diff --git a/.gitignore b/.gitignore
index 8890d879..28ba0c21 100755
--- a/.gitignore
+++ b/.gitignore
@@ -18,6 +18,5 @@ vignettes/*.R
.DS_Store
.Rprofile
^CRAN-RELEASE$
-git_*.sh
packrat/lib*/
packrat/src/
diff --git a/DESCRIPTION b/DESCRIPTION
index d8a2055f..4ba3534f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 0.6.1.9003
+Version: 0.6.1.9033
Date: 2019-05-20
Title: Antimicrobial Resistance Analysis
Authors@R: c(
diff --git a/R/mdro.R b/R/mdro.R
index d0f00b3f..eba2b7cc 100755
--- a/R/mdro.R
+++ b/R/mdro.R
@@ -374,6 +374,9 @@ eucast_exceptional_phenotypes <- function(x, country = "EUCAST", ...) {
}
# is_ESBL <- function(x, col_mo = NULL, ...) {
+# get_ab_col <- function(columns, ab) {
+# columns[names(columns) == ab]
+# }
# col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
# cols_ab <- get_column_abx(tbl = x,
# soft_dependencies = c("AMX", "AMP"),
diff --git a/R/misc.R b/R/misc.R
index 6868bbd8..2739c5b1 100755
--- a/R/misc.R
+++ b/R/misc.R
@@ -154,10 +154,6 @@ search_type_in_df <- function(tbl, type) {
found
}
-get_ab_col <- function(columns, ab) {
- columns[names(columns) == ab]
-}
-
get_column_abx <- function(x,
soft_dependencies = NULL,
hard_dependencies = NULL,
diff --git a/README.md b/README.md
index adb301e1..afef5516 100755
--- a/README.md
+++ b/README.md
@@ -13,12 +13,12 @@
This is the **development source** of `AMR`, a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
## Authors
-Matthijs S. Berends 1,2,a,
-Christian F. Luz 1,a,
+Matthijs S. Berends 1,2,a,
+Christian F. Luz 1,a,
Erwin E.A. Hassing2,
-Corinna Glasner 1,b,
-Alex W. Friedrich 1,b,
-Bhanu N.M. Sinha 1,b
+Corinna Glasner 1,b,
+Alex W. Friedrich 1,b,
+Bhanu N.M. Sinha 1,b
1 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl) [umcg.nl](http://www.umcg.nl)
2 Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index e547c6e3..545bc27f 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 52052430..2b66d591 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/authors.html b/docs/authors.html
index f1701d4f..c9a82572 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/index.html b/docs/index.html
index db1cc47a..4bfd1484 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -42,7 +42,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/news/index.html b/docs/news/index.html
index 26c844b2..c2b6a3c1 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html
index 9bfe09d9..25ae2a42 100644
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html
index f00f1d26..d89a0be2 100644
--- a/docs/reference/WHOCC.html
+++ b/docs/reference/WHOCC.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html
index ce7146e6..3f8089a4 100644
--- a/docs/reference/ab_property.html
+++ b/docs/reference/ab_property.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html
index 83beebe0..09922532 100644
--- a/docs/reference/age_groups.html
+++ b/docs/reference/age_groups.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html
index 3b2df153..6b728820 100644
--- a/docs/reference/antibiotics.html
+++ b/docs/reference/antibiotics.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/as.atc.html b/docs/reference/as.atc.html
index c19d1c9e..397f3065 100644
--- a/docs/reference/as.atc.html
+++ b/docs/reference/as.atc.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html
index ef4204ad..ee2662ac 100644
--- a/docs/reference/as.disk.html
+++ b/docs/reference/as.disk.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html
index b9af1cf8..2a0a58a9 100644
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html
index 0a754a70..d1046957 100644
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/count.html b/docs/reference/count.html
index 2bdd01e1..343beaed 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html
index 007c9f6f..71aeb914 100644
--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html
index 3bfcc5ab..6a6b13ea 100644
--- a/docs/reference/filter_ab_class.html
+++ b/docs/reference/filter_ab_class.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html
index c2a4e9d6..e62b2e6f 100644
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/freq.html b/docs/reference/freq.html
index 25a73355..a7716bb2 100644
--- a/docs/reference/freq.html
+++ b/docs/reference/freq.html
@@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html
index 0e4ac000..bb1d6dc5 100644
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html
index 5b41f545..d8a77b07 100644
--- a/docs/reference/guess_ab_col.html
+++ b/docs/reference/guess_ab_col.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 458600b0..c0e9f866 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html
index 43d7aa86..f0aa8d07 100644
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index 5bd628e8..0bfea458 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index 62f34126..e49b00c3 100644
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/portion.html b/docs/reference/portion.html
index 46251b39..10e24002 100644
--- a/docs/reference/portion.html
+++ b/docs/reference/portion.html
@@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html
index d02d4d91..dbbaf44c 100644
--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html
index fe532c2b..c3686354 100644
--- a/docs/reference/rsi_translation.html
+++ b/docs/reference/rsi_translation.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/docs/reference/translate.html b/docs/reference/translate.html
index aeb2e1fd..42f337ce 100644
--- a/docs/reference/translate.html
+++ b/docs/reference/translate.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9003
+ 0.6.1.9033
diff --git a/git_commit.sh b/git_commit.sh
new file mode 100755
index 00000000..e71cf26e
--- /dev/null
+++ b/git_commit.sh
@@ -0,0 +1,38 @@
+#######################################################################
+# To push new commits to the premaster branch, run: #
+# bash git_premaster.sh "commit message" #
+# #
+# After successful CRAN checks, merge it to the master branch with: #
+# bash git_merge.sh #
+#######################################################################
+
+if [ -z "$1" ]; then
+ echo "FATAL - no commit message"
+ exit 1
+fi
+
+echo "••••••••••••••••••••••••••••••••••••••••••••"
+echo "• Updating package date and version number •"
+echo "••••••••••••••••••••••••••••••••••••••••••••"
+sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
+# get latest tags
+git pull --tags --quiet
+# get version number: latest tag + .90 + number of commits (like 0.6.1.9033)
+newversion=`git describe --tags | sed 's/-/.90/' | sed 's/-.*//' | sed 's/v//'`
+sed -i -- "s/^Version: .*/Version: ${newversion}/" DESCRIPTION
+echo "First 3 lines of DESCRIPTION:"
+head -3 DESCRIPTION
+echo
+echo "•••••••••••••••••••••••"
+echo "• Documenting package •"
+echo "•••••••••••••••••••••••"
+Rscript -e "devtools::document()"
+echo
+echo "••••••••••••••"
+echo "• Committing •"
+echo "••••••••••••••"
+git add .
