species"	"Tcherpakov et al., 1999"	"e98e22d6a5472c702d773f45208b8d3f"	"CoL"	2	"430608007"
 "B_PNBCL_DNGD"	"Paenibacillus dongdonensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"dongdonensis"	""	"species"	"Son et al., 2014"	"792042"	"DSMZ"	2	
 "B_PNBCL_DSNN"	"Paenibacillus doosanensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"doosanensis"	""	"species"	"Kim et al., 2014"	"791705"	"DSMZ"	2	
+"B_PNBCL_DURM"	"Paenibacillus durum"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"durum"	""	"species"	"Collins et al., 1994"	"784553"	"DSMZ"	2	
 "B_PNBCL_DURS"	"Paenibacillus durus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"durus"	""	"species"	"Collins et al., 1994"	"3d10d59aee2784ef5fff65f7538ac245"	"CoL"	2	"114091008"
 "B_PNBCL_EDPH"	"Paenibacillus edaphicus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"edaphicus"	""	"species"	"Hu et al., 2010"	"55c35c5efb25e66c778cf6d60eac2e9a"	"CoL"	2	
 "B_PNBCL_EHMN"	"Paenibacillus ehimensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"ehimensis"	""	"species"	"Lee et al., 2004"	"977994e73d0595da2d2fdeaa365eb6cd"	"CoL"	2	"430609004"
@@ -42752,6 +42776,7 @@
 "B_PNBCL_KRBB"	"Paenibacillus kribbensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"kribbensis"	""	"species"	"Yoon et al., 2003"	"7990cce5493b343b4dd578b73c8da83e"	"CoL"	2	
 "B_PNBCL_KYNG"	"Paenibacillus kyungheensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"kyungheensis"	""	"species"	"Siddiqi et al., 2015"	"793494"	"DSMZ"	2	
 "B_PNBCL_LCTS"	"Paenibacillus lactis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"lactis"	""	"species"	"Scheldeman et al., 2004"	"a8fa50353b31da34a322d9fca3881572"	"CoL"	2	"430629003"
+"B_PNBCL_LACS"	"Paenibacillus lacus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"lacus"	""	"species"	"Chen et al., 2017"	"795288"	"DSMZ"	2	
 "B_PNBCL_LARV"	"Paenibacillus larvae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"larvae"	""	"species"	"Ash et al., 2006"	"9bfc05efd3eea0854db404760e482e1e"	"CoL"	2	"114098002"
 "B_PNBCL_LATS"	"Paenibacillus lautus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"lautus"	""	"species"	"Heyndrickx et al., 1996"	"b73ba9f5e23a3f1ddd34fcb98a3a10f8"	"CoL"	2	"114100002"
 "B_PNBCL_LEMN"	"Paenibacillus lemnae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Paenibacillaceae"	"Paenibacillus"	"lemnae"	""	"species"	"Kittiwongwattana et al., 2015"	"792440"	"DSMZ"	2	
@@ -43113,6 +43138,7 @@
 "B_PANTO"	"Pantoea"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Erwiniaceae"	"Pantoea"	""	""	"genus"	""	"5e1e7e2c2f3da486dfc2d89e6b75865e"	"CoL"	1	"115013001"
 "B_PANTO_AGGL"	"Pantoea agglomerans"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Erwiniaceae"	"Pantoea"	"agglomerans"	""	"species"	"Gavini et al., 1989"	"a0ec10fe69cbe44b829f9c387c6d5ebd"	"CoL"	1	"115015008"
 "B_PANTO_ALLI"	"Pantoea allii"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Erwiniaceae"	"Pantoea"	"allii"	""	"species"	"Brady et al., 2011"	"4dd07886be48e1ae6e8ed37d203c0f84"	"CoL"	1	
+"B_PANTO_ANNS"	"Pantoea ananas"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Erwiniaceae"	"Pantoea"	"ananas"	""	"species"	"Mergaert et al., 1993"	"784563"	"DSMZ"	1	
 "B_PANTO_ANNT"	"Pantoea ananatis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Erwiniaceae"	"Pantoea"	"ananatis"	""	"species"	"Mergaert et al., 1993"	"2c54740884f84a1a71a5cd300a79d15a"	"CoL"	1	"115014007"
 "B_PANTO_ANTH"	"Pantoea anthophila"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Erwiniaceae"	"Pantoea"	"anthophila"	""	"species"	"Brady et al., 2009"	"e722c6d8bb737b44d817a317c8ef8013"	"CoL"	1	
 "B_PANTO_BRNN"	"Pantoea brenneri"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Erwiniaceae"	"Pantoea"	"brenneri"	""	"species"	"Brady et al., 2010"	"4431f9b8fd978b73e96e06a1286006c5"	"CoL"	1	
@@ -49833,6 +49859,7 @@
 "C_PRTNN_RNHL"	"Proteonina reinholdi"	"Chromista"	"Foraminifera"	"Globothalamea"	"Lituolida"	"Hormosinidae"	"Proteonina"	"reinholdi"	""	"species"	"Ten Dam, 1947"	"c05060e270f23cfba9b6e353efdb2769"	"CoL"	3	
 "B_PROTS"	"Proteus"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Proteus"	""	""	"genus"	""	"0f62bf27dd2e0a29481695b9c7a55fa5"	"CoL"	1	"50517009"
 "B_PROTS_ALMN"	"Proteus alimentorum"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Proteus"	"alimentorum"	""	"species"	"Dai et al., 2018"	"797660"	"DSMZ"	1	
+"B_PROTS_CBRS"	"Proteus cibarius"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Proteus"	"cibarius"	""	"species"	"Hyun et al., 2016"	"794180"	"DSMZ"	1	
 "B_PROTS_CIBI"	"Proteus cibi"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Proteus"	"cibi"	""	"species"	"Dai et al., 2019"	"800142"	"DSMZ"	1	
 "B_PROTS_CLMB"	"Proteus columbae"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Proteus"	"columbae"	""	"species"	"Dai et al., 2018"	"797522"	"DSMZ"	1	
 "B_PROTS_FACS"	"Proteus faecis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Proteus"	"faecis"	""	"species"	"Dai et al., 2019"	"800143"	"DSMZ"	1	
@@ -50641,6 +50668,7 @@
 "B_PSDMN_BRSS_NRNT"	"Pseudomonas brassicacearum neoaurantiaca"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"brassicacearum"	"neoaurantiaca"	"infraspecies"	"Ivanova et al., 2009"	"ec8927aacb91b3a6cc4ca4a685f3914b"	"CoL"	1	
 "B_PSDMN_BRNN"	"Pseudomonas brenneri"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"brenneri"	""	"species"	"Baida et al., 2002"	"49c16df22b9794811ee11992e802fb75"	"CoL"	1	"415188002"
 "B_PSDMN_CAEN"	"Pseudomonas caeni"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"caeni"	""	"species"	"Xiao et al., 2009"	"aa17e9af46852075ef859e600004f3e7"	"CoL"	1	
+"B_PSDMN_CNDN"	"Pseudomonas canadensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"canadensis"	""	"species"	"Tambong et al., 2017"	"795214"	"DSMZ"	1	
 "B_PSDMN_CNNB"	"Pseudomonas cannabina"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"cannabina"	""	"species"	"Gardan et al., 1999"	"eca546200fc614d4abd73c834d001c3c"	"CoL"	1	
 "B_PSDMN_CRBX"	"Pseudomonas carboxydohydrogena"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"carboxydohydrogena"	""	"species"	"Meyer et al., 1980"	"6b549eed20115e65b1a5a7551409e7a5"	"CoL"	1	
 "B_PSDMN_CRCP"	"Pseudomonas caricapapayae"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"caricapapayae"	""	"species"	"Robbs, 1956"	"b2197848de1e1c7c10e903a27ab04aba"	"CoL"	1	"76278000"
@@ -50791,6 +50819,7 @@
 "B_PSDMN_TNNS"	"Pseudomonas taeanensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"taeanensis"	""	"species"	"Lee et al., 2010"	"db0759c67acd25a657bdd93c8a41869e"	"CoL"	1	
 "B_PSDMN_TTRL"	"Pseudomonas taetrolens"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"taetrolens"	""	"species"	"Haynes, 1957"	"37765eb7414456ba397f87b02ab3965c"	"CoL"	1	"73287000"
 "B_PSDMN_TWNN"	"Pseudomonas taiwanensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"taiwanensis"	""	"species"	"Wang et al., 2010"	"8d20832d1ffec1d093791edab57c79df"	"CoL"	1	"450372006"
+"B_PSDMN_TRMN"	"Pseudomonas tarimensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"tarimensis"	""	"species"	"Anwar et al., 2017"	"796144"	"DSMZ"	1	
 "B_PSDMN_THRM"	"Pseudomonas thermotolerans"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"thermotolerans"	""	"species"	"Manaia et al., 2002"	"05b82ed17c4615effe847440ec86dfd1"	"CoL"	1	"438068005"
 "B_PSDMN_THVR"	"Pseudomonas thivervalensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"thivervalensis"	""	"species"	"Achouak et al., 2000"	"78fb8ff185618bc7c11c117c2f1551f3"	"CoL"	1	"438028006"
 "B_PSDMN_TNJN"	"Pseudomonas tianjinensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Pseudomonadales"	"Pseudomonadaceae"	"Pseudomonas"	"tianjinensis"	""	"species"	"Chen et al., 2018"	"797819"	"DSMZ"	1	
@@ -56894,12 +56923,14 @@
 "B_SPHNGB_ALKL"	"Sphingobacterium alkalisoli"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"alkalisoli"	""	"species"	"Xu et al., 2017"	"795403"	"DSMZ"	3	
 "B_SPHNGB_ANHN"	"Sphingobacterium anhuiense"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"anhuiense"	""	"species"	"Wei et al., 2008"	"7639c737c663d05e1aee5fd3fed2b3c8"	"CoL"	3	
 "B_SPHNGB_ANTR"	"Sphingobacterium antarcticum"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"antarcticum"	""	"species"	"Shivaji et al., 1992"	"e19db9fdbc0a7ab1bf11b50b7fa32deb"	"CoL"	3	
+"B_SPHNGB_CTCS"	"Sphingobacterium antarcticus"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"antarcticus"	""	"species"	"Shivaji et al., 1992"	"784914"	"DSMZ"	3	
 "B_SPHNGB_AREN"	"Sphingobacterium arenae"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"arenae"	""	"species"	"Jiang et al., 2014"	"791480"	"DSMZ"	3	
 "B_SPHNGB_ATHY"	"Sphingobacterium athyrii"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"athyrii"	""	"species"	"Cheng et al., 2019"	"800119"	"DSMZ"	3	
 "B_SPHNGB_BMBS"	"Sphingobacterium bambusae"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"bambusae"	""	"species"	"Duan et al., 2010"	"9d76b2529efee4d3b1965472384825b0"	"CoL"	3	
 "B_SPHNGB_BVSG"	"Sphingobacterium bovisgrunnientis"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"bovisgrunnientis"	""	"species"	"Kaur et al., 2018"	"797534"	"DSMZ"	3	
 "B_SPHNGB_CAEN"	"Sphingobacterium caeni"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"caeni"	""	"species"	"Sun et al., 2013"	"790835"	"DSMZ"	3	
 "B_SPHNGB_CNDN"	"Sphingobacterium canadense"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"canadense"	""	"species"	"Mehnaz et al., 2008"	"e0dd9101ff5b891528b9c312f348d715"	"CoL"	3	
+"B_SPHNGB_CLLL"	"Sphingobacterium cellulitidis"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"cellulitidis"	""	"species"	"Huys et al., 2017"	"795224"	"DSMZ"	3	
 "B_SPHNGB_CHNG"	"Sphingobacterium changzhouense"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"changzhouense"	""	"species"	"Liu et al., 2013"	"791381"	"DSMZ"	3	
 "B_SPHNGB_CHZH"	"Sphingobacterium chuzhouense"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"chuzhouense"	""	"species"	"Wang et al., 2016"	"794891"	"DSMZ"	3	
 "B_SPHNGB_CIBI"	"Sphingobacterium cibi"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"cibi"	""	"species"	"Lai et al., 2016"	"794899"	"DSMZ"	3	
@@ -56914,6 +56945,7 @@
 "B_SPHNGB_GRSF"	"Sphingobacterium griseoflavum"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"griseoflavum"	""	"species"	"Long et al., 2016"	"794133"	"DSMZ"	3	
 "B_SPHNGB_HLXY"	"Sphingobacterium haloxyli"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"haloxyli"	""	"species"	"Liu et al., 2018"	"797903"	"DSMZ"	3	
 "B_SPHNGB_HTNN"	"Sphingobacterium hotanense"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"hotanense"	""	"species"	"Xiao et al., 2013"	"790574"	"DSMZ"	3	
+"B_SPHNGB_HUMI"	"Sphingobacterium humi"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"humi"	""	"species"	"Lee et al., 2017"	"796154"	"DSMZ"	3	
 "B_SPHNGB_JJNS"	"Sphingobacterium jejuense"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"jejuense"	""	"species"	"Siddiqi et al., 2016"	"794795"	"DSMZ"	3	
 "B_SPHNGB_KTHR"	"Sphingobacterium kitahiroshimense"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"kitahiroshimense"	""	"species"	"Matsuyama et al., 2008"	"1b487ae730993a033dd44f4ec3221d2a"	"CoL"	3	
 "B_SPHNGB_KYNG"	"Sphingobacterium kyonggiense"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"kyonggiense"	""	"species"	"Choi et al., 2012"	"790272"	"DSMZ"	3	
@@ -56933,6 +56965,7 @@
 "B_SPHNGB_SOLI"	"Sphingobacterium soli"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"soli"	""	"species"	"Fu et al., 2017"	"795506"	"DSMZ"	3	
 "B_SPHNGB_SPRT"	"Sphingobacterium spiritivorum"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"spiritivorum"	""	"species"	"Yabuuchi et al., 1983"	"7d4093a1793e9c443c9697c57b1b5011"	"CoL"	3	"61675006"
 "B_SPHNGB_SUAD"	"Sphingobacterium suaedae"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"suaedae"	""	"species"	"Sun et al., 2015"	"793626"	"DSMZ"	3	
+"B_SPHNGB_TBCS"	"Sphingobacterium tabacisoli"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"tabacisoli"	""	"species"	"Zhou et al., 2017"	"796213"	"DSMZ"	3	
 "B_SPHNGB_TERR"	"Sphingobacterium terrae"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"terrae"	""	"species"	"Chaudhary et al., 2018"	"797530"	"DSMZ"	3	
 "B_SPHNGB_THLP"	"Sphingobacterium thalpophilum"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"thalpophilum"	""	"species"	"Takeuchi et al., 1993"	"f74e7f7b4ef1d3d157e02c43c944e41b"	"CoL"	3	"113954009"
 "B_SPHNGB_THRM"	"Sphingobacterium thermophilum"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"thermophilum"	""	"species"	"Yabe et al., 2016"	"790761"	"DSMZ"	3	
@@ -57001,8 +57034,10 @@
 "B_SNGMNS_AERL"	"Sphingomonas aerolata"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"aerolata"	""	"species"	"Busse et al., 2003"	"d71319c356a2c3522a7f29010b7d062d"	"CoL"	2	"438982007"
 "B_SNGMNS_AERP"	"Sphingomonas aerophila"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"aerophila"	""	"species"	"Kim et al., 2014"	"791661"	"DSMZ"	2	
 "B_SNGMNS_AEST"	"Sphingomonas aestuarii"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"aestuarii"	""	"species"	"Roh et al., 2009"	"9ee9164ad23512c6aa68e8e68b1ad8b5"	"CoL"	2	
+"B_SNGMNS_AGRI"	"Sphingomonas agri"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"agri"	""	"species"	"Siddiqi et al., 2017"	"796214"	"DSMZ"	2	
 "B_SNGMNS_ALPN"	"Sphingomonas alpina"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"alpina"	""	"species"	"Margesin et al., 2012"	"790013"	"DSMZ"	2	
 "B_SNGMNS_ANTR"	"Sphingomonas antarctica"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"antarctica"	""	"species"	"Huang et al., 2017"	"796054"	"DSMZ"	2	
+"B_SNGMNS_AQTC"	"Sphingomonas aquatica"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"aquatica"	""	"species"	"Choi et al., 2017"	"795211"	"DSMZ"	2	
 "B_SNGMNS_AQTL"	"Sphingomonas aquatilis"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"aquatilis"	""	"species"	"Lee et al., 2001"	"a0d00893c721d7c701437af6d0b68e37"	"CoL"	2	"438983002"
 "B_SNGMNS_ARNT"	"Sphingomonas arantia"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"arantia"	""	"species"	"Jia et al., 2016"	"793916"	"DSMZ"	2	
 "B_SNGMNS_ASCC"	"Sphingomonas asaccharolytica"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"asaccharolytica"	""	"species"	"Takeuchi et al., 1995"	"d0f62018c7890604901ac6b83768877f"	"CoL"	2	"439679006"
@@ -57030,6 +57065,7 @@
 "B_SNGMNS_FLAV"	"Sphingomonas flava"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"flava"	""	"species"	"Corrig Du et al., 2015"	"793390"	"DSMZ"	2	
 "B_SNGMNS_FNTC"	"Sphingomonas fonticola"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"fonticola"	""	"species"	"Sheu et al., 2015"	"793605"	"DSMZ"	2	
 "B_SNGMNS_FRMS"	"Sphingomonas formosensis"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"formosensis"	""	"species"	"Lin et al., 2012"	"790015"	"DSMZ"	2	
+"B_SNGMNS_FRGD"	"Sphingomonas frigidaeris"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"frigidaeris"	""	"species"	"Lee et al., 2017"	"796111"	"DSMZ"	2	
 "B_SNGMNS_GEI"	"Sphingomonas gei"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"gei"	""	"species"	"Zhu et al., 2015"	"792696"	"DSMZ"	2	
 "B_SNGMNS_GMNS"	"Sphingomonas gimensis"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"gimensis"	""	"species"	"Feng et al., 2014"	"792286"	"DSMZ"	2	
 "B_SNGMNS_GNSN"	"Sphingomonas ginsengisoli"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"ginsengisoli"	""	"species"	"An et al., 2013"	"777083"	"DSMZ"	2	
@@ -57062,6 +57098,7 @@
 "B_SNGMNS_MALI"	"Sphingomonas mali"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"mali"	""	"species"	"Takeuchi et al., 1995"	"14d21127ff1cd6290f9e142244dc243d"	"CoL"	2	"438538007"
 "B_SNGMNS_MLNS"	"Sphingomonas melonis"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"melonis"	""	"species"	"Buonaurio et al., 2002"	"5862b2dca76ce845bc6a61e42730d25b"	"CoL"	2	"437985007"
 "B_SNGMNS_MSPH"	"Sphingomonas mesophila"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"mesophila"	""	"species"	"Li et al., 2019"	"800696"	"DSMZ"	2	
+"B_SNGMNS_MTLL"	"Sphingomonas metalli"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"metalli"	""	"species"	"Feng et al., 2016"	"794142"	"DSMZ"	2	
 "B_SNGMNS_MLLS"	"Sphingomonas molluscorum"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"molluscorum"	""	"species"	"Romanenko et al., 2007"	"faae3d7c0df29170b19eda034247ace1"	"CoL"	2	"709300006"
 "B_SNGMNS_MNTN"	"Sphingomonas montana"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"montana"	""	"species"	"Manandhar et al., 2018"	"796387"	"DSMZ"	2	
 "B_SNGMNS_MNTS"	"Sphingomonas montis"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Sphingomonadaceae"	"Sphingomonas"	"montis"	""	"species"	"Chaudhary et al., 2019"	"798059"	"DSMZ"	2	
@@ -58149,6 +58186,7 @@
 "B_STPHY_CAEL"	"Staphylococcus caeli"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"caeli"	""	"species"	"MacFadyen et al., 2019"	"798096"	"DSMZ"	1	
 "B_STPHY_CPTS"	"Staphylococcus capitis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"capitis"	""	"species"	"Kloos et al., 1975"	"1193b8010f095b3f414b0b4a7e61d941"	"CoL"	1	"40347003"
 "B_STPHY_CPTS_URLY"	"Staphylococcus capitis urealyticus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"capitis"	"urealyticus"	"infraspecies"	"Bannerman et al., 1991"	"ce0c0335b06f21a72ac55f8b284d52f1"	"CoL"	1	"103492009"
+"B_STPHY_CPTS_YTCS"	"Staphylococcus capitis ureolyticus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"capitis"	"ureolyticus"	"species"	"Bannerman et al., 1991"	"784963"	"DSMZ"	1	
 "B_STPHY_CAPR"	"Staphylococcus caprae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"caprae"	""	"species"	"Devriese et al., 1998"	"bbe445567c16e696e54dc109ba6bc9b8"	"CoL"	1	"76969000"
 "B_STPHY_CRNS"	"Staphylococcus carnosus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"carnosus"	""	"species"	"Schleifer et al., 1982"	"6e3a53da19778d9db3bef31a02cab1c8"	"CoL"	1	"9784002"
 "B_STPHY_CRNS_UTLS"	"Staphylococcus carnosus utilis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"carnosus"	"utilis"	"infraspecies"	"Probst et al., 1998"	"4f69c1cb6be4cb74200fdab137ff0acc"	"CoL"	1	"438733001"
@@ -58201,6 +58239,7 @@
 "B_STPHY_SCCN"	"Staphylococcus succinus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"succinus"	""	"species"	"Lambert et al., 1998"	"97b472391b6336adfbe3f99fa8b10469"	"CoL"	1	"438729008"
 "B_STPHY_SCCN_CASE"	"Staphylococcus succinus casei"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"succinus"	"casei"	"infraspecies"	"Place et al., 2003"	"0926b1c776f856ed9a9f9c1a9fad60f2"	"CoL"	1	"440815004"
 "B_STPHY_VTLN"	"Staphylococcus vitulinus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"vitulinus"	""	"species"	"Webster et al., 2004"	"9caa058a9ea00c6454065dd426548abe"	"CoL"	1	"440569005"
+"B_STPHY_VTLS"	"Staphylococcus vitulus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"vitulus"	""	"species"	"Webster et al., 2004"	"784968"	"DSMZ"	1	
 "B_STPHY_WRNR"	"Staphylococcus warneri"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"warneri"	""	"species"	"Kloos et al., 1975"	"7ea86b655238a5c4ef000deada350eca"	"CoL"	1	"63550006"
 "B_STPHY_XYLS"	"Staphylococcus xylosus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Staphylococcaceae"	"Staphylococcus"	"xylosus"	""	"species"	"Schleifer et al., 1975"	"117a3247c6aff3f937e16f4efe1eb22c"	"CoL"	1	"32737005"
 "B_STPHYL"	"Staphylospora"	"Bacteria"	"Firmicutes"	"Bacilli"	"Bacillales"	"Thermoactinomycetaceae"	"Staphylospora"	""	""	"genus"		""	"DSMZ"	2	
@@ -58916,7 +58955,9 @@
 "B_STRPT_CAML"	"Streptococcus cameli"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"cameli"	""	"species"	"Kadri et al., 2015"	"792771"	"DSMZ"	1	
 "B_STRPT_CANS"	"Streptococcus canis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"canis"	""	"species"	"Devriese et al., 1986"	"0849b426bc0abdfe28d40c1495f1fd5e"	"CoL"	1	"88231003"
 "B_STRPT_CAPR"	"Streptococcus caprae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"caprae"	""	"species"	"Vela et al., 2016"	"793751"	"DSMZ"	1	
+"B_STRPT_CSSL"	"Streptococcus casseliflavus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"casseliflavus"	""	"species"	"Vaughan et al., 1979"	"781304"	"DSMZ"	1	
 "B_STRPT_CSTR"	"Streptococcus castoreus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"castoreus"	""	"species"	"Lawson et al., 2005"	"2a64aa1e506cfff4215fc3ad53922a79"	"CoL"	1	
+"B_STRPT_CAVI"	"Streptococcus caviae"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"caviae"	""	"species"	"Palakawong Na Ayudthaya et al., 2017"	"795284"	"DSMZ"	1	
 "B_STRPT_CHNJ"	"Streptococcus chenjunshii"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"chenjunshii"	""	"species"	"Tian et al., 2019"	"800708"	"DSMZ"	1	
 "B_STRPT_CNST_PHRY"	"Streptococcus constellatus pharyngis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"constellatus"	"pharyngis"	"infraspecies"	"Whiley et al., 1999"	"ac1ecd4578b7331814b44a98c2f733a0"	"CoL"	1	"415602002"
 "B_STRPT_CNST_VBRG"	"Streptococcus constellatus viborgensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"constellatus"	"viborgensis"	"species"	"Jensen et al., 2013"	"790923"	"DSMZ"	1	
@@ -58986,6 +59027,7 @@
 "B_STRPT_ORSR"	"Streptococcus orisratti"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"orisratti"	""	"species"	"Zhu et al., 2000"	"6ee21abee87a261ed1b1efb79085d113"	"CoL"	1	"438034004"
 "B_STRPT_RSIS"	"Streptococcus orisuis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"orisuis"	""	"species"	"Takada et al., 2007"	"3fbb34ad017368789bbad1056730542c"	"CoL"	1	
 "B_STRPT_OVIS"	"Streptococcus ovis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"ovis"	""	"species"	"Collins et al., 2001"	"1fcad4cd3f156ca858b302d38971ee5e"	"CoL"	1	"438035003"
+"B_STRPT_OVBR"	"Streptococcus ovuberis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"ovuberis"	""	"species"	"Zamora et al., 2017"	"796216"	"DSMZ"	1	
 "B_STRPT_PNDN"	"Streptococcus panodentis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"panodentis"	""	"species"	"Okamoto et al., 2016"	"793690"	"DSMZ"	1	
 "B_STRPT_PNTH"	"Streptococcus pantholopis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"pantholopis"	""	"species"	"Bai et al., 2016"	"794568"	"DSMZ"	1	
 "B_STRPT_PRSN"	"Streptococcus parasanguinis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Streptococcaceae"	"Streptococcus"	"parasanguinis"	""	"species"	"Whiley et al., 1990"	"cb634a0af53fb79b57a68cf461079c04"	"CoL"	1	"113990002"
diff --git a/data-raw/reproduction_of_microorganisms.R b/data-raw/reproduction_of_microorganisms.R
index 4b2cfa95b..6237efaca 100644
--- a/data-raw/reproduction_of_microorganisms.R
+++ b/data-raw/reproduction_of_microorganisms.R
@@ -821,6 +821,18 @@ sum(duplicated(MOs$mo))
 sum(duplicated(MOs$fullname))
 colnames(MOs)
 
