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MDRO, freq tables, new print format for tibbles
This commit is contained in:
parent
3165c50d06
commit
2509e2413d
@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 0.1.2
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Version: 0.2.0
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Date: 2018-04-02
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Date: 2018-04-18
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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person(
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person(
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@ -28,9 +28,12 @@ Depends:
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R (>= 3.2.0)
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R (>= 3.2.0)
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Imports:
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Imports:
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dplyr (>= 0.7.0),
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dplyr (>= 0.7.0),
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data.table (>= 1.10.0),
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reshape2 (>= 1.4.0),
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reshape2 (>= 1.4.0),
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xml2 (>= 1.0.0),
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xml2 (>= 1.0.0),
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rvest (>= 0.3.2)
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knitr (>= 1.0.0),
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rvest (>= 0.3.2),
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tibble
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Suggests:
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Suggests:
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testthat (>= 1.0.2),
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testthat (>= 1.0.2),
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covr (>= 3.0.1)
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covr (>= 3.0.1)
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20
NAMESPACE
20
NAMESPACE
@ -7,11 +7,18 @@ S3method(barplot,mic)
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S3method(barplot,rsi)
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S3method(barplot,rsi)
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S3method(plot,mic)
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S3method(plot,mic)
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S3method(plot,rsi)
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S3method(plot,rsi)
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S3method(print,data.table)
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S3method(print,mic)
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S3method(print,mic)
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S3method(print,rsi)
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S3method(print,rsi)
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S3method(print,tbl)
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S3method(print,tbl_df)
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S3method(summary,mic)
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S3method(summary,mic)
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S3method(summary,rsi)
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S3method(summary,rsi)
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export("%like%")
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export(BRMO)
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export(EUCAST_rules)
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export(EUCAST_rules)
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export(MDRO)
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export(MRGN)
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export(abname)
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export(abname)
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export(anti_join_microorganisms)
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export(anti_join_microorganisms)
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export(as.mic)
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export(as.mic)
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@ -20,6 +27,8 @@ export(atc_property)
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export(clipboard_export)
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export(clipboard_export)
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export(clipboard_import)
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export(clipboard_import)
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export(first_isolate)
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export(first_isolate)
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export(freq)
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export(frequency_tbl)
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export(full_join_microorganisms)
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export(full_join_microorganisms)
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export(guess_bactid)
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export(guess_bactid)
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export(inner_join_microorganisms)
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export(inner_join_microorganisms)
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@ -41,8 +50,11 @@ exportMethods(barplot.mic)
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exportMethods(barplot.rsi)
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exportMethods(barplot.rsi)
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exportMethods(plot.mic)
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exportMethods(plot.mic)
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exportMethods(plot.rsi)
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exportMethods(plot.rsi)
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exportMethods(print.data.table)
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exportMethods(print.mic)
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exportMethods(print.mic)
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exportMethods(print.rsi)
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exportMethods(print.rsi)
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exportMethods(print.tbl)
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exportMethods(print.tbl_df)
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exportMethods(summary.mic)
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exportMethods(summary.mic)
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exportMethods(summary.rsi)
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exportMethods(summary.rsi)
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importFrom(dplyr,"%>%")
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importFrom(dplyr,"%>%")
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@ -52,15 +64,19 @@ importFrom(dplyr,arrange)
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importFrom(dplyr,arrange_at)
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importFrom(dplyr,arrange_at)
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importFrom(dplyr,as_tibble)
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importFrom(dplyr,as_tibble)
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importFrom(dplyr,between)
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importFrom(dplyr,between)
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importFrom(dplyr,desc)
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importFrom(dplyr,filter)
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importFrom(dplyr,filter)
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importFrom(dplyr,filter_at)
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importFrom(dplyr,filter_at)
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importFrom(dplyr,group_by)
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importFrom(dplyr,group_by)
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importFrom(dplyr,group_by_at)
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importFrom(dplyr,group_by_at)
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importFrom(dplyr,group_size)
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importFrom(dplyr,group_vars)
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importFrom(dplyr,if_else)
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importFrom(dplyr,if_else)
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importFrom(dplyr,lag)
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importFrom(dplyr,lag)
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importFrom(dplyr,left_join)
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importFrom(dplyr,left_join)
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importFrom(dplyr,mutate)
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importFrom(dplyr,mutate)
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importFrom(dplyr,n_distinct)
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importFrom(dplyr,n_distinct)
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importFrom(dplyr,n_groups)
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importFrom(dplyr,progress_estimated)
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importFrom(dplyr,progress_estimated)
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importFrom(dplyr,pull)
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importFrom(dplyr,pull)
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importFrom(dplyr,row_number)
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importFrom(dplyr,row_number)
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@ -69,6 +85,7 @@ importFrom(dplyr,slice)
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importFrom(dplyr,summarise)
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importFrom(dplyr,summarise)
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importFrom(dplyr,tibble)
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importFrom(dplyr,tibble)
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importFrom(dplyr,vars)
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importFrom(dplyr,vars)
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importFrom(grDevices,boxplot.stats)
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importFrom(graphics,axis)
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importFrom(graphics,axis)
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importFrom(graphics,barplot)
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importFrom(graphics,barplot)
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importFrom(graphics,plot)
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importFrom(graphics,plot)
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@ -76,6 +93,9 @@ importFrom(graphics,text)
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importFrom(reshape2,dcast)
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importFrom(reshape2,dcast)
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importFrom(rvest,html_nodes)
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importFrom(rvest,html_nodes)
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importFrom(rvest,html_table)
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importFrom(rvest,html_table)
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importFrom(stats,fivenum)
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importFrom(stats,quantile)
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importFrom(stats,sd)
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importFrom(utils,object.size)
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importFrom(utils,object.size)
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importFrom(utils,packageDescription)
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importFrom(utils,packageDescription)
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importFrom(utils,read.delim)
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importFrom(utils,read.delim)
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28
NEWS
28
NEWS
@ -1,28 +0,0 @@
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## 0.1.2
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- Added full support for Windows, Linux and macOS
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- New function `guess_bactid` to determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
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- New functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
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- New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
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- Renamed dataset `ablist` to `antibiotics`
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- Renamed dataset `bactlist` to `microorganisms`
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- Added more microorganisms to `bactlist`
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- Added analysis examples on help page of dataset `septic_patients`
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- Added support for character vector in join functions
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- Added warnings when applying a join results in more rows after than before the join
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- Altered `%like%` to make it case insensitive
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- For parameters of functions `first_isolate`, `EUCAST_rules` the column names are now case-insensitive
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- Functions `as.rsi` and `as.mic` now add the package name and version as attribute
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- Expanded README.md
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- Added unit testing with the `testthat` package
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- Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
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- Added Line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
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## 0.1.1
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- `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
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- Edited column names to comply with GLIMS, the laboratory information system
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- Added more valid MIC values
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- Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
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- Added barplots for `rsi` and `mic` classes
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## 0.1.0
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- First submission to CRAN.