+git commit -a -m "$1" --quiet
+
+echo
+echo "Done."
diff --git a/git_merge.sh b/git_merge.sh
new file mode 100755
index 00000000..0e088a54
--- /dev/null
+++ b/git_merge.sh
@@ -0,0 +1,26 @@
+#######################################################################
+# To push new commits to the premaster branch, run: #
+# bash git_premaster.sh "commit message" #
+# #
+# After successful CRAN checks, merge it to the master branch with: #
+# bash git_merge.sh #
+#######################################################################
+
+# stash current changes
+# git stash --quiet
+
+# go to master
+git checkout master --quiet
+echo "changed branch to master"
+# import everything from premaster
+git merge premaster
+# and send it to git
+git push
+# echo "pushed changes to master"
+# return to premaster
+git checkout premaster --quiet
+echo "changed branch back to premaster"
+
+# and get stashed changes back
+# git stash apply --quiet
+
diff --git a/git_premaster.sh b/git_premaster.sh
new file mode 100755
index 00000000..aba302f6
--- /dev/null
+++ b/git_premaster.sh
@@ -0,0 +1,62 @@
+#######################################################################
+# To push new commits to the premaster branch, run: #
+# bash git_premaster.sh "commit message" #
+# #
+# After successful CRAN checks, merge it to the master branch with: #
+# bash git_merge.sh #
+#######################################################################
+
+if [ -z "$1" ]; then
+ echo "FATAL - no commit message"
+ exit 1
+fi
+
+echo "••••••••••••••••••••••••••••••••••••••••••••"
+echo "• Updating package date and version number •"
+echo "••••••••••••••••••••••••••••••••••••••••••••"
+sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
+# get latest tags
+git pull --tags --quiet
+# get version number: latest tag + .90 + number of commits (like 0.6.1.9033)
+newversion=`git describe --tags | sed 's/-/.90/' | sed 's/-.*//' | sed 's/v//'`
+sed -i -- "s/^Version: .*/Version: ${newversion}/" DESCRIPTION
+echo "First 3 lines of DESCRIPTION:"
+head -3 DESCRIPTION
+echo
+echo "•••••••••••••••••••••••••••••••••"
+echo "• Reloading/Documenting package •"
+echo "•••••••••••••••••••••••••••••••••"
+Rscript -e "devtools::load_all(quiet = TRUE)"
+Rscript -e "suppressMessages(devtools::document())"
+Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
+echo
+echo "•••••••••••••••••"
+echo "• Building site •"
+echo "•••••••••••••••••"
+Rscript -e "suppressMessages(pkgdown::build_site(lazy = TRUE, examples = FALSE))"
+
+echo
+echo "•••••••••••••••••••••••••"
+echo "• List of changed files •"
+echo "•••••••••••••••••••••••••"
+git status --short
+echo
+
+read -p "Continue (Y/n)? " choice
+case "$choice" in
+ n|N ) exit 1;;
+ * ) ;;
+esac
+
+echo
+echo "•••••••••••••••••••••••••••"
+echo "• Uploading to repository •"
+echo "•••••••••••••••••••••••••••"
+git add .
+git commit -a -m "$1" --quiet
+git push --quiet
+echo "Comparison:"
+echo "https://gitlab.com/msberends/AMR/compare/master...premaster?view=inline"
+
+echo
+echo "Done."
diff --git a/git_siteonly.sh b/git_siteonly.sh
new file mode 100755
index 00000000..7e6470ae
--- /dev/null
+++ b/git_siteonly.sh
@@ -0,0 +1,38 @@
+#######################################################################
+# To push new commits to the premaster branch, run: #
+# bash git_premaster.sh "commit message" #
+# #
+# After successful CRAN checks, merge it to the master branch with: #
+# bash git_merge.sh #
+#######################################################################
+
+echo "•••••••••••••••••••••"
+echo "• Reloading package •"
+echo "•••••••••••••••••••••"
+Rscript -e "devtools::load_all()"
+Rscript -e "devtools::document()"
+Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
+echo
+echo "•••••••••••••••••"
+echo "• Building site •"
+echo "•••••••••••••••••"
+Rscript -e "suppressMessages(pkgdown::build_site(lazy = TRUE, examples = FALSE))"
+
+echo
+read -p "Continue (Y/n)? " choice
+case "$choice" in
+ n|N ) exit 1;;
+ * ) ;;
+esac
+
+echo
+echo "•••••••••••••••••••••••••••"
+echo "• Uploading to repository •"
+echo "•••••••••••••••••••••••••••"
+git add .
+git commit -a -m "website update" --quiet
+# git push --quiet
+git checkout master
+git merge premaster
+git push --quiet
+git checkout premaster