+# add the ones we would delete now, that have unexisting codes and names (also in the old names)
+MOs <- MOs %>% 
+  mutate(mo = as.character(mo)) %>% 
+  bind_rows(
+    AMR::microorganisms %>%
+      mutate(mo = as.character(mo)) %>% 
+      filter(genus %in% gen & !fullname %in% AMR::microorganisms$fullname & 
+               !fullname %in% AMR::microorganisms.old$fullname &
+               !mo  %in% microorganisms$mo) %>%
+      select(all_of(colnames(AMR::microorganisms)))
+  )
+
 # here we welcome the new ones:
 MOs %>% arrange(fullname) %>% filter(!fullname %in% AMR::microorganisms$fullname) %>% View()
 MOs.old %>% arrange(fullname) %>% filter(!fullname %in% AMR::microorganisms.old$fullname) %>% View()
diff --git a/data/microorganisms.rda b/data/microorganisms.rda
index db8f7a99b..a0714ce56 100644
Binary files a/data/microorganisms.rda and b/data/microorganisms.rda differ
diff --git a/docs/404.html b/docs/404.html
index 21defab20..e1f668e28 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -9,12 +9,12 @@
 <title>Page not found (404) • AMR (for R)</title>
 
 <!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="https://msberends.gitlab.io/AMR/favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="https://msberends.gitlab.io/AMR/favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="https://msberends.gitlab.io/AMR/apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="https://msberends.gitlab.io/AMR/apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="https://msberends.gitlab.io/AMR/apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="https://msberends.gitlab.io/AMR/apple-touch-icon-60x60.png" />
+<link rel="icon" type="image/png" sizes="16x16" href="https://msberends.github.io/AMR/favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="https://msberends.github.io/AMR/favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="https://msberends.github.io/AMR/apple-touch-icon.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="https://msberends.github.io/AMR/apple-touch-icon-120x120.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="https://msberends.github.io/AMR/apple-touch-icon-76x76.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="https://msberends.github.io/AMR/apple-touch-icon-60x60.png" />
 
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
@@ -25,8 +25,8 @@
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
 
 <!-- bootstrap-toc -->
-<link rel="stylesheet" href="https://msberends.gitlab.io/AMR/bootstrap-toc.css">
-<script src="https://msberends.gitlab.io/AMR/bootstrap-toc.js"></script>
+<link rel="stylesheet" href="https://msberends.github.io/AMR/bootstrap-toc.css">
+<script src="https://msberends.github.io/AMR/bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
@@ -40,16 +40,16 @@
 <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
-<link href="https://msberends.gitlab.io/AMR/pkgdown.css" rel="stylesheet">
-<script src="https://msberends.gitlab.io/AMR/pkgdown.js"></script>
+<link href="https://msberends.github.io/AMR/pkgdown.css" rel="stylesheet">
+<script src="https://msberends.github.io/AMR/pkgdown.js"></script>
 
 
 
-  <link href="https://msberends.gitlab.io/AMR/extra.css" rel="stylesheet">
-  <script src="https://msberends.gitlab.io/AMR/extra.js"></script>
+  <link href="https://msberends.github.io/AMR/extra.css" rel="stylesheet">
+  <script src="https://msberends.github.io/AMR/extra.js"></script>
 
 <meta property="og:title" content="Page not found (404)" />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -80,8 +80,8 @@
         <span class="icon-bar"></span>
       </button>
       <span class="navbar-brand">
-        <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
+        <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -199,8 +199,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 1d8b6b328..a1b3c299f 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -49,7 +49,7 @@
   <script src="extra.js"></script>
 
 <meta property="og:title" content="License" />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -199,8 +199,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index bbceaf2fb..29f5ece23 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -49,7 +49,7 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="Articles" />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -199,8 +199,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
diff --git a/docs/authors.html b/docs/authors.html
index ed52a0181..3d8f1e1aa 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -49,7 +49,7 @@
   <script src="extra.js"></script>
 