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37
NEWS.md
Normal file
37
NEWS.md
Normal file
@ -0,0 +1,37 @@
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## 0.2.0
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#### New
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- Full support for Windows, Linux and macOS
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- Function `guess_bactid` to determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
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- Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
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- Function `MDRO` to determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines. Suggest your own via https://github.com/msberends/AMR/issues/new. Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
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- Function `freq` to create frequency tables, with additional info in a header
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- New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
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- New print format for tibbles and data.tables
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#### Changed
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- Renamed dataset `ablist` to `antibiotics`
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- Renamed dataset `bactlist` to `microorganisms`
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- Added more microorganisms to `bactlist`
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- Added analysis examples on help page of dataset `septic_patients`
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- Added support for character vector in `join` functions
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- Added warnings when a join results in more rows after than before the join
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- Altered `%like%` to make it case insensitive
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- For parameters of functions `first_isolate` and `EUCAST_rules` the column names are now case-insensitive
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- Functions `as.rsi` and `as.mic` now add the package name and version as attribute
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#### Other
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- Expanded README.md with more examples
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- Added ORC IDs of authors to DESCRIPTION file
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- Added unit testing with the `testthat` package
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- Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
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- Added Line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
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## 0.1.1
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- `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
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- Edited column names to comply with GLIMS, the laboratory information system
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- Added more valid MIC values
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- Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
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- Added barplots for `rsi` and `mic` classes
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## 0.1.0
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- First submission to CRAN.
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@ -439,45 +439,26 @@ key_antibiotics <- function(tbl,
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col.list <- c(amox, cfot, cfta, cftr, cfur, cipr, clar,
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col.list <- c(amox, cfot, cfta, cftr, cfur, cipr, clar,
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clin, clox, doxy, gent, line, mero, peni,
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clin, clox, doxy, gent, line, mero, peni,
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pita, rifa, teic, trsu, vanc)
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pita, rifa, teic, trsu, vanc)
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col.list <- col.list[!is.na(col.list)]
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col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
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col.list.bak <- col.list
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amox <- col.list[amox]
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# are they available as upper case or lower case then?
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cfot <- col.list[cfot]
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for (i in 1:length(col.list)) {
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cfta <- col.list[cfta]
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if (toupper(col.list[i]) %in% colnames(tbl)) {
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cftr <- col.list[cftr]
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col.list[i] <- toupper(col.list[i])
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cfur <- col.list[cfur]
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} else if (tolower(col.list[i]) %in% colnames(tbl)) {
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cipr <- col.list[cipr]
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col.list[i] <- tolower(col.list[i])
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clar <- col.list[clar]
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} else if (!col.list[i] %in% colnames(tbl)) {
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clin <- col.list[clin]
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col.list[i] <- NA
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clox <- col.list[clox]
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}
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doxy <- col.list[doxy]
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}
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gent <- col.list[gent]
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if (!all(col.list %in% colnames(tbl))) {
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line <- col.list[line]
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if (info == TRUE) {
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mero <- col.list[mero]
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warning('These columns do not exist and will be ignored: ',
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peni <- col.list[peni]
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col.list.bak[!(col.list %in% colnames(tbl))] %>% toString(),
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pita <- col.list[pita]
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immediate. = TRUE,
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rifa <- col.list[rifa]
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call. = FALSE)
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teic <- col.list[teic]
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}
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trsu <- col.list[trsu]
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}
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vanc <- col.list[vanc]
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amox <- col.list[1]
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cfot <- col.list[2]
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cfta <- col.list[3]
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cftr <- col.list[4]
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cfur <- col.list[5]
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cipr <- col.list[6]
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clar <- col.list[7]
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clin <- col.list[8]
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clox <- col.list[9]
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doxy <- col.list[10]
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gent <- col.list[11]
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line <- col.list[12]
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mero <- col.list[13]
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peni <- col.list[14]
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pita <- col.list[15]
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rifa <- col.list[16]
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teic <- col.list[17]
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trsu <- col.list[18]
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vanc <- col.list[19]
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# join microorganisms
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# join microorganisms
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tbl <- tbl %>% left_join_microorganisms(col_bactid)
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tbl <- tbl %>% left_join_microorganisms(col_bactid)
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361
R/freq.R
Normal file
361
R/freq.R
Normal file
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Frequency table
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#'
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#' Create a frequency table of a vector of data, a single column or a maximum of 9 columns of a data frame. Supports markdown for reports.
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#' @param x data
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#' @param sort.count Sort on count. Use \code{FALSE} to sort alphabetically on item.
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#' @param nmax number of row to print. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.
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#' @param na.rm a logical value indicating whether NA values should be removed from the frequency table. The header will always print the amount of\code{NA}s.
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#' @param markdown print table in markdown format (this forces \code{nmax = NA})
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#' @param toConsole Print table to the console. Use \code{FALSE} to assign the table to an object.
