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dr. M.S. (Matthijs) Berends
2019-05-20 14:16:53 +02:00
parent 4ca00e1868
commit 6eb08a2ea3
38 changed files with 202 additions and 40 deletions
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1
.gitignore vendored
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@@ -18,6 +18,5 @@ vignettes/*.R
.DS_Store
.Rprofile
^CRAN-RELEASE$
git_*.sh
packrat/lib*/
packrat/src/

2
DESCRIPTION
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@@ -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(

3
R/mdro.R
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@@ -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"),

4
R/misc.R
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@@ -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,

10
README.md
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@@ -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 <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>,
Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,a</sup>,
Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>,
Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,a</sup>,
Erwin E.A. Hassing<sup>2</sup>,
Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
<sup>1</sup> 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)<br>
<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>

2
docs/LICENSE-text.html
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@@ -78,7 +78,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/articles/index.html
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@@ -78,7 +78,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/authors.html
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@@ -78,7 +78,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/index.html
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@@ -42,7 +42,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/news/index.html
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@@ -78,7 +78,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/AMR-deprecated.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/WHOCC.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/ab_property.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/age_groups.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/antibiotics.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/as.atc.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/as.disk.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/as.mic.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/as.rsi.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/count.html
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@@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/eucast_rules.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/filter_ab_class.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/first_isolate.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/freq.html
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@@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/guess_ab_col.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/index.html
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@@ -78,7 +78,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/key_antibiotics.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/mdro.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/microorganisms.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/portion.html
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@@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/resistance_predict.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/rsi_translation.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

2
docs/reference/translate.html
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@@ -80,7 +80,7 @@
</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="Released version">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
</span>
</div>

38
git_commit.sh Executable file
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@@ -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."

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git_merge.sh Executable file
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@@ -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

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git_premaster.sh Executable file
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@@ -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."

38
git_siteonly.sh Executable file
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@@ -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