 <meta property="og:title" content="Citation and Authors" />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -199,8 +199,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -226,7 +226,7 @@
   <div class="contents col-md-9">
     <div class="page-header">
       <h1>Citation</h1>
-      <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
+      <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
     </div>
 
     <p>Berends MS, Luz CF et al. (2019). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622</p>
diff --git a/docs/extra.css b/docs/extra.css
index 4d4be3514..5886f4205 100644
--- a/docs/extra.css
+++ b/docs/extra.css
@@ -4,7 +4,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -17,7 +17,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 */
 
diff --git a/docs/extra.js b/docs/extra.js
index 61e7c25ca..2a7781fe1 100644
--- a/docs/extra.js
+++ b/docs/extra.js
@@ -4,7 +4,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -17,7 +17,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 */
 
@@ -88,6 +88,7 @@ $( document ).ready(function() {
       x = x.replace("Sofia", "Dr. Sofia");
       x = x.replace("Dennis", "Dr. Dennis");
       x = x.replace("Judith", "Dr. Judith");
+      x = x.replace("Gwen", "Dr. Gwen");
     }
     return(x);
   }
diff --git a/docs/index.html b/docs/index.html
index 526597767..14ac1afe3 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -24,7 +24,7 @@
     using evidence-based methods, like those defined by Leclercq et al. (2013) 
     &lt;doi:10.1111/j.1469-0691.2011.03703.x&gt; and the Clinical and Laboratory 
     Standards Institute (2014) &lt;isbn: 1-56238-899-1&gt;.">
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg">
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -161,8 +161,8 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -199,8 +199,8 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
 <a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
 <p><em>(To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.)</em></p>
 <p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
-<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
-<p>This package was created for both routine data analysis and academic research, at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>). It is fully independent of any other R package, works with all versions of R since R-3.0.0 (April 2013) and has a total file size of only 5 MB. It was designed to work in any setting, including those with very limited resources.</p>
+<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
+<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
 <div class="main-content">
 <p>
 <a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in more than 100 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from more than 100 countries <small>(source: <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge, to see the names of the countries.
@@ -371,9 +371,9 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
 <ul class="list-unstyled">
 <li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=AMR">https://​cloud.r-project.org/​package=AMR</a>
 </li>
-<li>Browse source code at <br><a href="https://gitlab.com/msberends/AMR/">https://​gitlab.com/​msberends/​AMR/​</a>
+<li>Browse source code at <br><a href="https://github.com/msberends/AMR/">https://​github.com/​msberends/​AMR/​</a>
 </li>
-<li>Report a bug at <br><a href="https://gitlab.com/msberends/AMR/issues">https://​gitlab.com/​msberends/​AMR/​issues</a>
+<li>Report a bug at <br><a href="https://github.com/msberends/AMR/issues">https://​github.com/​msberends/​AMR/​issues</a>
 </li>
 </ul>
 </div>
diff --git a/docs/news/index.html b/docs/news/index.html
index cd378f4db..b0a0d2153 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -49,7 +49,7 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="Changelog" />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -199,8 +199,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -226,16 +226,16 @@
   <div class="col-md-9 contents">
     <div class="page-header">
       <h1 data-toc-skip>Changelog <small></small></h1>
-      <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
+      <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209025" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9025">
-<a href="#amr-1209025" class="anchor"></a>AMR 1.2.0.9025<small> Unreleased </small>
+    <div id="amr-1209026" class="section level1">
+<h1 class="page-header" data-toc-text="1.2.0.9026">
+<a href="#amr-1209026" class="anchor"></a>AMR 1.2.0.9026<small> Unreleased </small>
 </h1>
-<div id="last-updated-03-jul-2020" class="section level2">
+<div id="last-updated-08-jul-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-03-jul-2020" class="anchor"></a><small>Last updated: 03-Jul-2020</small>
+<a href="#last-updated-08-jul-2020" class="anchor"></a><small>Last updated: 08-Jul-2020</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@@ -266,7 +266,7 @@
 <ul>
 <li>95% speed improvement (!) by using other base R functions for calculation</li>
 <li>Using unexisting columns wil now return an error instead of dropping them silently</li>
-<li>Using variables for column names (as well as <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again</li>
+<li>Using variables for column names (as well as selectors like <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again</li>
 </ul>
 </li>
 <li>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 9342630f1..2881a1840 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,8 +10,8 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-07-03T10:14Z
+last_built: 2020-07-08T12:47Z
 urls:
-  reference: https://msberends.gitlab.io/AMR/reference
-  article: https://msberends.gitlab.io/AMR/articles
+  reference: https://msberends.github.io/AMR/reference
+  article: https://msberends.github.io/AMR/articles
 
diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html
index 81947548b..3b333d83a 100644
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Deprecated functions — AMR-deprecated" />
 <meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Deprecated functions</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
     <div class="hidden name"><code>AMR-deprecated.Rd</code></div>
     </div>
 
@@ -258,7 +258,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html
index b7587f79d..d544e5055 100644
--- a/docs/reference/AMR.html
+++ b/docs/reference/AMR.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="The <code>AMR</code> Package — AMR" />
 <meta property="og:description" content="Welcome to the AMR package." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>The <code>AMR</code> Package</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
     <div class="hidden name"><code>AMR.Rd</code></div>
     </div>
 
@@ -263,7 +263,7 @@
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>
 
     
@@ -278,7 +278,7 @@ Post Office Box 30001 <br />
 9700 RB Groningen <br />
 The Netherlands</p>
 <p>If you have found a bug, please file a new issue at: <br />
-<a href='https://gitlab.com/msberends/AMR/issues'>https://gitlab.com/msberends/AMR/issues</a></p>
+<a href='https://github.com/msberends/AMR/issues'>https://github.com/msberends/AMR/issues</a></p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html
index 2f397f2c1..c3097eda0 100644
--- a/docs/reference/WHOCC.html
+++ b/docs/reference/WHOCC.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC" />
 <meta property="og:description" content="All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
     <div class="hidden name"><code>WHOCC.Rd</code></div>
     </div>
 
@@ -250,7 +250,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"meropenem"</span>)
diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html
index 1c678316d..ba7e18978 100644
--- a/docs/reference/WHONET.html
+++ b/docs/reference/WHONET.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Data set with 500 isolates - WHONET example — WHONET" />
 <meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our example_isolates data set." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Data set with 500 isolates - WHONET example</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>WHONET.Rd</code></div>
     </div>
 
@@ -273,7 +273,7 @@
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/ab_from_text.html b/docs/reference/ab_from_text.html
index b2d2fdc21..2beae0e04 100644
--- a/docs/reference/ab_from_text.html
+++ b/docs/reference/ab_from_text.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Retrieve antimicrobial drug names and doses from clinical text — ab_from_text" />
 <meta property="og:description" content="Use this function on e.g. clinical texts from health care records. It returns a list with all antimicrobial drugs, doses and forms of administration found in the texts." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Retrieve antimicrobial drug names and doses from clinical text</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
     <div class="hidden name"><code>ab_from_text.Rd</code></div>
     </div>
 
@@ -299,12 +299,12 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>
diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html
index 1d598718a..ac866358f 100644
--- a/docs/reference/ab_property.html
+++ b/docs/reference/ab_property.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Property of an antibiotic — ab_property" />
 <meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Property of an antibiotic</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
     <div class="hidden name"><code>ab_property.Rd</code></div>
     </div>
 
@@ -330,7 +330,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>
diff --git a/docs/reference/age.html b/docs/reference/age.html
index 805ebac03..6932ebaf8 100644
--- a/docs/reference/age.html
+++ b/docs/reference/age.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Age in years of individuals — age" />
 <meta property="og:description" content="Calculates age in years based on a reference date, which is the sytem date at default." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Age in years of individuals</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
     <div class="hidden name"><code>age.Rd</code></div>
     </div>
 
@@ -272,7 +272,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>
diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html
index b8efb20b5..8ce9572b9 100644
--- a/docs/reference/age_groups.html
+++ b/docs/reference/age_groups.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Split ages into age groups — age_groups" />
 <meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Split ages into age groups</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
     <div class="hidden name"><code>age_groups.Rd</code></div>
     </div>
 
@@ -281,7 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>
diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html
index d6f585e9a..2a558a114 100644
--- a/docs/reference/antibiotics.html
+++ b/docs/reference/antibiotics.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Data sets with 558 antimicrobials — antibiotics" />
 <meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_property() functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Data sets with 558 antimicrobials</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>antibiotics.Rd</code></div>
     </div>
 
@@ -291,13 +291,13 @@
 
 
 <p>These data sets are available as 'flat files' for use even without R - you can find the files here:</p><ul>
-<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
-<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
+<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
+<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
 </ul>
 
 <p>Files in R format (with preserved data structure) can be found here:</p><ul>
-<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda'>https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda</a></p></li>
-<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda'>https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda</a></p></li>
+<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antibiotics.rda'>https://github.com/msberends/AMR/raw/master/data/antibiotics.rda</a></p></li>
+<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antivirals.rda'>https://github.com/msberends/AMR/raw/master/data/antivirals.rda</a></p></li>
 </ul>
 
 
@@ -314,7 +314,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html
index 88709ef9e..6f6e87d5e 100644
--- a/docs/reference/as.ab.html
+++ b/docs/reference/as.ab.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Transform to antibiotic ID — as.ab" />
 <meta property="og:description" content="Use this function to determine the antibiotic code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Transform to antibiotic ID</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
     <div class="hidden name"><code>as.ab.Rd</code></div>
     </div>
 
@@ -282,7 +282,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
     <h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
 
     
@@ -296,7 +296,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'>
diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html
index ce24cf291..c5b869af0 100644
--- a/docs/reference/as.disk.html
+++ b/docs/reference/as.disk.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Class 'disk' — as.disk" />
 <meta property="og:description" content="This transforms a vector to a new class disk, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Class 'disk'</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
     <div class="hidden name"><code>as.disk.Rd</code></div>
     </div>
 
@@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html
index d89457ab0..827d7eb5c 100644
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Class 'mic' — as.mic" />
 <meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Class 'mic'</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
     <div class="hidden name"><code>as.mic.Rd</code></div>
     </div>
 
@@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index 54b936058..a9983ffbd 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Transform to microorganism ID — as.mo" />
 <meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like &quot;Staphylococcus aureus&quot;), an abbreviated name (like &quot;S. aureus&quot;), an abbreviation known in the field (like &quot;MRSA&quot;), or just a genus. Please see Examples." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Transform to microorganism ID</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
     <div class="hidden name"><code>as.mo.Rd</code></div>
     </div>
 
@@ -378,7 +378,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a> for the <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that is being used to determine ID's.</p>
diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html
index 87c8ae266..2cdc45028 100644
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Class 'rsi' — as.rsi" />
 <meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Class 'rsi'</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
     <div class="hidden name"><code>as.rsi.Rd</code></div>
     </div>
 
@@ -308,7 +308,7 @@
 
     <p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p>
 <p>Supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p>
-<p>The repository of this package <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This <strong>allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
+<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This <strong>allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
 <p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
 <p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
     <h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@@ -336,7 +336,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div>
diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html
index 3d7fd6bba..77e06cb6e 100644
--- a/docs/reference/atc_online.html
+++ b/docs/reference/atc_online.html
@@ -51,7 +51,7 @@
 <meta property="og:title" content="Get ATC properties from WHOCC website — atc_online_property" />
 <meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
 This function requires an internet connection." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -83,7 +83,7 @@ This function requires an internet connection." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -201,8 +201,8 @@ This function requires an internet connection." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -228,7 +228,7 @@ This function requires an internet connection." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Get ATC properties from WHOCC website</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
     <div class="hidden name"><code>atc_online.Rd</code></div>
     </div>
 
@@ -312,7 +312,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
diff --git a/docs/reference/availability.html b/docs/reference/availability.html
index b1ca9639b..e600f0efc 100644
--- a/docs/reference/availability.html
+++ b/docs/reference/availability.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Check availability of columns — availability" />
 <meta property="og:description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Check availability of columns</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
     <div class="hidden name"><code>availability.Rd</code></div>
     </div>
 
@@ -267,7 +267,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>availability</span>(<span class='no'>example_isolates</span>)
diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html
index fcd717542..7473b468d 100644
--- a/docs/reference/bug_drug_combinations.html
+++ b/docs/reference/bug_drug_combinations.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Determine bug-drug combinations — bug_drug_combinations" />
 <meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Determine bug-drug combinations</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
     <div class="hidden name"><code>bug_drug_combinations.Rd</code></div>
     </div>
 
@@ -333,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># \donttest{</span>
diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html
index ed7cf2c52..689b12023 100644
--- a/docs/reference/catalogue_of_life.html
+++ b/docs/reference/catalogue_of_life.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
 <meta property="og:description" content="This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>The Catalogue of Life</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
     <div class="hidden name"><code>catalogue_of_life.Rd</code></div>
     </div>
 
@@ -258,12 +258,12 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 </ul>
 
 <p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
-<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
+<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />
diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html
index 836074f6c..6b3ed87bf 100644
--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
 <meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Version info of included Catalogue of Life</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
     <div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
     </div>
 
@@ -255,7 +255,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
diff --git a/docs/reference/count.html b/docs/reference/count.html
index f70225a26..955601c86 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -51,7 +51,7 @@
 <meta property="og:title" content="Count available isolates — count" />
 <meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, please see Examples.
 count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -201,8 +201,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -228,7 +228,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Count available isolates</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
     <div class="hidden name"><code>count.Rd</code></div>
     </div>
 
@@ -360,7 +360,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='proportion.html'>proportion_*</a></code> to calculate microbial resistance and susceptibility.</p></div>
diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html
index ad203be41..a0b131007 100644
--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@@ -51,7 +51,7 @@
 <meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
 <meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.
 To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -201,8 +201,8 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -228,7 +228,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Apply EUCAST rules</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
     <div class="hidden name"><code>eucast_rules.Rd</code></div>
     </div>
 
@@ -307,7 +307,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 </ul>
 
 <p>These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use <code>eucast_rules(..., rules = "all")</code>, or set the default behaviour of the <code>[eucast_rules()]</code> function with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code> (or any other valid input value(s) to the <code>rules</code> parameter).</p>
-<p>The file containing all EUCAST rules is located here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
+<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
     <h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
 
     
@@ -398,12 +398,12 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># \donttest{</span>
diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html
index 19c332ce6..0233a31ce 100644
--- a/docs/reference/example_isolates.html
+++ b/docs/reference/example_isolates.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Data set with 2,000 example isolates — example_isolates" />
 <meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,12 +227,12 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Data set with 2,000 example isolates</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>example_isolates.Rd</code></div>
     </div>
 
     <div class="ref-description">
-    <p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
+    <p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read <a href='https://msberends.github.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
     </div>
 
     <pre class="usage"><span class='no'>example_isolates</span></pre>
@@ -257,7 +257,7 @@
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html
index 9f84ea4fd..918ddb4f9 100644
--- a/docs/reference/example_isolates_unclean.html
+++ b/docs/reference/example_isolates_unclean.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Data set with unclean data — example_isolates_unclean" />
 <meta property="og:description" content="A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Data set with unclean data</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>example_isolates_unclean.Rd</code></div>
     </div>
 