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#' @param digits how many significant digits are to be used for numeric values (not for the items themselves, that depends on \code{\link{getOption}("digits")})
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#' @param sep a character string to separate the terms when selecting multiple columns
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#' @details For numeric values, the next values will be calculated and shown into the header:
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#' \itemize{
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#' \item{Mean, using \code{\link[base]{mean}}}
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#' \item{Standard deviation, using \code{\link[stats]{sd}}}
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#' \item{Five numbers of Tukey (min, Q1, median, Q3, max), using \code{\link[stats]{fivenum}}}
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#' \item{Outliers (count and list), using \code{\link{boxplot.stats}}}
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#' \item{Coefficient of variation (CV), the standard deviation divided by the mean}
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#' \item{Coefficient of quartile variation (CQV, sometimes called coefficient of dispersion), calculated as \code{(Q3 - Q1) / (Q3 + Q1)} using \code{\link{quantile}} with \code{type = 6} as quantile algorithm to comply with SPSS standards}
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#' }
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#' @importFrom stats fivenum sd quantile
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#' @importFrom grDevices boxplot.stats
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#' @importFrom dplyr %>% select pull n_distinct group_by arrange desc mutate summarise
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#' @keywords summary summarise frequency freq
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#' @rdname freq
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#' @export
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#' @examples
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#' library(dplyr)
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#'
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#' freq(septic_patients$hospital_id)
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#'
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#' septic_patients %>%
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#' filter(hospital_id == "A") %>%
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#' select(bactid) %>%
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#' freq()
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#'
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#' # select multiple columns; they will be pasted together
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#' septic_patients %>%
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#' left_join_microorganisms %>%
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#' filter(hospital_id == "A") %>%
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#' select(genus, species) %>%
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#' freq()
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#'
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#' # save frequency table to an object
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#' years <- septic_patients %>%
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#' mutate(year = format(date, "%Y")) %>%
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#' select(year) %>%
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#' freq(toConsole = FALSE)
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freq <- function(x,
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sort.count = TRUE,
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nmax = 15,
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na.rm = TRUE,
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markdown = FALSE,
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toConsole = TRUE,
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digits = 2,
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sep = " ") {
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||||||
|
mult.columns <- 0
|
||||||
|
|
||||||
|
if (NROW(x) == 0) {
|
||||||
|
cat('\nNo observations.\n')
|
||||||
|
return(invisible())
|
||||||
|
}
|
||||||
|
|
||||||
|
if (!is.null(ncol(x))) {
|
||||||
|
if (ncol(x) == 1 & any(class(x) == 'data.frame')) {
|
||||||
|
x <- x %>% pull(1)
|
||||||
|
} else if (ncol(x) < 10) {
|
||||||
|
|
||||||
|
mult.columns <- ncol(x)
|
||||||
|
|
||||||
|
colnames(x) <- LETTERS[1:ncol(x)]
|
||||||
|
if (ncol(x) == 2) {
|
||||||
|
x$total <- paste(x$A %>% as.character(),
|
||||||
|
x$B %>% as.character(),
|
||||||
|
sep = sep)
|
||||||
|
} else if (ncol(x) == 3) {
|
||||||
|
x$total <- paste(x$A %>% as.character(),
|
||||||
|
x$B %>% as.character(),
|
||||||
|
x$C %>% as.character(),
|
||||||
|
sep = sep)
|
||||||
|
} else if (ncol(x) == 4) {
|
||||||
|
x$total <- paste(x$A %>% as.character(),
|
||||||
|
x$B %>% as.character(),
|
||||||
|
x$C %>% as.character(),
|
||||||
|
x$D %>% as.character(),
|
||||||
|
sep = sep)
|
||||||
|
} else if (ncol(x) == 5) {
|
||||||
|
x$total <- paste(x$A %>% as.character(),
|
||||||
|
x$B %>% as.character(),
|
||||||
|
x$C %>% as.character(),
|
||||||
|
x$D %>% as.character(),
|
||||||
|
x$E %>% as.character(),
|
||||||
|
sep = sep)
|
||||||
|
} else if (ncol(x) == 6) {
|
||||||
|
x$total <- paste(x$A %>% as.character(),
|
||||||
|
x$B %>% as.character(),
|
||||||
|
x$C %>% as.character(),
|
||||||
|
x$D %>% as.character(),
|
||||||
|
x$E %>% as.character(),
|
||||||
|
x$F %>% as.character(),
|
||||||
|
sep = sep)
|
||||||
|
} else if (ncol(x) == 7) {
|
||||||
|
x$total <- paste(x$A %>% as.character(),
|
||||||
|
x$B %>% as.character(),
|
||||||
|
x$C %>% as.character(),
|
||||||
|
x$D %>% as.character(),
|
||||||
|
x$E %>% as.character(),
|
||||||
|
x$F %>% as.character(),
|
||||||
|
x$G %>% as.character(),
|
||||||
|
sep = sep)
|
||||||
|
} else if (ncol(x) == 8) {
|
||||||
|
