diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml deleted file mode 100644 index e3077c82..00000000 --- a/.gitlab-ci.yml +++ /dev/null @@ -1,36 +0,0 @@ -# ==================================================================== # -# 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. # -# ==================================================================== # - -# as long as GitLab used - make sure the website will be updated -stages: - - deploy - -pages: - stage: deploy - allow_failure: true - when: always - only: - - master - script: - - mv docs public - artifacts: - paths: - - public diff --git a/DESCRIPTION b/DESCRIPTION index e97dd90d..3f7b4567 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.2.0.9031 +Version: 1.2.0.9032 Date: 2020-07-09 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 90a0ffaa..722eac91 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.2.0.9031 +# AMR 1.2.0.9032 ## Last updated: 09-Jul-2020 ### New @@ -38,7 +38,7 @@ * Any progress bar will now only show in interactive mode (i.e. not in R Markdown) ### Other -* Project moved to GitHub +* Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI. # AMR 1.2.0 diff --git a/R/translate.R b/R/translate.R index f57d4704..fe9f282d 100755 --- a/R/translate.R +++ b/R/translate.R @@ -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://github.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE) + warning("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE) return(FALSE) }) if (NROW(df_trans) == 0 | !any_form_in_patterns) { diff --git a/README.md b/README.md index 6f6dfa6d..17155054 100755 --- a/README.md +++ b/README.md @@ -1,18 +1,18 @@ % AMR (for R) # `AMR` (for R) - + 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 GitHub (https://github.com/msberends/AMR) and GitLab (https://gitlab.com/msberends/AMR).* +*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to GitLab (https://gitlab.com/msberends/AMR).* ### How to get this package Please see [our website](https://msberends.github.io/AMR/#get-this-package). ### Copyright -This R package is licensed under the [GNU General Public License (GPL) v2.0](https://gitlab.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package: +This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package: - May be used for commercial purposes diff --git a/data-raw/country_analysis.R b/data-raw/country_analysis.R index 11e90808..f25f8ea4 100644 --- a/data-raw/country_analysis.R +++ b/data-raw/country_analysis.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. # # ==================================================================== # # Read and format data ---------------------------------------------------- diff --git a/data-raw/internals.R b/data-raw/internals.R index f3493fa5..8075461e 100644 --- a/data-raw/internals.R +++ b/data-raw/internals.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. # # ==================================================================== # # Run this file to update the package using: ------------------------------- diff --git a/data-raw/loinc.R b/data-raw/loinc.R index 2f34fcc6..c6a4b23b 100644 --- a/data-raw/loinc.R +++ b/data-raw/loinc.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. # # ==================================================================== # # last updated: 20 January 2020 - Loinc_2.67 diff --git a/data-raw/poorman_prepend.R b/data-raw/poorman_prepend.R index afa3a68f..41181ea8 100644 --- a/data-raw/poorman_prepend.R +++ b/data-raw/poorman_prepend.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/data-raw/read_EUCAST.R b/data-raw/read_EUCAST.R index 78fbfcda..646d5108 100644 --- a/data-raw/read_EUCAST.R +++ b/data-raw/read_EUCAST.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(openxlsx) diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index fac3b94f..ede153bb 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_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. # # ==================================================================== # library(dplyr) diff --git a/data-raw/reproduction_of_antivirals.R b/data-raw/reproduction_of_antivirals.R index f1a32fd8..0167f06c 100644 --- a/data-raw/reproduction_of_antivirals.R +++ b/data-raw/reproduction_of_antivirals.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 all data from the WHOCC website diff --git a/data-raw/reproduction_of_example_isolates_unclean.R b/data-raw/reproduction_of_example_isolates_unclean.R index 9d34e990..c49baa26 100644 --- a/data-raw/reproduction_of_example_isolates_unclean.R +++ b/data-raw/reproduction_of_example_isolates_unclean.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. # # ==================================================================== # patients <- unlist(lapply(LETTERS, paste0, 1:10)) diff --git a/data-raw/reproduction_of_microorganisms.R b/data-raw/reproduction_of_microorganisms.R index 6237efac..3abec2f7 100644 --- a/data-raw/reproduction_of_microorganisms.R +++ b/data-raw/reproduction_of_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. # # ==================================================================== # # Reproduction of the `microorganisms` data set diff --git a/data-raw/snomed.R b/data-raw/snomed.R index abf40a2a..30b753f1 100644 --- a/data-raw/snomed.R +++ b/data-raw/snomed.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(AMR) diff --git a/docs/404.html b/docs/404.html index b12eb2a0..1db1be6b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9031 + 1.2.0.9032 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index b5885137..ad2fe669 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9031 + 1.2.0.9032 diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html index 148cf2f9..ffb8199c 100644 --- a/docs/articles/SPSS.html +++ b/docs/articles/SPSS.html @@ -39,7 +39,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/articles/WHONET.html b/docs/articles/WHONET.html index f825cfbf..46684c5e 100644 --- a/docs/articles/WHONET.html +++ b/docs/articles/WHONET.html @@ -39,7 +39,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 @@ -202,7 +202,7 @@