@@ -252,7 +252,7 @@
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html
index 36a19be30..bc0576d68 100644
--- a/docs/reference/filter_ab_class.html
+++ b/docs/reference/filter_ab_class.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Filter isolates on result in antimicrobial class — filter_ab_class" />
 <meta property="og:description" content="Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Filter isolates on result in antimicrobial class</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
     <div class="hidden name"><code>filter_ab_class.Rd</code></div>
     </div>
 
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html
index 2bf68dc24..fd0d8cee8 100644
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Determine first (weighted) isolates — first_isolate" />
 <meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Determine first (weighted) isolates</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
     <div class="hidden name"><code>first_isolate.Rd</code></div>
     </div>
 
@@ -393,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='key_antibiotics.html'>key_antibiotics()</a></code></p></div>
diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html
index bafe27042..17d7d0847 100644
--- a/docs/reference/g.test.html
+++ b/docs/reference/g.test.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="<em>G</em>-test for Count Data — g.test" />
 <meta property="og:description" content="g.test() performs chi-squared contingency table tests and goodness-of-fit tests, just like chisq.test() but is more reliable (1). A G-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a G-test of goodness-of-fit), or to see whether the proportions of one variable are different for different values of the other variable (called a G-test of independence)." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1><em>G</em>-test for Count Data</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
     <div class="hidden name"><code>g.test.Rd</code></div>
     </div>
 
@@ -334,7 +334,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
     
diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html
index 817366853..a9b9d8dd4 100644
--- a/docs/reference/ggplot_pca.html
+++ b/docs/reference/ggplot_pca.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="PCA biplot with <code>ggplot2</code> — ggplot_pca" />
 <meta property="og:description" content="Produces a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>PCA biplot with <code>ggplot2</code></h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
     <div class="hidden name"><code>ggplot_pca.Rd</code></div>
     </div>
 
@@ -376,7 +376,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html
index c5c210578..aca21a720 100644
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@@ -49,8 +49,8 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
-<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot2 functions." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on ggplot2 functions." />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,12 +227,12 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>AMR plots with <code>ggplot2</code></h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
     <div class="hidden name"><code>ggplot_rsi.Rd</code></div>
     </div>
 
     <div class="ref-description">
-    <p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
+    <p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
     </div>
 
     <pre class="usage"><span class='fu'>ggplot_rsi</span>(
@@ -393,10 +393,10 @@
 
 <p><code>geom_rsi()</code> will take any variable from the data that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
 <p><code>facet_rsi()</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>ggplot2::facet_wrap()</a></code>.</p>
-<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code>ggplot2::scale_continuous()</code>.</p>
-<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code>ggplot2::scale_brewer()</code>.</p>
+<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>ggplot2::scale_y_continuous()</a></code>.</p>
+<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code><a href='https://ggplot2.tidyverse.org/reference/scale_manual.html'>ggplot2::scale_fill_manual()</a></code>.</p>
 <p><code>theme_rsi()</code> is a [ggplot2 theme][<code><a href='https://ggplot2.tidyverse.org/reference/theme.html'>ggplot2::theme()</a></code> with minimal distraction.</p>
-<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code></p>
+<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code>.</p>
 <p><code>ggplot_rsi()</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p>
 
     <h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
@@ -404,12 +404,12 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>) <span class='kw'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html
index 043a291d3..0478d8c9e 100644
--- a/docs/reference/guess_ab_col.html
+++ b/docs/reference/guess_ab_col.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Guess antibiotic column — guess_ab_col" />
 <meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Guess antibiotic column</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
     <div class="hidden name"><code>guess_ab_col.Rd</code></div>
     </div>
 
@@ -265,12 +265,12 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"S"</span>,
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 118cdf9f0..9ff31e9e1 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -49,7 +49,7 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="Function reference" />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -199,8 +199,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -484,7 +484,7 @@
         <td>
           <p><code><a href="microorganisms.html">microorganisms</a></code> </p>
         </td>
-        <td><p>Data set with 67,108 microorganisms</p></td>
+        <td><p>Data set with 67,150 microorganisms</p></td>
       </tr><tr>
         
         <td>
diff --git a/docs/reference/join.html b/docs/reference/join.html
index 2f7f8a229..fccd684b4 100644
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Join <a href='microorganisms.html'>microorganisms</a> to a data set — join" />
 <meta property="og:description" content="Join the data set microorganisms easily to an existing table or character vector." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Join <a href='microorganisms.html'>microorganisms</a> to a data set</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
     <div class="hidden name"><code>join.Rd</code></div>
     </div>
 
@@ -283,7 +283,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))
diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html
index 21ef75b39..785ff3cbd 100644
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Key antibiotics for first <em>weighted</em> isolates — key_antibiotics" />
 <meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Key antibiotics for first <em>weighted</em> isolates</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/key_antibiotics.R'><code>R/key_antibiotics.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/key_antibiotics.R'><code>R/key_antibiotics.R</code></a></small>
     <div class="hidden name"><code>key_antibiotics.Rd</code></div>
     </div>
 
@@ -379,7 +379,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>
diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html
index c963c0601..a482ad841 100644
--- a/docs/reference/kurtosis.html
+++ b/docs/reference/kurtosis.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Kurtosis of the sample — kurtosis" />
 <meta property="og:description" content="Kurtosis is a measure of the &quot;tailedness&quot; of the probability distribution of a real-valued random variable." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Kurtosis of the sample</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/kurtosis.R'><code>R/kurtosis.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/kurtosis.R'><code>R/kurtosis.R</code></a></small>
     <div class="hidden name"><code>kurtosis.Rd</code></div>
     </div>
 
@@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='skewness.html'>skewness()</a></code></p></div>
diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html
index 098218f17..233b6f04f 100644
--- a/docs/reference/lifecycle.html
+++ b/docs/reference/lifecycle.html
@@ -52,7 +52,7 @@
 <meta property="og:description" content="Functions in this AMR package are categorised using the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle.
  
 This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -202,8 +202,8 @@ This page contains a section for every lifecycle (with text borrowed from the af
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -229,7 +229,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Lifecycles of functions in the <code>AMR</code> package</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
     <div class="hidden name"><code>lifecycle.Rd</code></div>
     </div>
 
@@ -252,7 +252,7 @@ The lifecycle of this function is <strong>experimental</strong>. An experimental
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
 
     
diff --git a/docs/reference/like.html b/docs/reference/like.html
index a04e2e5ce..2eb06caa9 100644
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Pattern Matching — like" />
 <meta property="og:description" content="Convenient wrapper around grep() to match a pattern: x %like% pattern. It always returns a logical vector and is always case-insensitive (use x %like_case% pattern for case-sensitive matching). Also, pattern can be as long as x to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Pattern Matching</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/like.R'><code>R/like.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/like.R'><code>R/like.R</code></a></small>
     <div class="hidden name"><code>like.Rd</code></div>
     </div>
 
@@ -285,7 +285,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>base::grep()</a></code></p></div>
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index 138b989a4..d702b31b2 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Determine multidrug-resistant organisms (MDRO) — mdro" />
 <meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Determine multidrug-resistant organisms (MDRO)</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mdro.R'><code>R/mdro.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mdro.R'><code>R/mdro.R</code></a></small>
     <div class="hidden name"><code>mdro.Rd</code></div>
     </div>
 
@@ -326,14 +326,14 @@ The German national guideline - Mueller et al. (2015) Antimicrobial Resistance a
 The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<a href='https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'>link</a>)</p></li>
 </ul>
 
-<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://gitlab.com/msberends/AMR/issues/new'>https://gitlab.com/msberends/AMR/issues/new</a>.</p>
+<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://github.com/msberends/AMR/issues/new'>https://github.com/msberends/AMR/issues/new</a>.</p>
 <p><strong>Note:</strong> Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu <em>et al.</em> in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this <code>mdro()</code> function makes sure that results from before 2016 and after 2016 are identical.</p>
     <h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
 
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
     <h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
 
     
@@ -437,7 +437,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html
index f4ef168e6..90e3df158 100644
--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Translation table with 5,582 common microorganism codes — microorganisms.codes" />
 <meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Translation table with 5,582 common microorganism codes</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>microorganisms.codes.Rd</code></div>
     </div>
 
@@ -256,7 +256,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index 6ec1c4cfc..aa3a95cd4 100644
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Data set with 67,108 microorganisms — microorganisms • AMR (for R)</title>
+<title>Data set with 67,150 microorganisms — microorganisms • AMR (for R)</title>
 
 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,9 +48,9 @@
   <link href="../extra.css" rel="stylesheet">
   <script src="../extra.js"></script>
 
-<meta property="og:title" content="Data set with 67,108 microorganisms — microorganisms" />
+<meta property="og:title" content="Data set with 67,150 microorganisms — microorganisms" />
 <meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo()." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -226,8 +226,8 @@
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Data set with 67,108 microorganisms</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
+    <h1>Data set with 67,150 microorganisms</h1>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>microorganisms.Rd</code></div>
     </div>
 
@@ -240,7 +240,7 @@
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 67,108 observations and 16 variables:</p><ul>
+    <p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 67,150 observations and 16 variables:</p><ul>
 <li><p><code>mo</code><br /> ID of microorganism as used by this package</p></li>
 <li><p><code>fullname</code><br /> Full name, like <code>"Escherichia coli"</code></p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br /> Taxonomic rank of the microorganism</p></li>
@@ -266,17 +266,17 @@
 <li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
 <li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
 <li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
-<li><p>7,369 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
+<li><p>7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
 </ul>
 <h3>Direct download</h3>
 
 
 <p>This data set is available as 'flat file' for use even without R - you can find the file here:</p><ul>
-<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
+<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
 </ul>
 
 <p>The file in R format (with preserved data structure) can be found here:</p><ul>
-<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda'>https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda</a></p></li>
+<li><p><a href='https://github.com/msberends/AMR/raw/master/data/microorganisms.rda'>https://github.com/msberends/AMR/raw/master/data/microorganisms.rda</a></p></li>
 </ul>
 
 
@@ -297,7 +297,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code>, <code><a href='mo_property.html'>mo_property()</a></code>, <a href='microorganisms.codes.html'>microorganisms.codes</a></p></div>
diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html
index 5ef7a925b..924348aa1 100644
--- a/docs/reference/microorganisms.old.html
+++ b/docs/reference/microorganisms.old.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Data set with previously accepted taxonomic names — microorganisms.old" />
 <meta property="og:description" content="A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by as.mo()." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Data set with previously accepted taxonomic names</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>microorganisms.old.Rd</code></div>
     </div>
 
@@ -262,7 +262,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <code><a href='mo_property.html'>mo_property()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html
index 7e9d3b807..80e4ccb62 100644
--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Property of a microorganism — mo_property" />
 <meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Property of a microorganism</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_property.R'><code>R/mo_property.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_property.R'><code>R/mo_property.R</code></a></small>
     <div class="hidden name"><code>mo_property.Rd</code></div>
     </div>
 
@@ -361,7 +361,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html
index d57db0173..d6e63d637 100644
--- a/docs/reference/mo_source.html
+++ b/docs/reference/mo_source.html
@@ -51,7 +51,7 @@
 <meta property="og:title" content="User-defined reference data set for microorganisms — mo_source" />
 <meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
 This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -201,8 +201,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -228,7 +228,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>User-defined reference data set for microorganisms</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo_source.R'><code>R/mo_source.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_source.R'><code>R/mo_source.R</code></a></small>
     <div class="hidden name"><code>mo_source.Rd</code></div>
     </div>
 
@@ -316,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/p_symbol.html b/docs/reference/p_symbol.html
index e0af51ccd..a8ca70496 100644
--- a/docs/reference/p_symbol.html
+++ b/docs/reference/p_symbol.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Symbol of a p-value — p_symbol" />
 <meta property="og:description" content="Return the symbol related to the p-value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above p = 1 will return NA." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Symbol of a p-value</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/p_symbol.R'><code>R/p_symbol.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/p_symbol.R'><code>R/p_symbol.R</code></a></small>
     <div class="hidden name"><code>p_symbol.Rd</code></div>
     </div>
 
@@ -263,7 +263,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/pca.html b/docs/reference/pca.html
index f8b748e38..65f3ca3ee 100644
--- a/docs/reference/pca.html
+++ b/docs/reference/pca.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Principal Component Analysis (for AMR) — pca" />
 <meta property="og:description" content="Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Principal Component Analysis (for AMR)</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
     <div class="hidden name"><code>pca.Rd</code></div>
     </div>
 
@@ -309,7 +309,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html
index 06312d910..d813340b4 100644
--- a/docs/reference/proportion.html
+++ b/docs/reference/proportion.html
@@ -51,7 +51,7 @@
 <meta property="og:title" content="Calculate microbial resistance — proportion" />
 <meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, please see Examples.
 resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -201,8 +201,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -228,7 +228,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Calculate microbial resistance</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/proportion.R'><code>R/proportion.R</code></a>, <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi_df.R'><code>R/rsi_df.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/proportion.R'><code>R/proportion.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/rsi_df.R'><code>R/rsi_df.R</code></a></small>
     <div class="hidden name"><code>proportion.Rd</code></div>
     </div>
 
@@ -379,10 +379,10 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p><code><a href='count.html'>AMR::count()</a></code> to count resistant and susceptible isolates.</p></div>
+    <div class='dont-index'><p><code><a href='count.html'>count()</a></code> to count resistant and susceptible isolates.</p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html
index 62dae6fdb..3c83d01c2 100644
--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Predict antimicrobial resistance — resistance_predict" />
 <meta property="og:description" content="Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Predict antimicrobial resistance</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/resistance_predict.R'><code>R/resistance_predict.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/resistance_predict.R'><code>R/resistance_predict.R</code></a></small>
     <div class="hidden name"><code>resistance_predict.Rd</code></div>
     </div>
 
@@ -362,7 +362,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
     <h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
 
     
@@ -381,7 +381,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>The <code><a href='proportion.html'>proportion()</a></code> functions to calculate resistance</p>
diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html
index 0e781a49a..a643e648f 100644
--- a/docs/reference/rsi_translation.html
+++ b/docs/reference/rsi_translation.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Data set for R/SI interpretation — rsi_translation" />
 <meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Data set for R/SI interpretation</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>rsi_translation.Rd</code></div>
     </div>
 
@@ -255,12 +255,12 @@
 
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p>
+    <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html
index 8225249df..e9eee5995 100644
--- a/docs/reference/skewness.html
+++ b/docs/reference/skewness.html
@@ -51,7 +51,7 @@
 <meta property="og:title" content="Skewness of the sample — skewness" />
 <meta property="og:description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
 When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -201,8 +201,8 @@ When negative: the left tail is longer; the mass of the distribution is concentr
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -228,7 +228,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Skewness of the sample</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/skewness.R'><code>R/skewness.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/skewness.R'><code>R/skewness.R</code></a></small>
     <div class="hidden name"><code>skewness.Rd</code></div>
     </div>
 
@@ -271,7 +271,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='kurtosis.html'>kurtosis()</a></code></p></div>
diff --git a/docs/reference/translate.html b/docs/reference/translate.html
index c23a5d7e2..b105c9de5 100644
--- a/docs/reference/translate.html
+++ b/docs/reference/translate.html
@@ -50,7 +50,7 @@
 
 <meta property="og:title" content="Translate strings from AMR package — translate" />
 <meta property="og:description" content="For language-dependent output of AMR functions, like mo_name(), mo_gramstain(), mo_type() and ab_name()." />
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
 