x$total <- paste(x$A %>% as.character(),
|
||||||
|
x$B %>% as.character(),
|
||||||
|
x$C %>% as.character(),
|
||||||
|
x$D %>% as.character(),
|
||||||
|
x$E %>% as.character(),
|
||||||
|
x$F %>% as.character(),
|
||||||
|
x$G %>% as.character(),
|
||||||
|
x$H %>% as.character(),
|
||||||
|
sep = sep)
|
||||||
|
} else if (ncol(x) == 9) {
|
||||||
|
x$total <- paste(x$A %>% as.character(),
|
||||||
|
x$B %>% as.character(),
|
||||||
|
x$C %>% as.character(),
|
||||||
|
x$D %>% as.character(),
|
||||||
|
x$E %>% as.character(),
|
||||||
|
x$F %>% as.character(),
|
||||||
|
x$G %>% as.character(),
|
||||||
|
x$H %>% as.character(),
|
||||||
|
x$I %>% as.character(),
|
||||||
|
sep = sep)
|
||||||
|
}
|
||||||
|
|
||||||
|
x <- x$total
|
||||||
|
|
||||||
|
} else {
|
||||||
|
stop('A maximum of 9 columns can be analysed at the same time.', call. = FALSE)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (markdown == TRUE & toConsole == FALSE) {
|
||||||
|
warning('`toConsole = FALSE` will be ignored when `markdown = TRUE`.')
|
||||||
|
}
|
||||||
|
|
||||||
|
if (mult.columns > 1) {
|
||||||
|
NAs <- x[is.na(x) | x == trimws(strrep('NA ', mult.columns))]
|
||||||
|
} else {
|
||||||
|
NAs <- x[is.na(x)]
|
||||||
|
}
|
||||||
|
if (na.rm == TRUE) {
|
||||||
|
x <- x[!x %in% NAs]
|
||||||
|
}
|
||||||
|
|
||||||
|
if (missing(sort.count) & any(class(x) %in% c('double', 'integer', 'numeric', 'raw', 'single', 'factor'))) {
|
||||||
|
# sort on item/level at default when x is numeric or a factor and sort.count is not set
|
||||||
|
sort.count <- FALSE
|
||||||
|
}
|
||||||
|
|
||||||
|
header <- character(0)
|
||||||
|
|
||||||
|
markdown_line <- ''
|
||||||
|
if (markdown == TRUE) {
|
||||||
|
markdown_line <- '\n'
|
||||||
|
}
|
||||||
|
x_align <- 'l'
|
||||||
|
|
||||||
|
if (mult.columns > 0) {
|
||||||
|
header <- header %>% paste0(markdown_line, 'Columns: ', mult.columns)
|
||||||
|
} else {
|
||||||
|
header <- header %>% paste0(markdown_line, 'Class: ', class(x) %>% rev() %>% paste(collapse = " > "))
|
||||||
|
}
|
||||||
|
|
||||||
|
if (is.list(x) | is.matrix(x) | is.environment(x) | is.function(x)) {
|
||||||
|
cat(header, "\n")
|
||||||
|
stop('`freq()` does not support lists, matrices, environments or functions.', call. = FALSE)
|
||||||
|
}
|
||||||
|
|
||||||
|
header <- header %>% paste0(markdown_line, '\nLength: ', (NAs %>% length() + x %>% length()) %>% format(),
|
||||||
|
' (of which NA: ', NAs %>% length() %>% format(),
|
||||||
|
' = ', (NAs %>% length() / (NAs %>% length() + x %>% length())) %>% percent(force_zero = TRUE), ')')
|
||||||
|
header <- header %>% paste0(markdown_line, '\nUnique: ', x %>% n_distinct() %>% format())
|
||||||
|
|
||||||
|
header.numbers.done <- FALSE
|
||||||
|
if (any(class(x) %in% c('double', 'integer', 'numeric', 'raw', 'single'))) {
|
||||||
|
# right align number
|
||||||
|
x_align <- 'r'
|
||||||
|
header <- header %>% paste0('\n')
|
||||||
|
header <- header %>% paste(markdown_line, '\nMean: ', x %>% base::mean(na.rm = TRUE) %>% format(digits = digits))
|
||||||
|
header <- header %>% paste0(markdown_line, '\nStd. dev.: ', x %>% stats::sd(na.rm = TRUE) %>% format(digits = digits),
|
||||||
|
' (CV: ', x %>% cv(na.rm = TRUE) %>% format(digits = digits), ')')
|
||||||
|
header <- header %>% paste0(markdown_line, '\nFive-Num: ', x %>% stats::fivenum(na.rm = TRUE) %>% format(digits = digits) %>% trimws() %>% paste(collapse = ' | '),
|
||||||
|
' (CQV: ', x %>% cqv(na.rm = TRUE) %>% format(digits = digits), ')')
|
||||||
|
outlier_length <- length(boxplot.stats(x)$out)
|
||||||
|
header <- header %>% paste0(markdown_line, '\nOutliers: ', outlier_length)
|
||||||
|
if (outlier_length > 0) {
|
||||||
|
header <- header %>% paste0(' (unique: ', boxplot.stats(x)$out %>% unique() %>% length(), ')')
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
formatdates <- "%e %B %Y" # = d mmmm yyyy
|
||||||
|
if (any(class(x) == 'hms')) {
|
||||||
|
x <- x %>% as.POSIXlt()
|
||||||
|
formatdates <- "%H:%M:%S"
|
||||||
|
}
|
||||||
|
if (any(class(x) %in% c('Date', 'POSIXct', 'POSIXlt'))) {
|
||||||
|
header <- header %>% paste0('\n')
|
||||||
|
mindatum <- x %>% min()
|
||||||
|
maxdatum <- x %>% max()
|
||||||
|
header <- header %>% paste0(markdown_line, '\nOldest: ', mindatum %>% format(formatdates) %>% trimws())
|
||||||
|
header <- header %>% paste0(markdown_line, '\nNewest: ', maxdatum %>% format(formatdates) %>% trimws(),
|
||||||
|
' (+', difftime(maxdatum, mindatum, units = 'auto') %>% as.double() %>% format(), ')')
|
||||||
|
}
|
||||||
|
if (any(class(x) == 'POSIXlt')) {
|
||||||
|
x <- x %>% format(formatdates)
|
||||||
|
}
|
||||||
|
|
||||||
|
if (toConsole == TRUE) {
|
||||||
|
cat(header)
|
||||||
|
}
|
||||||
|
|
||||||
|
if (all(is.na(x))) {
|
||||||
|
cat('\n\nNo observations.\n')
|
||||||
|
return(invisible())
|
||||||
|
}
|
||||||
|
if (n_distinct(x) == length(x)) {
|
||||||
|
warning('All observations are unique.', call. = FALSE)
|
||||||
|
}
|
||||||
|
|
||||||
|
if (nmax == 0 | is.na(nmax)) {
|
||||||
|
nmax <- length(x)
|
||||||
|
}
|
||||||
|
nmax.1 <- min(length(x), nmax + 1)
|
||||||
|
|
||||||
|
# create table with counts and percentages
|
||||||
|
if (any(class(x) == 'factor')) {
|
||||||
|
df <- tibble::tibble(Item = x,
|
||||||
|
Fctlvl = x %>% as.integer()) %>%
|
||||||
|
group_by(Item, Fctlvl)
|
||||||
|
column_names <- c('Item', 'Count', 'Percent', 'Cum. Count', 'Cum. Percent', '(Factor Level)')
|
||||||
|
column_align <- c('l', 'r', 'r', 'r', 'r', 'r')
|
||||||
|
} else {
|
||||||
|
df <- tibble::tibble(Item = x) %>%
|
||||||
|
group_by(Item)
|
||||||
|
column_names <- c('Item', 'Count', 'Percent', 'Cum. Count', 'Cum. Percent')
|
||||||
|
column_align <- c(x_align, 'r', 'r', 'r', 'r')
|
||||||
|
}
|
||||||
|
df <- df %>%
|
||||||
|
summarise(Count = n(),
|
||||||
|
Percent = (n() / length(x)) %>% percent(force_zero = TRUE))
|
||||||
|
|
||||||
|
if (df$Item %>% paste(collapse = ',') %like% '\033') {
|
||||||
|
df <- df %>%
|
||||||
|
mutate(Item = Item %>%
|
||||||
|
# remove escape char
|
||||||
|
# see https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
|
||||||
|
gsub('\033', ' ', ., fixed = TRUE))
|
||||||
|
}
|
||||||
|
|
||||||
|
# sort according to setting
|
||||||
|
if (sort.count == TRUE) {