An example syntax could look like this:

library(readxl)
 data <- read_excel(path = "path/to/your/file.xlsx")
-

This package comes with an example data set WHONET. We will use it for this analysis.

+

This package comes with an example data set WHONET. We will use it for this analysis.

@@ -214,7 +214,7 @@ library(cleaner) # to create frequency tables

We will have to transform some variables to simplify and automate the analysis:

# transform variables
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 840fdf32..2bd5ee92 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -81,7 +81,7 @@
       
       
         AMR (for R)
-        1.2.0.9031
+        1.2.0.9032
diff --git a/docs/authors.html b/docs/authors.html index 063ae201..b682fe49 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9031 + 1.2.0.9032 diff --git a/docs/index.html b/docs/index.html index f91a11e0..2dfebaa1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.2.0.9031 + 1.2.0.9032 diff --git a/docs/news/index.html b/docs/news/index.html index cdd07390..d36a9a62 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9031 + 1.2.0.9032 @@ -229,9 +229,9 @@ Source: NEWS.md -
-

-AMR 1.2.0.9031 Unreleased +
+

+AMR 1.2.0.9032 Unreleased

@@ -292,7 +292,7 @@

Other

    -
  • Project moved to GitHub
    • +
  • Moved primary location of this project from GitLab to GitHub, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9a8184eb..4bc83d8c 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-07-09T14:11Z +last_built: 2020-07-09T18:06Z urls: 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 f65d4f2f..e46ed965 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032

diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html index c34cd76d..4c448649 100644 --- a/docs/reference/AMR.html +++ b/docs/reference/AMR.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html index bea57b2a..753da0cf 100644 --- a/docs/reference/WHOCC.html +++ b/docs/reference/WHOCC.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html index 2463807a..440a6267 100644 --- a/docs/reference/WHONET.html +++ b/docs/reference/WHONET.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/ab_from_text.html b/docs/reference/ab_from_text.html index 3d1f53f4..c4536b2b 100644 --- a/docs/reference/ab_from_text.html +++ b/docs/reference/ab_from_text.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index 77662783..d4148b1d 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/age.html b/docs/reference/age.html index 8405126f..7088155a 100644 --- a/docs/reference/age.html +++ b/docs/reference/age.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index 2814f41c..83e7a05d 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 8616a950..bf1444f0 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index 0b0820aa..19e95438 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index 746fd787..41bd4c88 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index 853d51ec..7ccfe916 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index 704adfcd..722a1926 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index fee7e121..e8909e13 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index a9dae051..31944846 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -83,7 +83,7 @@ This function requires an internet connection." /> AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/availability.html b/docs/reference/availability.html index 461aadc5..3ec059c8 100644 --- a/docs/reference/availability.html +++ b/docs/reference/availability.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index d30b4884..6bafa339 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index 20c5a14e..b2ba47b0 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html index 38d3ad6c..9ee14870 100644 --- a/docs/reference/catalogue_of_life_version.html +++ b/docs/reference/catalogue_of_life_version.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/count.html b/docs/reference/count.html index 64e529e8..6b8d553a 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index cdd0d08a..901e70ae 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html index eaf17bed..f954b10d 100644 --- a/docs/reference/example_isolates.html +++ b/docs/reference/example_isolates.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html index 8eefe38a..9a5e372b 100644 --- a/docs/reference/example_isolates_unclean.html +++ b/docs/reference/example_isolates_unclean.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index f1884400..9f737481 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index beff502f..dfa01482 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html index efd133f0..5dd3fcec 100644 --- a/docs/reference/g.test.html +++ b/docs/reference/g.test.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index 0a70fffb..8789aae8 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index 0235922f..8592936e 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index 6ac64817..def158da 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/index.html b/docs/reference/index.html index afa988a1..bd20d1db 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9031 + 1.2.0.9032 diff --git a/docs/reference/join.html b/docs/reference/join.html index b713504b..b87b284d 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html index 589b8db1..bfc73187 100644 --- a/docs/reference/key_antibiotics.html +++ b/docs/reference/key_antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html index 5c6d91bb..b89a5ada 100644 --- a/docs/reference/kurtosis.html +++ b/docs/reference/kurtosis.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html index f69de213..60764f16 100644 --- a/docs/reference/lifecycle.html +++ b/docs/reference/lifecycle.html @@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/like.html b/docs/reference/like.html index c11b88ca..8d0326b1 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index a548b02d..e5fafdf1 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 16f72ecf..810ecda3 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 2665bfb1..6fd58dce 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 709e7039..d699f0f3 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 6e9108e3..1c350fa8 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html index c1d85619..b234b67b 100644 --- a/docs/reference/mo_source.html +++ b/docs/reference/mo_source.html @@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/p_symbol.html b/docs/reference/p_symbol.html index 4fdf9fca..8ae9c516 100644 --- a/docs/reference/p_symbol.html +++ b/docs/reference/p_symbol.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/pca.html b/docs/reference/pca.html index 44ddcac0..37e33d21 100644 --- a/docs/reference/pca.html +++ b/docs/reference/pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index 0a921422..e0aed1d2 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index 34cc2622..7a267a91 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index 385d8d99..268029c2 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index 3873286d..f2a0b8d7 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/reference/translate.html b/docs/reference/translate.html index d04aae50..0c8650b9 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9030 + 1.2.0.9032 diff --git a/docs/works_great_on.png b/docs/works_great_on.png new file mode 100644 index 00000000..0feb5c9d Binary files /dev/null and b/docs/works_great_on.png differ diff --git a/pkgdown/logos/works_great_on.png b/pkgdown/logos/works_great_on.png new file mode 100644 index 00000000..0feb5c9d Binary files /dev/null and b/pkgdown/logos/works_great_on.png differ diff --git a/vignettes/WHONET.Rmd b/vignettes/WHONET.Rmd index f798fe3a..10bb65f9 100644 --- a/vignettes/WHONET.Rmd +++ b/vignettes/WHONET.Rmd @@ -34,7 +34,7 @@ library(readxl) data <- read_excel(path = "path/to/your/file.xlsx") ``` -This package comes with an [example data set `WHONET`](https://msberends.gitlab.io/AMR/reference/WHONET.html). We will use it for this analysis. +This package comes with an [example data set `WHONET`](https://msberends.github.io/AMR/reference/WHONET.html). We will use it for this analysis. ### Preparation @@ -49,7 +49,7 @@ library(cleaner) # to create frequency tables We will have to transform some variables to simplify and automate the analysis: -* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.gitlab.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms. +* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms. * Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.rsi()` function is for. ```{r}