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
       </span>
     </div>
 
@@ -200,8 +200,8 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="https://gitlab.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+  <a href="https://github.com/msberends/AMR">
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -227,7 +227,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Translate strings from AMR package</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/translate.R'><code>R/translate.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/translate.R'><code>R/translate.R</code></a></small>
     <div class="hidden name"><code>translate.Rd</code></div>
     </div>
 
@@ -240,9 +240,9 @@
 
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>.</p>
-<p>Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Not all these languages currently have translations available for all antimicrobial agents and colloquial microorganism names.</p>
-<p>Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
+    <p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>.</p>
+<p>Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
+<p>Please suggest your own translations <a href='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p>
 <p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property()</a></code> functions (<code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.).</p>
 <p>The system language will be used at default, if that language is supported. The system language can be overwritten with <code><a href='https://rdrr.io/r/base/Sys.setenv.html'>Sys.setenv(AMR_locale = yourlanguage)</a></code>.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@@ -256,7 +256,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># The 'language' parameter of below functions</span>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 5dd3ef714..732bf7711 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -1,174 +1,174 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
-    <loc>https://msberends.gitlab.io/AMR/index.html</loc>
+    <loc>https://msberends.github.io/AMR/index.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/AMR-deprecated.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/AMR-deprecated.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/AMR.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/AMR.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/WHOCC.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/WHOCC.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/WHONET.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/WHONET.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/ab_from_text.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/ab_from_text.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/ab_property.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/ab_property.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/age.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/age.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/age_groups.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/age_groups.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/antibiotic_class_selectors.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/antibiotics.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/antibiotics.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/as.ab.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/as.ab.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/as.disk.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/as.disk.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/as.mic.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/as.mic.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/as.mo.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/as.mo.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/as.rsi.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/as.rsi.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/atc_online.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/atc_online.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/availability.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/availability.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/bug_drug_combinations.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/bug_drug_combinations.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/catalogue_of_life.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/catalogue_of_life.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/catalogue_of_life_version.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/catalogue_of_life_version.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/count.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/count.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/eucast_rules.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/eucast_rules.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/example_isolates.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/example_isolates.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/example_isolates_unclean.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/example_isolates_unclean.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/filter_ab_class.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/filter_ab_class.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/first_isolate.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/first_isolate.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/g.test.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/g.test.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/ggplot_pca.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/ggplot_pca.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/ggplot_rsi.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/ggplot_rsi.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/guess_ab_col.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/guess_ab_col.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/join.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/join.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/key_antibiotics.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/key_antibiotics.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/kurtosis.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/kurtosis.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/lifecycle.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/lifecycle.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/like.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/like.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/mdro.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/mdro.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/microorganisms.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/microorganisms.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/microorganisms.codes.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/microorganisms.codes.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/microorganisms.old.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/microorganisms.old.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/mo_property.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/mo_property.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/mo_source.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/mo_source.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/p_symbol.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/p_symbol.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/pca.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/pca.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/proportion.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/proportion.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/resistance_predict.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/resistance_predict.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/rsi_translation.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/rsi_translation.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/skewness.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/skewness.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/reference/translate.html</loc>
+    <loc>https://msberends.github.io/AMR/reference/translate.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/AMR.html</loc>
+    <loc>https://msberends.github.io/AMR/articles/AMR.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/EUCAST.html</loc>
+    <loc>https://msberends.github.io/AMR/articles/EUCAST.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/MDR.html</loc>
+    <loc>https://msberends.github.io/AMR/articles/MDR.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/PCA.html</loc>
+    <loc>https://msberends.github.io/AMR/articles/PCA.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/SPSS.html</loc>
+    <loc>https://msberends.github.io/AMR/articles/SPSS.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/WHONET.html</loc>
+    <loc>https://msberends.github.io/AMR/articles/WHONET.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/benchmarks.html</loc>
+    <loc>https://msberends.github.io/AMR/articles/benchmarks.html</loc>
   </url>
   <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/resistance_predict.html</loc>
+    <loc>https://msberends.github.io/AMR/articles/resistance_predict.html</loc>
   </url>
 </urlset>
diff --git a/git_merge.sh b/git_merge.sh
index 9f9404ccd..caca81c78 100755
--- a/git_merge.sh
+++ b/git_merge.sh
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,13 +16,13 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 ########################################################################
 # `git_premaster.sh` takes 3 parameters:                               #
 #   1. Commit message (character) [mandatory]                          #
-#   2. Lazy website generation (logical), with FALSE only changed      #
+#   2. Lazy website generation (logical), with TRUE only changed       #
 #      files will be processed [defaults to TRUE]                      #
 #   3. Version number to be used in DESCRIPTION and NEWS.md            #
 #      [defaults to current tag and last commit number + 9000]         #
diff --git a/git_premaster.sh b/git_premaster.sh
index f5d9e7e67..1aa872ddd 100755
--- a/git_premaster.sh
+++ b/git_premaster.sh
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,13 +16,13 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 ########################################################################
 # `git_premaster.sh` takes 3 parameters:                               #
 #   1. Commit message (character) [mandatory]                          #
-#   2. Lazy website generation (logical), with FALSE only changed      #
+#   2. Lazy website generation (logical), with TRUE only changed       #
 #      files will be processed [defaults to TRUE]                      #
 #   3. Version number to be used in DESCRIPTION and NEWS.md            #
 #      [defaults to current tag and last commit number + 9000]         #
@@ -139,10 +139,13 @@ echo
 echo "•••••••••••••••••••••••••••"
 echo "• Uploading to repository •"
 echo "•••••••••••••••••••••••••••"
+# save latest changes as well
+git add .
+# and commit
 git commit -a -m "(v$new_version) $1" --quiet
 git push --quiet
 echo "Comparison:"
-echo "https://gitlab.com/msberends/AMR/compare/master...premaster?view=inline"
+echo "https://github.com/msberends/AMR/compare/master...premaster?view=inline"
 
 echo
 echo "•••••••••"
diff --git a/git_siteonly.sh b/git_siteonly.sh
index 0c7df013e..da1354343 100755
--- a/git_siteonly.sh
+++ b/git_siteonly.sh
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,13 +16,13 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 ########################################################################
 # `git_premaster.sh` takes 3 parameters:                               #
 #   1. Commit message (character) [mandatory]                          #
-#   2. Lazy website generation (logical), with FALSE only changed      #
+#   2. Lazy website generation (logical), with TRUE only changed       #
 #      files will be processed [defaults to TRUE]                      #
 #   3. Version number to be used in DESCRIPTION and NEWS.md            #
 #      [defaults to current tag and last commit number + 9000]         #
diff --git a/index.md b/index.md
index 71f34b1d0..24e76d715 100644
--- a/index.md
+++ b/index.md
@@ -9,9 +9,9 @@
 
 `AMR` is a free, open-source and independent [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
 
-After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
 
-This package was created for both routine data analysis and academic research, at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)). It is fully independent of any other R package, works with all versions of R since R-3.0.0 (April 2013) and has a total file size of only 5 MB. It was designed to work in any setting, including those with very limited resources.
+This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
 
 <div class="main-content"> 
   <p>
diff --git a/man/AMR-deprecated.Rd b/man/AMR-deprecated.Rd
index 456c38d25..27ef3c166 100644
--- a/man/AMR-deprecated.Rd
+++ b/man/AMR-deprecated.Rd
@@ -28,12 +28,12 @@ These functions are so-called '\link{Deprecated}'. They will be removed in a fut
 \section{Retired lifecycle}{
 
 \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
+The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \keyword{internal}
diff --git a/man/AMR.Rd b/man/AMR.Rd
index 97a8c1aed..1fca5bdd4 100644
--- a/man/AMR.Rd
+++ b/man/AMR.Rd
@@ -32,7 +32,7 @@ This package can be used for:
 }
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \section{Contact Us}{
@@ -49,6 +49,6 @@ Post Office Box 30001 \cr
 The Netherlands
 
 If you have found a bug, please file a new issue at: \cr
-\url{https://gitlab.com/msberends/AMR/issues}
+\url{https://github.com/msberends/AMR/issues}
 }
 
diff --git a/man/WHOCC.Rd b/man/WHOCC.Rd
index a3c8d6281..2b7d4c4ae 100644
--- a/man/WHOCC.Rd
+++ b/man/WHOCC.Rd
@@ -20,7 +20,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/WHONET.Rd b/man/WHONET.Rd
index 3cfd18872..4a46724ce 100644
--- a/man/WHONET.Rd
+++ b/man/WHONET.Rd
@@ -43,7 +43,7 @@ This example data set has the exact same structure as an export file from WHONET
 }
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \keyword{datasets}
diff --git a/man/ab_from_text.Rd b/man/ab_from_text.Rd
index e759299fc..1d305ecc8 100644
--- a/man/ab_from_text.Rd
+++ b/man/ab_from_text.Rd
@@ -57,12 +57,12 @@ With using \code{collapse}, this function will return a \link{character}:\cr
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/ab_property.Rd b/man/ab_property.Rd
index e1fea2b4b..84551a67d 100644
--- a/man/ab_property.Rd
+++ b/man/ab_property.Rd
@@ -79,7 +79,7 @@ The function \code{\link[=ab_url]{ab_url()}} will return the direct URL to the o
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
@@ -95,7 +95,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/age.Rd b/man/age.Rd
index 3d0d34831..7778f9119 100644
--- a/man/age.Rd
+++ b/man/age.Rd
@@ -24,14 +24,14 @@ Calculates age in years based on a reference date, which is the sytem date at de
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/age_groups.Rd b/man/age_groups.Rd
index c019e59a4..c1215399f 100644
--- a/man/age_groups.Rd
+++ b/man/age_groups.Rd
@@ -36,14 +36,14 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd
index aaf228bf0..a45258feb 100644
--- a/man/antibiotics.Rd
+++ b/man/antibiotics.Rd
@@ -64,14 +64,14 @@ Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and co
 
 These data sets are available as 'flat files' for use even without R - you can find the files here:
 \itemize{
-\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt}
-\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt}
+\item \url{https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt}
+\item \url{https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt}
 }
 
 Files in R format (with preserved data structure) can be found here:
 \itemize{
-\item \url{https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda}
-\item \url{https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda}
+\item \url{https://github.com/msberends/AMR/raw/master/data/antibiotics.rda}
+\item \url{https://github.com/msberends/AMR/raw/master/data/antivirals.rda}
 }
 }
 }
@@ -89,7 +89,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \seealso{
diff --git a/man/as.ab.Rd b/man/as.ab.Rd
index 28cb99116..7d43dce5b 100644
--- a/man/as.ab.Rd
+++ b/man/as.ab.Rd
@@ -48,7 +48,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \section{WHOCC}{
@@ -65,7 +65,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/as.disk.Rd b/man/as.disk.Rd
index ce721f981..70e67586c 100644
--- a/man/as.disk.Rd
+++ b/man/as.disk.Rd
@@ -27,14 +27,14 @@ Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It sup
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/as.mic.Rd b/man/as.mic.Rd
index 819e53547..0f5bb533f 100755
--- a/man/as.mic.Rd
+++ b/man/as.mic.Rd
@@ -27,14 +27,14 @@ To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MI
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/as.mo.Rd b/man/as.mo.Rd
index 446b970bb..49dacd786 100644
--- a/man/as.mo.Rd
+++ b/man/as.mo.Rd
@@ -133,7 +133,7 @@ Group 3 (least prevalent microorganisms) consists of all other microorganisms.
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
@@ -148,7 +148,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd
index ddfec9ee3..e434b75db 100755
--- a/man/as.rsi.Rd
+++ b/man/as.rsi.Rd
@@ -64,7 +64,7 @@ When using \code{\link[=as.rsi]{as.rsi()}} on untransformed data, the data will
 
 Supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using \code{"CLSI"} or \code{"EUCAST"} for input will automatically select the latest version of that guideline.
 
-The repository of this package \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This \strong{allows for easy implementation of these rules in laboratory information systems (LIS)}.
+The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This \strong{allows for easy implementation of these rules in laboratory information systems (LIS)}.
 
 After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rules]{eucast_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
 
@@ -88,14 +88,14 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/atc_online.Rd b/man/atc_online.Rd
index 6ae5223bb..17ddca8ee 100644
--- a/man/atc_online.Rd
+++ b/man/atc_online.Rd
@@ -66,12 +66,12 @@ Abbreviations of return values when using \code{property = "U"} (unit):
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
+The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/availability.Rd b/man/availability.Rd
index a27da6db4..54f4621a0 100644
--- a/man/availability.Rd
+++ b/man/availability.Rd
@@ -23,14 +23,14 @@ The function returns a \code{\link{data.frame}} with columns \code{"resistant"}
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/bug_drug_combinations.Rd b/man/bug_drug_combinations.Rd
index 3681ccbf6..de1dfa569 100644
--- a/man/bug_drug_combinations.Rd
+++ b/man/bug_drug_combinations.Rd
@@ -68,14 +68,14 @@ The language of the output can be overwritten with \code{options(AMR_locale)}, p
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/catalogue_of_life.Rd b/man/catalogue_of_life.Rd
index 1aa7dc127..7a32307d1 100644
--- a/man/catalogue_of_life.Rd
+++ b/man/catalogue_of_life.Rd
@@ -28,12 +28,12 @@ Included are:
 
 The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
 
-The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
+The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/catalogue_of_life_version.Rd b/man/catalogue_of_life_version.Rd
index 57207c409..166a023c6 100644
--- a/man/catalogue_of_life_version.Rd
+++ b/man/catalogue_of_life_version.Rd
@@ -25,7 +25,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \seealso{
diff --git a/man/count.Rd b/man/count.Rd
index e772a1c70..eb6c316d7 100644
--- a/man/count.Rd
+++ b/man/count.Rd
@@ -75,7 +75,7 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
@@ -128,7 +128,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd
index 1ee06851d..8bbc6e080 100644
--- a/man/eucast_rules.Rd
+++ b/man/eucast_rules.Rd
@@ -64,7 +64,7 @@ Before further processing, some non-EUCAST rules can be applied to improve the e
 
 These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use \code{eucast_rules(..., rules = "all")}, or set the default behaviour of the \verb{[eucast_rules()]} function with \code{options(AMR.eucast_rules = "all")} (or any other valid input value(s) to the \code{rules} parameter).
 