|
||||||
|
df <- df %>% arrange(desc(Count))
|
||||||
|
} else {
|
||||||
|
if (any(class(x) == 'factor')) {
|
||||||
|
df <- df %>% arrange(Fctlvl)
|
||||||
|
} else {
|
||||||
|
df <- df %>% arrange(Item)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# add cumulative values
|
||||||
|
df$Cum <- cumsum(df$Count)
|
||||||
|
df$CumTot <- (df$Cum / sum(df$Count, na.rm = TRUE)) %>% percent(force_zero = TRUE)
|
||||||
|
df$Cum <- df$Cum %>% format()
|
||||||
|
|
||||||
|
if (any(class(x) == 'factor')) {
|
||||||
|
# put factor last
|
||||||
|
df <- df %>% select(Item, Count, Percent, Cum, CumTot, Fctlvl)
|
||||||
|
}
|
||||||
|
|
||||||
|
if (markdown == TRUE) {
|
||||||
|
tblformat <- 'markdown'
|
||||||
|
} else {
|
||||||
|
tblformat <- 'pandoc'
|
||||||
|
}
|
||||||
|
|
||||||
|
if (toConsole == FALSE) {
|
||||||
|
# assign to object
|
||||||
|
df[, 3] <- df[, 2] / sum(df[, 2], na.rm = TRUE)
|
||||||
|
df[, 4] <- cumsum(df[, 2])
|
||||||
|
df[, 5] <- df[, 4] / sum(df[, 2], na.rm = TRUE)
|
||||||
|
return(df)
|
||||||
|
|
||||||
|
} else {
|
||||||
|
|
||||||
|
# save old NA setting for kable
|
||||||
|
opt.old <- options()$knitr.kable.NA
|
||||||
|
options(knitr.kable.NA = "<NA>")
|
||||||
|
|
||||||
|
Count.rest <- sum(df[nmax.1:nrow(df), 'Count'], na.rm = TRUE)
|
||||||
|
if (any(class(x) %in% c('double', 'integer', 'numeric', 'raw', 'single'))) {
|
||||||
|
df <- df %>% mutate(Item = format(Item))
|
||||||
|
}
|
||||||
|
df <- df %>% mutate(Count = format(Count))
|
||||||
|
|
||||||
|
if (nrow(df) > nmax.1 & markdown == FALSE) {
|
||||||
|
df2 <- df[1:nmax,]
|
||||||
|
print(
|
||||||
|
knitr::kable(df2,
|
||||||
|
format = tblformat,
|
||||||
|
col.names = column_names,
|
||||||
|
align = column_align,
|
||||||
|
padding = 1)
|
||||||
|
)
|
||||||
|
cat('... and ',
|
||||||
|
format(nrow(df) - nmax),
|
||||||
|
' more ',
|
||||||
|
paste0('(n = ',
|
||||||
|
format(Count.rest),
|
||||||
|
'; ',
|
||||||
|
(Count.rest / length(x)) %>% percent(force_zero = TRUE),
|
||||||
|
')'),
|
||||||
|
'. Use `nmax` to show more rows.\n\n', sep = '')
|
||||||
|
|
||||||
|
} else {
|
||||||
|
print(
|
||||||
|
knitr::kable(df,
|
||||||
|
format = tblformat,
|
||||||
|
col.names = column_names,
|
||||||
|
align = column_align,
|
||||||
|
padding = 1)
|
||||||
|
)
|
||||||
|
}
|
||||||
|
cat('\n')
|
||||||
|
|
||||||
|
# reset old kable setting
|
||||||
|
options(knitr.kable.NA = opt.old)
|
||||||
|
return(invisible())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname freq
|
||||||
|
#' @export
|
||||||
|
frequency_tbl <- freq
|
||||||
13
R/globals.R
13
R/globals.R
@ -16,16 +16,20 @@
|
|||||||
# GNU General Public License for more details. #
|
# GNU General Public License for more details. #
|
||||||
# ==================================================================== #
|
# ==================================================================== #
|
||||||
|
|
||||||
globalVariables(c('.',
|
globalVariables(c('abname',
|
||||||
'abname',
|
|
||||||
'bactid',
|
'bactid',
|
||||||
'cnt',
|
'cnt',
|
||||||
|
'Count',
|
||||||
|
'Cum',
|
||||||
|
'CumTot',
|
||||||
'date_lab',
|
'date_lab',
|
||||||
'days_diff',
|
'days_diff',
|
||||||
|
'Fctlvl',
|
||||||
'first_isolate_row_index',
|
'first_isolate_row_index',
|
||||||
'fullname',
|
'fullname',
|
||||||
'genus',
|
'genus',
|
||||||
'gramstain',
|
'gramstain',
|
||||||
|
'Item',
|
||||||
'key_ab',
|
'key_ab',
|
||||||
'key_ab_lag',
|
'key_ab_lag',
|
||||||
'key_ab_other',
|
'key_ab_other',
|
||||||
@ -34,6 +38,9 @@ globalVariables(c('.',
|
|||||||
'n',
|
'n',
|
||||||
'other_pat_or_mo',
|
'other_pat_or_mo',
|
||||||
'patient_id',
|
'patient_id',
|
||||||
|
'Percent',
|
||||||
|
'quantile',
|
||||||
'real_first_isolate',
|
'real_first_isolate',
|
||||||
'species',
|
'species',
|
||||||
'y'))
|
'y',
|
||||||
|
'.'))
|
||||||
|
|||||||
203
R/mdro.R
Normal file
203
R/mdro.R
Normal file
@ -0,0 +1,203 @@
|
|||||||
|
# ==================================================================== #
|
||||||
|
# TITLE #
|
||||||
|
# Antimicrobial Resistance (AMR) Analysis #
|
||||||
|
# #
|
||||||
|
# AUTHORS #
|
||||||
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||||
|
# #
|
||||||
|
# LICENCE #
|
||||||
|
# This program is free software; you can redistribute it and/or modify #
|
||||||
|
# it under the terms of the GNU General Public License version 2.0, #
|
||||||
|
# as published by the Free Software Foundation. #
|
||||||
|
# #
|
||||||
|
# This program is distributed in the hope that it will be useful, #
|
||||||
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||||
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||||
|
# GNU General Public License for more details. #
|
||||||
|
# ==================================================================== #
|
||||||
|
|
||||||
|
#' Determine multidrug-resistant organisms (MDRO)
|
||||||
|
#'
|
||||||
|
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
|
||||||
|
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
|
||||||
|
#' @param country country to determine guidelines. Should be a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).
|
||||||
|
#' @param col_bactid column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$bactid}, see \code{\link{microorganisms}}
|
||||||
|
#' @param info print progress
|
||||||
|
#' @param aminoglycosides,quinolones,carbapenems character vector with column names of antibiotics
|
||||||
|
#' @param ceftazidime,piperacillin,trimethoprim_sulfa,penicillin,vancomycin column names of antibiotics
|
||||||
|
#' @param ... parameters that are passed on to \code{MDR}
|
||||||
|
#' @return Ordered factor with values \code{Positive}, \code{Unconfirmed}, \code{Negative}.
|
||||||
|
#' @rdname MDRO
|
||||||
|
#' @export
|
||||||
|
MDRO <- function(tbl,
|
||||||
|
country,
|
||||||
|
col_bactid = 'bactid',
|
||||||
|
info = TRUE,
|
||||||
|
aminoglycosides = c('gent', 'tobr', 'kana'),
|
||||||
|
quinolones = c('cipr', 'norf'),
|
||||||
|
carbapenems = c('imip', 'mero', 'erta'),
|
||||||
|
ceftazidime = 'cfta',
|
||||||
|
piperacillin = 'pita',
|
||||||
|
trimethoprim_sulfa = 'trsu',
|
||||||
|
penicillin = 'peni',
|
||||||
|
vancomycin = 'vanc') {
|
||||||
|
|
||||||
|
# strip whitespaces
|
||||||
|
country <- trimws(country)
