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