-The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
+The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
 }
 \section{Antibiotics}{
 
@@ -156,12 +156,12 @@ The following antibiotics are used for the functions \code{\link[=eucast_rules]{
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/example_isolates.Rd b/man/example_isolates.Rd
index a3a1859ee..149957cbb 100644
--- a/man/example_isolates.Rd
+++ b/man/example_isolates.Rd
@@ -23,11 +23,11 @@ A \code{\link{data.frame}} with 2,000 observations and 49 variables:
 example_isolates
 }
 \description{
-A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
+A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read \href{https://msberends.github.io/AMR/articles/AMR.html}{the tutorial on our website}.
 }
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \keyword{datasets}
diff --git a/man/example_isolates_unclean.Rd b/man/example_isolates_unclean.Rd
index 2e48933c5..fdf5dfe40 100644
--- a/man/example_isolates_unclean.Rd
+++ b/man/example_isolates_unclean.Rd
@@ -22,7 +22,7 @@ A data set containing 3,000 microbial isolates that are not cleaned up and conse
 }
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \keyword{datasets}
diff --git a/man/filter_ab_class.Rd b/man/filter_ab_class.Rd
index c3c7f8906..1f99f2433 100644
--- a/man/filter_ab_class.Rd
+++ b/man/filter_ab_class.Rd
@@ -65,7 +65,7 @@ All columns of \code{x} will be searched for known antibiotic names, abbreviatio
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd
index 5302942e9..a25a58f20 100755
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@@ -125,14 +125,14 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/g.test.Rd b/man/g.test.Rd
index c153147e0..18e71e506 100644
--- a/man/g.test.Rd
+++ b/man/g.test.Rd
@@ -100,12 +100,12 @@ If there are more than two categories and you want to find out which ones are si
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
+The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/ggplot_pca.Rd b/man/ggplot_pca.Rd
index 0bae27cc1..542fc2fce 100644
--- a/man/ggplot_pca.Rd
+++ b/man/ggplot_pca.Rd
@@ -107,7 +107,7 @@ The colours for labels and points can be changed by adding another scale layer f
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \examples{
diff --git a/man/ggplot_rsi.Rd b/man/ggplot_rsi.Rd
index 381e0fa04..88f65253d 100644
--- a/man/ggplot_rsi.Rd
+++ b/man/ggplot_rsi.Rd
@@ -114,7 +114,7 @@ labels_rsi_count(
 \item{...}{other parameters passed on to \code{\link[=geom_rsi]{geom_rsi()}}}
 }
 \description{
-Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \link[ggplot2:ggplot]{ggplot2} functions.
+Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on \link[ggplot2:ggplot]{ggplot2} functions.
 }
 \details{
 At default, the names of antibiotics will be shown on the plots using \code{\link[=ab_name]{ab_name()}}. This can be set with the \code{translate_ab} parameter. See \code{\link[=count_df]{count_df()}}.
@@ -124,13 +124,13 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
 
 \code{\link[=facet_rsi]{facet_rsi()}} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2:facet_wrap]{ggplot2::facet_wrap()}}.
 
-\code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_continuous]{ggplot2::scale_continuous()}}.
+\code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_continuous]{ggplot2::scale_y_continuous()}}.
 
-\code{\link[=scale_rsi_colours]{scale_rsi_colours()}} sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using \code{\link[ggplot2:scale_brewer]{ggplot2::scale_brewer()}}.
+\code{\link[=scale_rsi_colours]{scale_rsi_colours()}} sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using \code{\link[ggplot2:scale_manual]{ggplot2::scale_fill_manual()}}.
 
 \code{\link[=theme_rsi]{theme_rsi()}} is a [ggplot2 theme][\code{\link[ggplot2:theme]{ggplot2::theme()}} with minimal distraction.
 
-\code{\link[=labels_rsi_count]{labels_rsi_count()}} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}
+\code{\link[=labels_rsi_count]{labels_rsi_count()}} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.
 
 \code{\link[=ggplot_rsi]{ggplot_rsi()}} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\verb{\%>\%}). See Examples.
 }
@@ -138,12 +138,12 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/guess_ab_col.Rd b/man/guess_ab_col.Rd
index aaab938c2..a6893c4a0 100644
--- a/man/guess_ab_col.Rd
+++ b/man/guess_ab_col.Rd
@@ -25,12 +25,12 @@ You can look for an antibiotic (trade) name or abbreviation and it will search \
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/join.Rd b/man/join.Rd
index d668b67fd..d439e3a66 100755
--- a/man/join.Rd
+++ b/man/join.Rd
@@ -43,14 +43,14 @@ These functions rely on \code{\link[=merge]{merge()}}, a base R function to do j
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/key_antibiotics.Rd b/man/key_antibiotics.Rd
index 8d759d83a..236a8d7ab 100755
--- a/man/key_antibiotics.Rd
+++ b/man/key_antibiotics.Rd
@@ -109,7 +109,7 @@ The function \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}} check
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
@@ -129,7 +129,7 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/kurtosis.Rd b/man/kurtosis.Rd
index 2f710cc20..8afada07c 100644
--- a/man/kurtosis.Rd
+++ b/man/kurtosis.Rd
@@ -26,12 +26,12 @@ Kurtosis is a measure of the "tailedness" of the probability distribution of a r
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
+The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \seealso{
diff --git a/man/lifecycle.Rd b/man/lifecycle.Rd
index a2d1f1517..08d9bff2c 100644
--- a/man/lifecycle.Rd
+++ b/man/lifecycle.Rd
@@ -12,19 +12,19 @@ This page contains a section for every lifecycle (with text borrowed from the af
 \section{Experimental lifecycle}{
 
 \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
+The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
 }
 
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
@@ -32,12 +32,12 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
 \section{Retired lifecycle}{
 
 \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
+The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
 }
 
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
+The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
diff --git a/man/like.Rd b/man/like.Rd
index ffdd8f4bf..604cddb36 100755
--- a/man/like.Rd
+++ b/man/like.Rd
@@ -42,14 +42,14 @@ Using RStudio? This function can also be inserted from the Addins menu and can h
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/mdro.Rd b/man/mdro.Rd
index eb07bc41a..fadb959bf 100644
--- a/man/mdro.Rd
+++ b/man/mdro.Rd
@@ -88,14 +88,14 @@ The German national guideline - Mueller et al. (2015) Antimicrobial Resistance a
 The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})
 }
 
-Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
+Please suggest your own (country-specific) guidelines by letting us know: \url{https://github.com/msberends/AMR/issues/new}.
 
 \strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{\link[=mdro]{mdro()}} function makes sure that results from before 2016 and after 2016 are identical.
 }
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \section{Antibiotics}{
@@ -202,7 +202,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd
index 84e5dc4c1..a23c19dd0 100755
--- a/man/microorganisms.Rd
+++ b/man/microorganisms.Rd
@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms}
 \alias{microorganisms}
-\title{Data set with 67,108 microorganisms}
+\title{Data set with 67,150 microorganisms}
 \format{
-A \code{\link{data.frame}} with 67,108 observations and 16 variables:
+A \code{\link{data.frame}} with 67,150 observations and 16 variables:
 \itemize{
 \item \code{mo}\cr ID of microorganism as used by this package
 \item \code{fullname}\cr Full name, like \code{"Escherichia coli"}
@@ -40,18 +40,18 @@ Manually added were:
 \item 1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
 \item 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
 \item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
-\item 7,369 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
+\item 7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
 }
 \subsection{Direct download}{
 
 This data set is available as 'flat file' for use even without R - you can find the file here:
 \itemize{
-\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt}
+\item \url{https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt}
 }
 
 The file in R format (with preserved data structure) can be found here:
 \itemize{
-\item \url{https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda}
+\item \url{https://github.com/msberends/AMR/raw/master/data/microorganisms.rda}
 }
 }
 }
@@ -72,7 +72,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \seealso{
diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd
index 373b1b87a..778377620 100644
--- a/man/microorganisms.codes.Rd
+++ b/man/microorganisms.codes.Rd
@@ -27,7 +27,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \seealso{
diff --git a/man/microorganisms.old.Rd b/man/microorganisms.old.Rd
index f62305fd7..9fa493923 100644
--- a/man/microorganisms.old.Rd
+++ b/man/microorganisms.old.Rd
@@ -34,7 +34,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \seealso{
diff --git a/man/mo_property.Rd b/man/mo_property.Rd
index cd7e95fe1..9c9ac9cb0 100644
--- a/man/mo_property.Rd
+++ b/man/mo_property.Rd
@@ -119,7 +119,7 @@ The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the o
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
@@ -144,7 +144,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/mo_source.Rd b/man/mo_source.Rd
index 0dd376a62..5c759c8de 100644
--- a/man/mo_source.Rd
+++ b/man/mo_source.Rd
@@ -84,13 +84,13 @@ If the original Excel file is moved or deleted, the mo_source file will be remov
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
diff --git a/man/p_symbol.Rd b/man/p_symbol.Rd
index 154de7732..c604964a5 100644
--- a/man/p_symbol.Rd
+++ b/man/p_symbol.Rd
@@ -20,11 +20,11 @@ Return the symbol related to the p-value: 0 '\verb{***}' 0.001 '\verb{**}' 0.01
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
+The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
diff --git a/man/pca.Rd b/man/pca.Rd
index 744f3b550..cb83c28e0 100644
--- a/man/pca.Rd
+++ b/man/pca.Rd
@@ -62,7 +62,7 @@ The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object,
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \examples{
diff --git a/man/proportion.Rd b/man/proportion.Rd
index 22ea1a55c..b62507bf4 100644
--- a/man/proportion.Rd
+++ b/man/proportion.Rd
@@ -83,7 +83,7 @@ The function \code{\link[=resistance]{resistance()}} is equal to the function \c
 
 \strong{Remember that you should filter your table to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set.
 
-These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[AMR:count]{count()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
+These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[=count]{count()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
 
 The function \code{\link[=proportion_df]{proportion_df()}} takes any variable from \code{data} that has an \code{\link{rsi}} class (created with \code{\link[=as.rsi]{as.rsi()}}) and calculates the proportions R, I and S. It also supports grouped variables. The function \code{\link[=rsi_df]{rsi_df()}} works exactly like \code{\link[=proportion_df]{proportion_df()}}, but adds the number of isolates.
 }
@@ -121,7 +121,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
@@ -143,7 +143,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
@@ -229,5 +229,5 @@ if (require("dplyr")) {
 }
 }
 \seealso{
-\code{\link[AMR:count]{AMR::count()}} to count resistant and susceptible isolates.
+\code{\link[=count]{count()}} to count resistant and susceptible isolates.
 }
diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd
index 91157993c..c44bba5d0 100644
--- a/man/resistance_predict.Rd
+++ b/man/resistance_predict.Rd
@@ -103,7 +103,7 @@ Valid options for the statistical model (parameter \code{model}) are:
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
+The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
 }
 
 \section{Interpretation of R and S/I}{
@@ -123,7 +123,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/man/rsi_translation.Rd b/man/rsi_translation.Rd
index 6a313e98a..23dd966b7 100644
--- a/man/rsi_translation.Rd
+++ b/man/rsi_translation.Rd
@@ -26,11 +26,11 @@ rsi_translation
 Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
 }
 \details{
-The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
+The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
 }
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \keyword{datasets}
diff --git a/man/skewness.Rd b/man/skewness.Rd
index ffa8b2e9f..986a79f84 100644
--- a/man/skewness.Rd
+++ b/man/skewness.Rd
@@ -28,12 +28,12 @@ When negative: the left tail is longer; the mass of the distribution is concentr
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
+The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \seealso{
diff --git a/man/translate.Rd b/man/translate.Rd
index f1016e852..4f0bfd6c0 100644
--- a/man/translate.Rd
+++ b/man/translate.Rd
@@ -11,11 +11,11 @@ get_locale()
 For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}.
 }
 \details{
-Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv}.
+Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv}.
 
-Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Not all these languages currently have translations available for all antimicrobial agents and colloquial microorganism names.
+Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.
 
-Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
+Please suggest your own translations \href{https://github.com/msberends/AMR/issues/new?title=Translations}{by creating a new issue on our repository}.
 
 This file will be read by all functions where a translated output can be desired, like all \code{\link[=mo_property]{mo_property()}} functions (\code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}}, etc.).
 
@@ -24,14 +24,14 @@ The system language will be used at default, if that language is supported. The
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
+The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
 If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{
 
-On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
 \examples{
diff --git a/pkgdown/extra.css b/pkgdown/extra.css
index 4d4be3514..5886f4205 100644
--- a/pkgdown/extra.css
+++ b/pkgdown/extra.css
@@ -4,7 +4,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -17,7 +17,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 */
 
diff --git a/pkgdown/extra.js b/pkgdown/extra.js
index 61e7c25ca..2a7781fe1 100644
--- a/pkgdown/extra.js
+++ b/pkgdown/extra.js
@@ -4,7 +4,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -17,7 +17,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 */
 