|
||||||
|
if (length(country) > 1) {
|
||||||
|
stop('`country` must be a length one character string.', call. = FALSE)
|
||||||
|
}
|
||||||
|
if (!country %like% '^[a-z]{2}$') {
|
||||||
|
stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?MDRO.', call. = FALSE)
|
||||||
|
}
|
||||||
|
|
||||||
|
# create list and make country code case-independent
|
||||||
|
guideline <- list(country = list(code = tolower(country)))
|
||||||
|
|
||||||
|
# support per country
|
||||||
|
if (guideline$country$code == 'de') {
|
||||||
|
guideline$country$name <- 'Germany'
|
||||||
|
guideline$name <- ''
|
||||||
|
guideline$version <- ''
|
||||||
|
guideline$source <- ''
|
||||||
|
} else if (guideline$country$code == 'nl') {
|
||||||
|
guideline$country$name <- 'The Netherlands'
|
||||||
|
guideline$name <- 'WIP-Richtlijn BRMO'
|
||||||
|
guideline$version <- 'Revision of December 2017'
|
||||||
|
guideline$source <- 'https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'
|
||||||
|
# add here more countries like this:
|
||||||
|
# } else if (country$code == 'AA') {
|
||||||
|
# country$name <- 'country name'
|
||||||
|
} else {
|
||||||
|
stop('This country code is currently unsupported: ', guideline$country$code, call. = FALSE)
|
||||||
|
}
|
||||||
|
|
||||||
|
# Console colours
|
||||||
|
# source: http://www.tldp.org/HOWTO/Bash-Prompt-HOWTO/x329.html
|
||||||
|
ANSI_red <- "\033[31m"
|
||||||
|
ANSI_blue <- "\033[34m"
|
||||||
|
ANSI_reset <- "\033[0m"
|
||||||
|
|
||||||
|
if (info == TRUE) {
|
||||||
|
cat("Determining Highly Resistant Microorganisms (MDRO), according to:\n",
|
||||||
|
"Guideline: ", ANSI_red, guideline$name, ", ", guideline$version, ANSI_reset, "\n",
|
||||||
|
"Country : ", ANSI_red, guideline$country$name, ANSI_reset, "\n",
|
||||||
|
"Source : ", ANSI_blue, guideline$source, ANSI_reset, "\n",
|
||||||
|
"\n", sep = "")
|
||||||
|
}
|
||||||
|
|
||||||
|
# join microorganisms
|
||||||
|
tbl <- tbl %>% left_join_microorganisms(col_bactid)
|
||||||
|
|
||||||
|
tbl$MDRO <- 1
|
||||||
|
|
||||||
|
if (guideline$country$code == 'nl') {
|
||||||
|
# BRMO; Bijzonder Resistente Micro-Organismen
|
||||||
|
aminoglycosides <- aminoglycosides[aminoglycosides %in% colnames(tbl)]
|
||||||
|
quinolones <- quinolones[quinolones %in% colnames(tbl)]
|
||||||
|
carbapenems <- carbapenems[carbapenems %in% colnames(tbl)]
|
||||||
|
if (!ceftazidime %in% colnames(tbl)) { ceftazidime <- NA }
|
||||||
|
if (!piperacillin %in% colnames(tbl)) { piperacillin <- NA }
|
||||||
|
if (!trimethoprim_sulfa %in% colnames(tbl)) { trimethoprim_sulfa <- NA }
|
||||||
|
if (!penicillin %in% colnames(tbl)) { penicillin <- NA }
|
||||||
|
if (!vancomycin %in% colnames(tbl)) { vancomycin <- NA }
|
||||||
|
|
||||||
|
# Table 1
|
||||||
|
tbl[which(
|
||||||
|
tbl$family == 'Enterobacteriaceae'
|
||||||
|
& rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
|
||||||
|
& rowSums(tbl[, quinolones] == 'R', na.rm = TRUE) >= 1
|
||||||
|
), 'MDRO'] <- 4
|
||||||
|
tbl[which(
|
||||||
|
tbl$family == 'Enterobacteriaceae'
|
||||||
|
& rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
|
||||||
|
), 'MDRO'] <- 3
|
||||||
|
# rest is negative
|
||||||
|
tbl[which(
|
||||||
|
tbl$family == 'Enterobacteriaceae'
|
||||||
|
& tbl$MDRO == 1
|
||||||
|
), 'MDRO'] <- 2
|
||||||
|
|
||||||
|
# Table 2
|
||||||
|
tbl[which(
|
||||||
|
tbl$genus == 'Acinetobacter'
|
||||||
|
& rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
|
||||||
|
), 'MDRO'] <- 3
|
||||||
|
tbl[which(
|
||||||
|
tbl$genus == 'Acinetobacter'
|
||||||
|
& rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
|
||||||
|
& rowSums(tbl[, quinolones] == 'R', na.rm = TRUE) >= 1
|
||||||
|
), 'MDRO'] <- 4
|
||||||
|
# rest of Acinetobacter is negative
|
||||||
|
tbl[which(
|
||||||
|
tbl$genus == 'Acinetobacter'
|
||||||
|
& tbl$MDRO == 1
|
||||||
|
), 'MDRO'] <- 2
|
||||||
|
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Stenotrophomonas maltophilia'
|
||||||
|
& tbl[, trimethoprim_sulfa] == 'R'
|
||||||
|
), 'MDRO'] <- 4
|
||||||
|
# rest of Stenotrophomonas is negative
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Stenotrophomonas maltophilia'
|
||||||
|
& tbl$MDRO == 1
|
||||||
|
), 'MDRO'] <- 2
|
||||||
|
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Pseudomonas aeruginosa'
|
||||||
|
& sum(rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1,
|
||||||
|
rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1,
|
||||||
|
rowSums(tbl[, quinolones] == 'R', na.rm = TRUE) >= 1,
|
||||||
|
tbl[, ceftazidime] == 'R',
|
||||||
|
tbl[, piperacillin] == 'R') >= 3
|
||||||
|
), 'MDRO'] <- 4
|
||||||
|
# rest of Pseudomonas is negative
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Pseudomonas aeruginosa'
|
||||||
|
& tbl$MDRO == 1
|
||||||
|
), 'MDRO'] <- 2
|
||||||
|
|
||||||
|
# Table 3
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Streptococcus pneumoniae'
|
||||||
|
& tbl[, penicillin] == 'R'
|
||||||
|
), 'MDRO'] <- 4
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Streptococcus pneumoniae'
|
||||||
|
& tbl[, vancomycin] == 'R'
|
||||||
|
), 'MDRO'] <- 4
|
||||||
|
# rest of Streptococcus pneumoniae is negative
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Streptococcus pneumoniae'
|
||||||
|
& tbl$MDRO == 1
|
||||||
|
), 'MDRO'] <- 2
|
||||||
|
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Enterococcus faecium'
|
||||||
|
& rowSums(tbl[, c(penicillin, vancomycin)] == 'R', na.rm = TRUE) >= 1
|
||||||
|
), 'MDRO'] <- 4
|
||||||
|
# rest of Enterococcus faecium is negative
|
||||||
|
tbl[which(
|
||||||
|
tbl$fullname %like% 'Enterococcus faecium'
|
||||||
|
& tbl$MDRO == 1
|
||||||
|
), 'MDRO'] <- 2
|
||||||
|
}
|
||||||
|
|
||||||
|
factor(x = tbl$MDRO,
|
||||||
|
levels = c(1:4),
|
||||||
|
labels = c('Unknown', 'Negative', 'Unconfirmed', 'Positive'),
|
||||||
|
ordered = TRUE)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname MDRO
|
||||||
|
#' @export
|
||||||
|
BRMO <- function(tbl, country = "nl", ...) {
|
||||||
|
MDRO(tbl = tbl, country = country, ...)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname MDRO
|
||||||
|
#' @export
|
||||||
|
MRGN <- function(tbl, country = "de", ...) {
|
||||||
|
MDRO(tbl = tbl, country = country, ...)