@@ -88,6 +88,7 @@ $( document ).ready(function() {
       x = x.replace("Sofia", "Dr. Sofia");
       x = x.replace("Dennis", "Dr. Dennis");
       x = x.replace("Judith", "Dr. Judith");
+      x = x.replace("Gwen", "Dr. Gwen");
     }
     return(x);
   }
diff --git a/tests/appveyor/appveyor_tool.ps1 b/tests/appveyor/appveyor_tool.ps1
deleted file mode 100644
index 7badcc073..000000000
--- a/tests/appveyor/appveyor_tool.ps1
+++ /dev/null
@@ -1,213 +0,0 @@
-# from https://github.com/krlmlr/r-appveyor/tree/master/scripts
-
-if ( -not(Test-Path Env:\CRAN) ) {
-  $CRAN = "https://cran.rstudio.com"
-}
-Else {
-  $CRAN = $env:CRAN
-}
-
-
-# Found at http://zduck.com/2012/powershell-batch-files-exit-codes/
-Function Exec
-{
-    [CmdletBinding()]
-    param (
-        [Parameter(Position=0, Mandatory=1)]
-        [scriptblock]$Command,
-        [Parameter(Position=1, Mandatory=0)]
-        [string]$ErrorMessage = "Execution of command failed.`n$Command"
-    )
-    $ErrorActionPreference = "Continue"
-    & $Command 2>&1 | %{ "$_" }
-    if ($LastExitCode -ne 0) {
-        throw "Exec: $ErrorMessage`nExit code: $LastExitCode"
-    }
-}
-
-Function Progress
-{
-    [CmdletBinding()]
-    param (
-        [Parameter(Position=0, Mandatory=0)]
-        [string]$Message = ""
-    )
-
-    $ProgressMessage = '== ' + (Get-Date) + ': ' + $Message
-
-    Write-Host $ProgressMessage -ForegroundColor Magenta
-}
-
-Function TravisTool
-{
-  [CmdletBinding()]
-  param (
-      [Parameter(Position=0, Mandatory=1)]
-      [string[]]$Params
-  )
-
-  Exec { bash.exe ../travis-tool.sh $Params }
-}
-
-Function InstallR {
-  [CmdletBinding()]
-  Param()
-
-  if ( -not(Test-Path Env:\R_VERSION) ) {
-    $version = "patched"
-  }
-  Else {
-    $version = $env:R_VERSION
-  }
-
-  if ( -not(Test-Path Env:\R_ARCH) ) {
-    $arch = "x64"
-  }
-  Else {
-    $arch = $env:R_ARCH
-  }
-
-  If ($arch -eq "i386") {
-    $mingw_path = "mingw_32"
-  }
-  Else {
-    $mingw_path = "mingw_64"
-  }
-
-  Progress ("Version: " + $version)
-
-  If ($version -eq "devel") {
-    $url_path = ""
-    $version = "devel"
-  }
-  ElseIf (($version -eq "stable") -or ($version -eq "release")) {
-    $url_path = ""
-    $version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-release-win).Content).version
-    If ($version -eq "3.2.4") {
-      $version = "3.2.4revised"
-    }
-  }
-  ElseIf ($version -eq "patched") {
-    $url_path = ""
-    $version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-release-win).Content).version + "patched"
-  }
-  ElseIf ($version -eq "oldrel") {
-    $version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-oldrel).Content).version
-    $url_path = ("old/" + $version + "/")
-  }
-  Else {
-      $url_path = ("old/" + $version + "/")
-  }
-
-  Progress ("URL path: " + $url_path)
-
-  $rurl = $CRAN + "/bin/windows/base/" + $url_path + "R-" + $version + "-win.exe"
-  $global:rversion = $version
-
-  Progress ("Downloading R from: " + $rurl)
-  & "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../R-win.exe -L $rurl
-
-  Progress "Running R installer"
-  Start-Process -FilePath ..\R-win.exe -ArgumentList "/VERYSILENT /DIR=C:\R" -NoNewWindow -Wait
-
-  $RDrive = "C:"
-  echo "R is now available on drive $RDrive"
-
-  Progress "Setting PATH"
-  $env:PATH = $RDrive + '\R\bin\' + $arch + ';' + 'C:\Rtools\' + $mingw_path + '\bin;' + 'C:\MinGW\msys\1.0\bin;' + $env:PATH
-
-  Progress "Testing R installation"
-  Rscript -e "sessionInfo()"
-}
-
-Function InstallRtools40 {
-  $rtoolsurl = $CRAN + "/bin/windows/Rtools/rtools40-x86_64.exe"
-
-  Progress ("Downloading Rtools40 from: " + $rtoolsurl)
-  & "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../rtools40-x86_64.exe -L $rtoolsurl
-
-  Progress "Running Rtools40 installer"
-  Start-Process -FilePath ..\rtools40-x86_64.exe -ArgumentList /VERYSILENT -NoNewWindow -Wait
-
-  Progress "Setting PATH"
-  $env:PATH = 'c:\rtools40\usr\bin;c:\rtools40\mingw64\bin;' + $env:PATH
-}
-
-Function InstallRtools {
-  if ( -not(Test-Path Env:\RTOOLS_VERSION) ) {
-    $rtoolsver = '35'
-  }
-  Else {
-    $rtoolsver = $env:RTOOLS_VERSION
-  }
-
-  $rtoolsurl = $CRAN + "/bin/windows/Rtools/Rtools$rtoolsver.exe"
-
-  Progress ("Downloading Rtools from: " + $rtoolsurl)
-  & "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../Rtools-current.exe -L $rtoolsurl
-
-  Progress "Running Rtools installer"
-  Start-Process -FilePath ..\Rtools-current.exe -ArgumentList /VERYSILENT -NoNewWindow -Wait
-
-  $RtoolsDrive = "C:"
-  echo "Rtools is now available on drive $RtoolsDrive"
-
-  Progress "Setting PATH"
-  if ( -not(Test-Path Env:\GCC_PATH) ) {
-    $gcc_path = "gcc-4.6.3"
-  }
-  Else {
-    $gcc_path = $env:GCC_PATH
-  }
-  $env:PATH = $RtoolsDrive + '\Rtools\bin;' + $RtoolsDrive + '\Rtools\MinGW\bin;' + $RtoolsDrive + '\Rtools\' + $gcc_path + '\bin;' + $env:PATH
-  $env:BINPREF=$RtoolsDrive + '/Rtools/mingw_$(WIN)/bin/'
-}
-
-Function Bootstrap {
-  [CmdletBinding()]
-  Param()
-
-  Progress "Bootstrap: Start"
-
-  Progress "Adding GnuWin32 tools to PATH"
-  $env:PATH = "C:\Program Files (x86)\Git\bin;" + $env:PATH
-
-  Progress "Setting time zone"
-  tzutil /g
-  tzutil /s "GMT Standard Time"
-  tzutil /g
-
-  InstallR
-
-  if ((Test-Path "src") -or ($env:USE_RTOOLS -eq "true") -or ($env:USE_RTOOLS -eq "yes")) {
-    if ($rversion.StartsWith("3")) {
-      InstallRtools
-    } Else {
-      InstallRtools40
-    }
-  }
-  Else {
-    Progress "Skipping download of Rtools because src/ directory is missing."
-  }
-
-  Progress "Downloading and installing travis-tool.sh"
-  cp "tests\appveyor\travis_tool.sh" "..\travis-tool.sh"
-  # Invoke-WebRequest https://raw.githubusercontent.com/krlmlr/r-appveyor/master/r-travis/scripts/travis-tool.sh -OutFile "..\travis-tool.sh"
-  echo '@bash.exe ../travis-tool.sh %*' | Out-File -Encoding ASCII .\travis-tool.sh.cmd
-  cat .\travis-tool.sh.cmd
-  bash -c "( echo; echo '^travis-tool\.sh\.cmd$' ) >> .Rbuildignore"
-  cat .\.Rbuildignore
-
-  $env:PATH.Split(";")
-
-  Progress "Setting R_LIBS_USER"
-  $env:R_LIBS_USER = 'c:\RLibrary\' + $rversion.Substring(0,3)
-  if ( -not(Test-Path $env:R_LIBS_USER) ) {
-    mkdir $env:R_LIBS_USER
-  }
-
-  Progress "Setting TAR to 'internal'"
-  $env:TAR = 'internal'
-
-  Progress "Bootstrap: Done"
-}
diff --git a/tests/appveyor/travis_tool.sh b/tests/appveyor/travis_tool.sh
deleted file mode 100644
index c0493277d..000000000
--- a/tests/appveyor/travis_tool.sh
+++ /dev/null
@@ -1,444 +0,0 @@
-#!/bin/bash
-# -*- sh-basic-offset: 4; sh-indentation: 4 -*-
-# Bootstrap an R/travis environment.
-
-set -e
-# Comment out this line for quieter output:
-set -x
-
-CRAN=${CRAN:-"https://cran.rstudio.com"}
-BIOC=${BIOC:-"http://bioconductor.org/biocLite.R"}
-PKGTYPE=${PKGTYPE:-"win.binary"}
-BIOC_USE_DEVEL=${BIOC_USE_DEVEL:-"TRUE"}
-OS=$(uname -s)
-DOWNLOAD_FILE_METHOD=${DOWNLOAD_FILE_METHOD:-"auto"}
-
-PANDOC_VERSION='1.13.1'
-PANDOC_DIR="${HOME}/opt/pandoc"
-PANDOC_URL="https://s3.amazonaws.com/rstudio-buildtools/pandoc-${PANDOC_VERSION}.zip"
-
-# MacTeX installs in a new $PATH entry, and there's no way to force
-# the *parent* shell to source it from here. So we just manually add
-# all the entries to a location we already know to be on $PATH.
-#
-# TODO(craigcitro): Remove this once we can add `/usr/texbin` to the
-# root path.
-PATH="${PATH}:/usr/texbin"
-
-R_BUILD_ARGS=${R_BUILD_ARGS-"--no-manual"}
-R_CHECK_ARGS=${R_CHECK_ARGS-"--no-manual --as-cran"}
-
-R_VERSION_TEST="getRversion() >= '3.5.0'"
-
-R_USE_BIOC_INST="source('${BIOC}');"\
-" tryCatch(useDevel(${BIOC_USE_DEVEL}),"\
-" error=function(e) {if (!grepl('already in use', e$message)) {e}});"\
-" options(repos=biocinstallRepos())"
-
-R_USE_BIOC_MNGR="if (!requireNamespace('BiocManager', quietly=TRUE))"\
-" install.packages('BiocManager', repos=c(CRAN='${CRAN}'));"\
-" if (${BIOC_USE_DEVEL})"\
-" BiocManager::install(version = 'devel', ask = FALSE);"\
-" options(repos=BiocManager::repositories())"
-
-R_USE_BIOC_CMDS="if (${R_VERSION_TEST}) {${R_USE_BIOC_MNGR}} else {${R_USE_BIOC_INST}};"
-
-BIOC_INSTALL="{if (${R_VERSION_TEST}) BiocManager::install else BiocInstaller::biocLite}"
-
-Bootstrap() {
-    if [[ "Darwin" == "${OS}" ]]; then
-        BootstrapMac
-    elif [[ "Linux" == "${OS}" ]]; then
-        BootstrapLinux
-    else
-        echo "Unknown OS: ${OS}"
-        exit 1
-    fi
-
-    if ! (test -e .Rbuildignore && grep -q 'travis_tool' .Rbuildignore); then
-        echo '^travis_tool\.sh$' >>.Rbuildignore
-    fi
-}
-
-InstallPandoc() {
-    local os_path="$1"
-    mkdir -p "${PANDOC_DIR}"
-    curl -o /tmp/pandoc-${PANDOC_VERSION}.zip ${PANDOC_URL}
-    unzip -j /tmp/pandoc-${PANDOC_VERSION}.zip "pandoc-${PANDOC_VERSION}/${os_path}/pandoc" -d "${PANDOC_DIR}"
-    chmod +x "${PANDOC_DIR}/pandoc"
-    sudo ln -s "${PANDOC_DIR}/pandoc" /usr/local/bin
-    unzip -j /tmp/pandoc-${PANDOC_VERSION}.zip "pandoc-${PANDOC_VERSION}/${os_path}/pandoc-citeproc" -d "${PANDOC_DIR}"
-    chmod +x "${PANDOC_DIR}/pandoc-citeproc"
-    sudo ln -s "${PANDOC_DIR}/pandoc-citeproc" /usr/local/bin
-}
-
-BootstrapLinux() {
-    # Set up our CRAN mirror.
-    sudo add-apt-repository "deb ${CRAN}/bin/linux/ubuntu $(lsb_release -cs)/"
-    sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
-
-    # Add marutter's c2d4u repository.
-    sudo add-apt-repository -y "ppa:marutter/rrutter"
-    sudo add-apt-repository -y "ppa:marutter/c2d4u"
-
-    # Update after adding all repositories.  Retry several times to work around
-    # flaky connection to Launchpad PPAs.
-    Retry sudo apt-get update -qq
-
-    # Install an R development environment. qpdf is also needed for
-    # --as-cran checks:
-    #   https://stat.ethz.ch/pipermail/r-help//2012-September/335676.html
-    Retry sudo apt-get install -y --no-install-recommends r-base-dev r-recommended qpdf
-
-    # Change permissions for /usr/local/lib/R/site-library
-    # This should really be via 'staff adduser travis staff'
-    # but that may affect only the next shell
-    sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library
-
-    # Process options
-    BootstrapLinuxOptions
-}
-
-BootstrapLinuxOptions() {
-    if [[ -n "$BOOTSTRAP_LATEX" ]]; then
-        # We add a backports PPA for more recent TeX packages.
-        sudo add-apt-repository -y "ppa:texlive-backports/ppa"
-
-        Retry sudo apt-get install -y --no-install-recommends \
-            texlive-base texlive-latex-base texlive-generic-recommended \
-            texlive-fonts-recommended texlive-fonts-extra \
-            texlive-extra-utils texlive-latex-recommended texlive-latex-extra \
-            texinfo lmodern
-    fi
-    if [[ -n "$BOOTSTRAP_PANDOC" ]]; then
-        InstallPandoc 'linux/debian/x86_64'
-    fi
-}
-
-BootstrapMac() {
-    # Install from latest CRAN binary build for OS X
-    wget ${CRAN}/bin/macosx/R-latest.pkg  -O /tmp/R-latest.pkg
-
-    echo "Installing OS X binary package for R"
-    sudo installer -pkg "/tmp/R-latest.pkg" -target /
-    rm "/tmp/R-latest.pkg"
-
-    # Process options
-    BootstrapMacOptions
-}
-
-BootstrapMacOptions() {
-    if [[ -n "$BOOTSTRAP_LATEX" ]]; then
-        # TODO: Install MacTeX.pkg once there's enough disk space
-        MACTEX=BasicTeX.pkg
-        wget http://ctan.math.utah.edu/ctan/tex-archive/systems/mac/mactex/$MACTEX -O "/tmp/$MACTEX"
-
-        echo "Installing OS X binary package for MacTeX"
-        sudo installer -pkg "/tmp/$MACTEX" -target /
-        rm "/tmp/$MACTEX"
-        # We need a few more packages than the basic package provides; this
-        # post saved me so much pain:
-        #   https://stat.ethz.ch/pipermail/r-sig-mac/2010-May/007399.html
-        sudo tlmgr update --self
-        sudo tlmgr install inconsolata upquote courier courier-scaled helvetic
-    fi
-    if [[ -n "$BOOTSTRAP_PANDOC" ]]; then
-        InstallPandoc 'mac'
-    fi
-}
-
-EnsureDevtools() {
-    if ! Rscript -e 'if (!("devtools" %in% rownames(installed.packages()))) q(status=1)' ; then
-        # Install devtools and testthat.
-        RBinaryInstall devtools testthat
-    fi
-}
-
-EnsureRemotes() {
-    if ! Rscript -e 'if (!("Rcpp" %in% rownames(installed.packages()))) q(status=1)' ; then
-        # Install remotes.
-        RBinaryInstall Rcpp
-    fi
-    if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then
-        # Install remotes.
-        RBinaryInstall remotes
-    fi
-    if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then
-        # Fallback: Install remotes from URL.
-        Rscript -e 'path <- file.path(tempdir(), "remotes_1.0.0.tar.gz"); download.file("https://cran.rstudio.com/src/contrib/Archive/remotes/remotes_1.0.0.tar.gz", path); install.packages(path, repos = NULL, type = "source")'
-    fi
-}
-
-AptGetInstall() {
-    if [[ "Linux" != "${OS}" ]]; then
-        echo "Wrong OS: ${OS}"
-        exit 1
-    fi
-
-    if [[ "" == "$*" ]]; then
-        echo "No arguments to aptget_install"
-        exit 1
-    fi
-
-    echo "Installing apt package(s) $@"
-    Retry sudo apt-get -y install "$@"
-}
-
-DpkgCurlInstall() {
-    if [[ "Linux" != "${OS}" ]]; then
-        echo "Wrong OS: ${OS}"
-        exit 1
-    fi
-
-    if [[ "" == "$*" ]]; then
-        echo "No arguments to dpkgcurl_install"
-        exit 1
-    fi
-
-    echo "Installing remote package(s) $@"
-    for rf in "$@"; do
-        curl -OL ${rf}
-        f=$(basename ${rf})
-        sudo dpkg -i ${f}
-        rm -v ${f}
-    done
-}
-
-RInstall() {
-    if [[ "" == "$*" ]]; then
-        echo "No arguments to r_install"
-        exit 1
-    fi
-
-    echo "Installing R package(s): $@"
-    Rscript -e 'install.packages(commandArgs(TRUE), repos="'"${CRAN}"'", INSTALL_opts="", type="'"${PKGTYPE}"'")' "$@"
-}
-
-BiocInstall() {
-    if [[ "" == "$*" ]]; then
-        echo "No arguments to bioc_install"
-        exit 1
-    fi
-
-    echo "Installing R Bioconductor package(s): $@"
-    Rscript -e "${R_USE_BIOC_CMDS}"" ${BIOC_INSTALL}(commandArgs(TRUE))" "$@"
-}
-
-RBinaryInstall() {
-    if [[ -z "$#" ]]; then
-        echo "No arguments to r_binary_install"
-        exit 1
-    fi
-
-    if [[ "Linux" != "${OS}" ]] || [[ -n "${FORCE_SOURCE_INSTALL}" ]]; then
-        echo "Fallback: Installing from source"
-        RInstall "$@"
-        return
-    fi
-
-    echo "Installing *binary* R packages: $*"
-    r_packages=$(echo $* | tr '[:upper:]' '[:lower:]')
-    r_debs=$(for r_package in ${r_packages}; do echo -n "r-cran-${r_package} "; done)
-
-    AptGetInstall ${r_debs}
-}
-
-InstallGithub() {
-    EnsureRemotes
-
-    echo "Installing GitHub packages: $@"
-    # Install the package.
-    Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_github(commandArgs(TRUE), type="'"${PKGTYPE}"'")' "$@"