|
||||||
|
}
|
||||||
98
R/misc.R
98
R/misc.R
@ -16,18 +16,98 @@
|
|||||||
# GNU General Public License for more details. #
|
# GNU General Public License for more details. #
|
||||||
# ==================================================================== #
|
# ==================================================================== #
|
||||||
|
|
||||||
# No export, no Rd
|
#' Pattern Matching
|
||||||
"%like%" <- function(vector, pattern) {
|
#'
|
||||||
# Source: https://github.com/Rdatatable/data.table/blob/master/R/like.R
|
#' Convenience function to compare a vector with a pattern, like \code{\link[base]{grep}}. It always returns a \code{logical} vector and is always case-insensitive.
|
||||||
# But made it case insensitive
|
#' @inheritParams base::grep
|
||||||
if (is.factor(vector)) {
|
#' @return A \code{logical} vector
|
||||||
as.integer(vector) %in% grep(pattern, levels(vector), ignore.case = TRUE)
|
#' @name like
|
||||||
|
#' @rdname like
|
||||||
|
#' @export
|
||||||
|
#' @source Inherited from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default.
|
||||||
|
#' @examples
|
||||||
|
#' library(dplyr)
|
||||||
|
#' # get unique occurences of bacteria whose name start with 'Ent'
|
||||||
|
#' septic_patients %>%
|
||||||
|
#' left_join_microorganisms() %>%
|
||||||
|
#' filter(fullname %like% '^Ent') %>%
|
||||||
|
#' pull(fullname) %>%
|
||||||
|
#' unique()
|
||||||
|
"%like%" <- function(x, pattern) {
|
||||||
|
if (length(pattern) > 1) {
|
||||||
|
pattern <- pattern[1]
|
||||||
|
warning('only the first element of argument `pattern` used for `%like%`', call. = FALSE)
|
||||||
|
}
|
||||||
|
if (is.factor(x)) {
|
||||||
|
as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE)
|
||||||
} else {
|
} else {
|
||||||
grepl(pattern, vector, ignore.case = TRUE)
|
base::grepl(pattern, x, ignore.case = TRUE)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
# No export, no Rd
|
# No export, no Rd
|
||||||
percent <- function(x, round = 1, ...) {
|
percent <- function(x, round = 1, force_zero = FALSE, ...) {
|
||||||
base::paste0(base::round(x * 100, digits = round), "%")
|
val <- base::round(x * 100, digits = round)
|
||||||
|
if (force_zero & any(val == as.integer(val))) {
|
||||||
|
val[val == as.integer(val)] <- paste0(val[val == as.integer(val)], ".", base::strrep(0, round))
|
||||||
|
}
|
||||||
|
base::paste0(val, "%")
|
||||||
|
}
|
||||||
|
|
||||||
|
check_available_columns <- function(tbl, col.list, info = TRUE) {
|
||||||
|
# check columns
|
||||||
|
col.list <- col.list[!is.na(col.list)]
|
||||||
|
names(col.list) <- col.list
|
||||||
|
col.list.bak <- col.list
|
||||||
|
# are they available as upper case or lower case then?
|
||||||
|
for (i in 1:length(col.list)) {
|
||||||
|
if (toupper(col.list[i]) %in% colnames(tbl)) {
|
||||||
|
col.list[i] <- toupper(col.list[i])
|
||||||
|
} else if (tolower(col.list[i]) %in% colnames(tbl)) {
|
||||||
|
col.list[i] <- tolower(col.list[i])
|
||||||
|
} else if (!col.list[i] %in% colnames(tbl)) {
|
||||||
|
col.list[i] <- NA
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (!all(col.list %in% colnames(tbl))) {
|
||||||
|
if (info == TRUE) {
|
||||||
|
warning('These columns do not exist and will be ignored: ',
|
||||||
|
col.list.bak[!(col.list %in% colnames(tbl))] %>% toString(),
|
||||||
|
immediate. = TRUE,
|
||||||
|
call. = FALSE)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
col.list
|
||||||
|
}
|
||||||
|
|
||||||
|
# Coefficient of variation (CV)
|
||||||
|
cv <- function(x, na.rm = TRUE) {
|
||||||
|
cv.x <- sd(x, na.rm = na.rm) / abs(mean(x, na.rm = na.rm))
|
||||||
|
cv.x
|
||||||
|
}
|
||||||
|
|
||||||
|
# Coefficient of dispersion, or coefficient of quartile variation (CQV).
|
||||||
|
# (Bonett et al., 2006: Confidence interval for a coefficient of quartile variation).
|
||||||
|
cqv <- function(x, na.rm = TRUE) {
|
||||||
|
cqv.x <-
|
||||||
|
(quantile(x, 0.75, na.rm = na.rm, type = 6) - quantile(x, 0.25, na.rm = na.rm, type = 6)) /
|
||||||
|
(quantile(x, 0.75, na.rm = na.rm, type = 6) + quantile(x, 0.25, na.rm = na.rm, type = 6))
|
||||||
|
unname(cqv.x)
|
||||||
|
}
|
||||||
|
|
||||||
|
# show bytes as kB/MB/GB
|
||||||
|
# size_humanreadable(123456) # 121 kB
|
||||||
|
# size_humanreadable(12345678) # 11.8 MB
|
||||||
|
size_humanreadable <- function(bytes, decimals = 1) {
|
||||||
|
bytes <- bytes %>% as.double()
|
||||||
|
# Adapted from:
|
||||||
|
# http://jeffreysambells.com/2012/10/25/human-readable-filesize-php
|
||||||
|
size <- c('B','kB','MB','GB','TB','PB','EB','ZB','YB')
|
||||||
|
factor <- floor((nchar(bytes) - 1) / 3)
|
||||||
|
# added slight improvement; no decimals for B and kB:
|
||||||
|
decimals <- rep(decimals, length(bytes))
|
||||||
|
decimals[size[factor + 1] %in% c('B', 'kB')] <- 0
|
||||||
|
|
||||||
|
out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1])
|
||||||
|
out
|
||||||
}
|
}
|
||||||
|
|||||||
349
R/print.R
Normal file
349
R/print.R
Normal file
@ -0,0 +1,349 @@
|
|||||||
|
# ==================================================================== #
|
||||||
|
# TITLE #
|
||||||
|
# Antimicrobial Resistance (AMR) Analysis #
|
||||||
|
# #
|
||||||
|
# AUTHORS #
|
||||||
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||||
|
# #
|
||||||
|
# LICENCE #
|
||||||
|
# This program is free software; you can redistribute it and/or modify #
|
||||||
|
# it under the terms of the GNU General Public License version 2.0, #
|
||||||
|
# as published by the Free Software Foundation. #
|
||||||
|
# #
|
||||||
|
# This program is distributed in the hope that it will be useful, #
|
||||||
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||||
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||||
|
# GNU General Public License for more details. #
|
||||||
|
# ==================================================================== #
|
||||||
|
|
||||||
|
#' Printing Data Tables and Tibbles
|
||||||
|
#'
|
||||||
|
#' Print a data table or tibble. It prints: \cr- The \strong{first and last rows} like \code{data.table}s are printed by the \code{data.table} package,\cr- A \strong{header} and \strong{left aligned text} like \code{tibble}s are printed by the \code{tibble} package with info about grouped variables,\cr- \strong{Unchanged values} and \strong{support for row names} like \code{data.frame}s are printed by the \code{base} package.