-}
-
-CleanLibrary() {
-    # removes all installed package so ensures a clean library
-    Rscript -e 'remove.packages(installed.packages()[is.na(installed.packages()[,"Priority"]), "Package"])'
-}
-
-InstallDeps() {
-    EnsureRemotes
-
-    echo "Installing dependencies"
-    Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_deps(dependencies = TRUE, type="'"${PKGTYPE}"'")'
-}
-
-InstallBiocDeps() {
-    EnsureDevtools
-    Rscript -e "${R_USE_BIOC_CMDS}"' library(devtools); install_deps(dependencies = TRUE, type="'"${PKGTYPE}"'")'
-}
-
-DumpSysinfo() {
-    echo "Dumping system information."
-    R -e '.libPaths(); sessionInfo(); installed.packages()'
-}
-
-DumpLogsByExtension() {
-    if [[ -z "$1" ]]; then
-        echo "dump_logs_by_extension requires exactly one argument, got: $@"
-        exit 1
-    fi
-    extension=$1
-    shift
-    package=$(find . -maxdepth 1 -name "*.Rcheck" -type d)
-    if [[ ${#package[@]} -ne 1 ]]; then
-        echo "Could not find package Rcheck directory, skipping log dump."
-        exit 0
-    fi
-    for name in $(find "${package}" -type f -name "*${extension}"); do
-        echo ">>> Filename: ${name} <<<"
-        cat ${name}
-    done
-}
-
-DumpLogs() {
-    echo "Dumping test execution logs."
-    DumpLogsByExtension "out"
-    DumpLogsByExtension "log"
-    DumpLogsByExtension "fail"
-}
-
-RunTests() {
-    Rscript -e 'sessionInfo()'
-    
-    echo "Building with: R CMD build ${R_BUILD_ARGS}"
-    if [[ "${KEEP_VIGNETTES}" == "" ]]; then
-        if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then
-            if [[ -d vignettes ]]; then
-                rm -rf vignettes
-                Rscript -e "d <- read.dcf('DESCRIPTION'); d[, colnames(d) == 'VignetteBuilder'] <- NA; write.dcf(d, 'DESCRIPTION')"
-            fi
-        fi
-    fi
-    R CMD build ${R_BUILD_ARGS} .
-    # We want to grab the version we just built.
-    FILE=$(ls -1t *.tar.gz | head -n 1)
-
-    # Create binary package (currently Windows only)
-    if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then
-        R_CHECK_INSTALL_ARGS="--install-args=--build"
-    fi
-
-    echo "Testing with: R CMD check \"${FILE}\" ${R_CHECK_ARGS} ${R_CHECK_INSTALL_ARGS}"
-    _R_CHECK_CRAN_INCOMING_=${_R_CHECK_CRAN_INCOMING_:-FALSE}
-    if [[ "$_R_CHECK_CRAN_INCOMING_" == "FALSE" ]]; then
-        echo "(CRAN incoming checks are off)"
-    fi
-    _R_CHECK_CRAN_INCOMING_=${_R_CHECK_CRAN_INCOMING_} R_QPDF=true R CMD check "${FILE}" ${R_CHECK_ARGS} ${R_CHECK_INSTALL_ARGS}
-
-    # Check reverse dependencies
-    if [[ -n "$R_CHECK_REVDEP" ]]; then
-        echo "Checking reverse dependencies"
-        EnsureDevtools
-        Rscript -e 'library(devtools); checkOutput <- unlist(revdep_check(as.package(".")$package));if (!is.null(checkOutput)) {print(data.frame(pkg = names(checkOutput), error = checkOutput));for(i in seq_along(checkOutput)){;cat("\n", names(checkOutput)[i], " Check Output:\n  ", paste(readLines(regmatches(checkOutput[i], regexec("/.*\\.out", checkOutput[i]))[[1]]), collapse = "\n  ", sep = ""), "\n", sep = "")};q(status = 1, save = "no")}'
-    fi
-
-    if [[ -n "${WARNINGS_ARE_ERRORS}" ]]; then
-        if DumpLogsByExtension "00check.log" | grep -q WARNING; then
-            echo "Found warnings, treated as errors."
-            echo "Clear or unset the WARNINGS_ARE_ERRORS environment variable to ignore warnings."
-            exit 1
-        fi
-    fi
-}
-
-Retry() {
-    if "$@"; then
-        return 0
-    fi
-    for wait_time in 5 20 30 60; do
-        echo "Command failed, retrying in ${wait_time} ..."
-        sleep ${wait_time}
-        if "$@"; then
-            return 0
-        fi
-    done
-    echo "Failed all retries!"
-    exit 1
-}
-
-COMMAND=$1
-echo "Running command: ${COMMAND}"
-shift
-case $COMMAND in
-    ##
-    ## Bootstrap a new core system
-    "bootstrap")
-        Bootstrap
-        ;;
-    ##
-    ## Clean library
-    "clean_library")
-        CleanLibrary
-        ;;
-    ##
-    ## Ensure devtools is loaded (implicitly called)
-    "install_devtools"|"devtools_install")
-        EnsureDevtools
-        ;;
-    ##
-    ## Ensure remotes is loaded (implicitly called)
-    "install_remotes"|"remotes_install")
-        EnsureRemotes
-        ;;
-    ##
-    ## Install a binary deb package via apt-get
-    "install_aptget"|"aptget_install")
-        AptGetInstall "$@"
-        ;;
-    ##
-    ## Install a binary deb package via a curl call and local dpkg -i
-    "install_dpkgcurl"|"dpkgcurl_install")
-        DpkgCurlInstall "$@"
-        ;;
-    ##
-    ## Install an R dependency from CRAN
-    "install_r"|"r_install")
-        RInstall "$@"
-        ;;
-    ##
-    ## Install an R dependency from Bioconductor
-    "install_bioc"|"bioc_install")
-        BiocInstall "$@"
-        ;;
-    ##
-    ## Install an R dependency as a binary (via c2d4u PPA)
-    "install_r_binary"|"r_binary_install")
-        RBinaryInstall "$@"
-        ;;
-    ##
-    ## Install a package from github sources (needs remotes)
-    "install_github"|"github_package")
-        InstallGithub "$@"
-        ;;
-    ##
-    ## Install package dependencies from CRAN (needs remotes)
-    "install_deps")
-        InstallDeps
-        ;;
-    ##
-    ## Install package dependencies from Bioconductor and CRAN (needs devtools)
-    "install_bioc_deps")
-        InstallBiocDeps
-        ;;
-    ##
-    ## Run the actual tests, ie R CMD check
-    "run_tests")
-        RunTests
-        ;;
-    ##
-    ## Dump information about installed packages
-    "dump_sysinfo")
-        DumpSysinfo
-        ;;
-    ##
-    ## Dump build or check logs
-    "dump_logs")
-        DumpLogs
-        ;;
-    ##
-    ## Dump selected build or check logs
-    "dump_logs_by_extension")
-        DumpLogsByExtension "$@"
-        ;;
-esac
diff --git a/tests/testthat.R b/tests/testthat.R
index 2c6738cf5..a1bf37359 100755
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 library(testthat)
diff --git a/tests/testthat/test-ab.R b/tests/testthat/test-ab.R
index 87aaa62ba..0c2713b69 100755
--- a/tests/testthat/test-ab.R
+++ b/tests/testthat/test-ab.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("ab.R")
diff --git a/tests/testthat/test-ab_from_text.R b/tests/testthat/test-ab_from_text.R
index e9b67b426..eefc472cd 100644
--- a/tests/testthat/test-ab_from_text.R
+++ b/tests/testthat/test-ab_from_text.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("ab_from_text.R")
diff --git a/tests/testthat/test-ab_property.R b/tests/testthat/test-ab_property.R
index f02778ad8..3e9447f94 100644
--- a/tests/testthat/test-ab_property.R
+++ b/tests/testthat/test-ab_property.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("ab_property.R")
diff --git a/tests/testthat/test-age.R b/tests/testthat/test-age.R
index 3cf32c351..d0f7341a4 100644
--- a/tests/testthat/test-age.R
+++ b/tests/testthat/test-age.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("age.R")
diff --git a/tests/testthat/test-antibiotic_class_selectors.R b/tests/testthat/test-antibiotic_class_selectors.R
index 9f45b70ac..a15e1541d 100644
--- a/tests/testthat/test-antibiotic_class_selectors.R
+++ b/tests/testthat/test-antibiotic_class_selectors.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("ab_class_selectors.R")
diff --git a/tests/testthat/test-availability.R b/tests/testthat/test-availability.R
index dfada3cd4..ec45fd974 100644
--- a/tests/testthat/test-availability.R
+++ b/tests/testthat/test-availability.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("availability.R")
diff --git a/tests/testthat/test-bug_drug_combinations.R b/tests/testthat/test-bug_drug_combinations.R
index 9e92d5ced..3cfdfa6b6 100644
--- a/tests/testthat/test-bug_drug_combinations.R
+++ b/tests/testthat/test-bug_drug_combinations.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("bug_drug_combinations.R")
diff --git a/tests/testthat/test-count.R b/tests/testthat/test-count.R
index 20e8e919e..49dba5c9a 100644
--- a/tests/testthat/test-count.R
+++ b/tests/testthat/test-count.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("count.R")
diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
index 91eafa078..ff5ab5d1d 100644
--- a/tests/testthat/test-data.R
+++ b/tests/testthat/test-data.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("data.R")
diff --git a/tests/testthat/test-deprecated.R b/tests/testthat/test-deprecated.R
index c771e1981..5fdd2d36f 100644
--- a/tests/testthat/test-deprecated.R
+++ b/tests/testthat/test-deprecated.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("deprecated.R")
diff --git a/tests/testthat/test-disk.R b/tests/testthat/test-disk.R
index 3336cd449..9c7d64610 100755
--- a/tests/testthat/test-disk.R
+++ b/tests/testthat/test-disk.R
@@ -3,7 +3,7 @@
 # Antidiskrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("disk.R")
diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R
index cfd875c00..4943a9f90 100755
--- a/tests/testthat/test-eucast_rules.R
+++ b/tests/testthat/test-eucast_rules.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("eucast_rules.R")
diff --git a/tests/testthat/test-filter_ab_class.R b/tests/testthat/test-filter_ab_class.R
index 84dc20d8e..9aabcaa63 100644
--- a/tests/testthat/test-filter_ab_class.R
+++ b/tests/testthat/test-filter_ab_class.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("filter_ab_class.R")
diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R
index 99b08efef..08270d69b 100755
--- a/tests/testthat/test-first_isolate.R
+++ b/tests/testthat/test-first_isolate.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("first_isolate.R")
diff --git a/tests/testthat/test-g.test.R b/tests/testthat/test-g.test.R
index ddd37b239..35fc17fae 100644
--- a/tests/testthat/test-g.test.R
+++ b/tests/testthat/test-g.test.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("g.test.R")
diff --git a/tests/testthat/test-get_locale.R b/tests/testthat/test-get_locale.R
index f69a7940b..9180fdfe2 100644
--- a/tests/testthat/test-get_locale.R
+++ b/tests/testthat/test-get_locale.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("get_locale.R")
diff --git a/tests/testthat/test-ggplot_rsi.R b/tests/testthat/test-ggplot_rsi.R
index 8f6c6ad20..7298e2033 100644
--- a/tests/testthat/test-ggplot_rsi.R
+++ b/tests/testthat/test-ggplot_rsi.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("ggplot_rsi.R")
diff --git a/tests/testthat/test-guess_ab_col.R b/tests/testthat/test-guess_ab_col.R
index 4447263f4..d1d59b025 100644
--- a/tests/testthat/test-guess_ab_col.R
+++ b/tests/testthat/test-guess_ab_col.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("guess_ab_col.R")
diff --git a/tests/testthat/test-join_microorganisms.R b/tests/testthat/test-join_microorganisms.R
index ab960f845..eeef5bbe1 100755
--- a/tests/testthat/test-join_microorganisms.R
+++ b/tests/testthat/test-join_microorganisms.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("join_microorganisms.R")
diff --git a/tests/testthat/test-key_antibiotics.R b/tests/testthat/test-key_antibiotics.R
index f66c718c9..463aea5e6 100644
--- a/tests/testthat/test-key_antibiotics.R
+++ b/tests/testthat/test-key_antibiotics.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("key_antibiotics.R")
diff --git a/tests/testthat/test-kurtosis.R b/tests/testthat/test-kurtosis.R
index f657e3ba4..bb3fd3b90 100644
--- a/tests/testthat/test-kurtosis.R
+++ b/tests/testthat/test-kurtosis.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("kurtosis.R")
diff --git a/tests/testthat/test-like.R b/tests/testthat/test-like.R
index 149490f31..7adee61bb 100644
--- a/tests/testthat/test-like.R
+++ b/tests/testthat/test-like.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("like.R")
diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R
index 651387205..fb7203614 100755
--- a/tests/testthat/test-mdro.R
+++ b/tests/testthat/test-mdro.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("mdro.R")
diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R
index b7cd335d9..d9045e849 100755
--- a/tests/testthat/test-mic.R
+++ b/tests/testthat/test-mic.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("mic.R")
diff --git a/tests/testthat/test-misc.R b/tests/testthat/test-misc.R
index c5f9c4ea4..62fa1557f 100755
--- a/tests/testthat/test-misc.R
+++ b/tests/testthat/test-misc.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("misc.R")
diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R
index 1c916f4de..4006b6d0e 100644
--- a/tests/testthat/test-mo.R
+++ b/tests/testthat/test-mo.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("mo.R")
diff --git a/tests/testthat/test-mo_history.R b/tests/testthat/test-mo_history.R
index a424b9278..4b7b04a05 100644
--- a/tests/testthat/test-mo_history.R
+++ b/tests/testthat/test-mo_history.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,5 +16,5 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R
index d2e4d6ddc..3dc41f3a7 100644
--- a/tests/testthat/test-mo_property.R
+++ b/tests/testthat/test-mo_property.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("mo_property.R")
diff --git a/tests/testthat/test-p_symbol.R b/tests/testthat/test-p_symbol.R
index 639405ba4..7fdcba53a 100644
--- a/tests/testthat/test-p_symbol.R
+++ b/tests/testthat/test-p_symbol.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("p_symbol.R")
diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R
index 63fb271c5..82f3ccc04 100644
--- a/tests/testthat/test-pca.R
+++ b/tests/testthat/test-pca.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("pca.R")
diff --git a/tests/testthat/test-proportion.R b/tests/testthat/test-proportion.R
index 511a1c010..8346ccdc6 100755
--- a/tests/testthat/test-proportion.R
+++ b/tests/testthat/test-proportion.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("proportion.R")
diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R
index fe02a1322..fd8f2aaf0 100644
--- a/tests/testthat/test-resistance_predict.R
+++ b/tests/testthat/test-resistance_predict.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("resistance_predict.R")
diff --git a/tests/testthat/test-rsi.R b/tests/testthat/test-rsi.R
index ac6b00bab..92313eb3a 100644
--- a/tests/testthat/test-rsi.R
+++ b/tests/testthat/test-rsi.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("rsi.R")
diff --git a/tests/testthat/test-skewness.R b/tests/testthat/test-skewness.R
index d1dc4f2b7..ad7e413b6 100644
--- a/tests/testthat/test-skewness.R
+++ b/tests/testthat/test-skewness.R
@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
+# https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,7 +16,7 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
 context("skewness.R")