|
||||||
|
#' @inheritParams base::print.data.frame
|
||||||
|
#' @param nmax amount of rows to print in total. When the total amount of rows exceeds this limit, the first and last \code{nmax / 2} rows will be printed. Use \code{nmax = NA} to print all rows.
|
||||||
|
#' @param header print header with information about data size and tibble grouping
|
||||||
|
#' @param print.keys print keys for \code{data.table}
|
||||||
|
#' @param na value to print instead of NA
|
||||||
|
#' @param width amount of white spaces to keep between columns, must be at least 1
|
||||||
|
#' @rdname print
|
||||||
|
#' @name print
|
||||||
|
#' @importFrom dplyr %>% n_groups group_vars group_size filter pull select
|
||||||
|
#' @exportMethod print.tbl_df
|
||||||
|
#' @export
|
||||||
|
#' @examples
|
||||||
|
#' # still showing all values unchanged:
|
||||||
|
#' library(dplyr)
|
||||||
|
#' starwars
|
||||||
|
#' print(starwars, width = 3)
|
||||||
|
#'
|
||||||
|
#' # compare the significance notation of this
|
||||||
|
#' starwars %>% select(birth_year)
|
||||||
|
#' # with this
|
||||||
|
#' tibble:::print.tbl_df(starwars %>% select(birth_year))
|
||||||
|
#'
|
||||||
|
#' # supports info about groups (look at header)
|
||||||
|
#' starwars %>% group_by(homeworld, gender)
|
||||||
|
print.tbl_df <- function(x,
|
||||||
|
nmax = 10,
|
||||||
|
header = TRUE,
|
||||||
|
row.names = TRUE,
|
||||||
|
right = FALSE,
|
||||||
|
width = 1,
|
||||||
|
na = "<NA>",
|
||||||
|
...) {
|
||||||
|
prettyprint_df(x = x,
|
||||||
|
nmax = nmax,
|
||||||
|
header = header,
|
||||||
|
row.names = row.names,
|
||||||
|
print.keys = FALSE,
|
||||||
|
right = right,
|
||||||
|
width = width,
|
||||||
|
na = na,
|
||||||
|
...)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname print
|
||||||
|
#' @exportMethod print.tbl
|
||||||
|
#' @export
|
||||||
|
print.tbl <- function(x, ...) {
|
||||||
|
prettyprint_df(x, ...)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @rdname print
|
||||||
|
#' @exportMethod print.data.table
|
||||||
|
#' @export
|
||||||
|
print.data.table <- function(x,
|
||||||
|
nmax = 10,
|
||||||
|
header = TRUE,
|
||||||
|
row.names = TRUE,
|
||||||
|
print.keys = FALSE,
|
||||||
|
right = FALSE,
|
||||||
|
width = 1,
|
||||||
|
na = "<NA>",
|
||||||
|
...) {
|
||||||
|
prettyprint_df(x = x,
|
||||||
|
nmax = nmax,
|
||||||
|
header = header,
|
||||||
|
row.names = row.names,
|
||||||
|
print.keys = print.keys,
|
||||||
|
right = right,
|
||||||
|
width = width,
|
||||||
|
na = na,
|
||||||
|
...)
|
||||||
|
}
|
||||||
|
|
||||||
|
printDT <- data.table:::print.data.table
|
||||||
|
prettyprint_df <- function(x,
|
||||||
|
nmax = 10,
|
||||||
|
header = TRUE,
|
||||||
|
row.names = TRUE,
|
||||||
|
print.keys = FALSE,
|
||||||
|
right = FALSE,
|
||||||
|
width = 1,
|
||||||
|
na = "<NA>",
|
||||||
|
...) {
|
||||||
|
|
||||||
|
ansi_reset <- "\u001B[0m"
|
||||||
|
ansi_black <- "\u001B[30m"
|
||||||
|
ansi_red <- "\u001B[31m"
|
||||||
|
ansi_green <- "\u001B[32m"
|
||||||
|
ansi_yellow <- "\u001B[33m"
|
||||||
|
ansi_blue <- "\u001B[34m"
|
||||||
|
ansi_purple <- "\u001B[35m"
|
||||||
|
ansi_cyan <- "\u001B[36m"
|
||||||
|
ansi_white <- "\u001B[37m"
|
||||||
|
ansi_gray <- "\u001B[38;5;246m"
|
||||||
|
|
||||||
|
if (width < 1) {
|
||||||
|
stop('`width` must be at least 1.', call. = FALSE)
|
||||||
|
}
|
||||||
|
|
||||||
|
if (is.na(nmax)) {
|
||||||
|
nmax <- NROW(x)
|
||||||
|
}
|
||||||
|
n <- nmax
|
||||||
|
if (n %% 2 == 1) {
|
||||||
|
# odd number; add 1
|
||||||
|
n <- n + 1
|
||||||
|
}
|
||||||
|
|
||||||
|
width <- width - 1
|
||||||
|
|
||||||
|
if ('tbl_df' %in% class(x)) {
|
||||||
|
type <- 'tibble'
|
||||||
|
} else if ('data.table' %in% class(x)) {
|
||||||
|
type <- 'data.table'
|
||||||
|
} else {
|
||||||
|
type <- 'data.frame'
|
||||||
|
}
|
||||||
|
|
||||||
|
if (header == TRUE) {
|
||||||
|
if (NCOL(x) == 1) {
|
||||||
|
vars <- 'variable'
|
||||||
|
} else {
|
||||||
|
vars <- 'variables'
|
||||||
|
}
|
||||||
|
|
||||||
|
size <- object.size(x) %>% as.double() %>% size_humanreadable()
|
||||||
|
|
||||||
|
cat(paste0("A ", type,": ",
|
||||||
|
format(NROW(x)),
|
||||||
|
" obs. of ",
|
||||||
|
format(NCOL(x)),
|
||||||
|
" ", vars,
|
||||||
|
ansi_gray, " (", size, ")\n", ansi_reset))
|
||||||
|
if ('grouped_df' %in% class(x) & n_groups(x) > 0) {
|
||||||
|
cat(paste0("Grouped by ",
|
||||||
|
x %>% group_vars() %>% paste0(ansi_red, ., ansi_reset) %>% paste0(collapse = " and "),
|
||||||
|
ansi_gray,
|
||||||
|
" (",
|
||||||
|
x %>% n_groups(),
|
||||||
|
" groups with sizes between ",
|
||||||
|
x %>% group_size() %>% min(),
|
||||||
|
" and ",
|
||||||
|
x %>% group_size() %>% max(),
|
||||||
|
")\n",
|
||||||
|
ansi_reset))
|
||||||
|
}
|
||||||
|
if (!is.null(attributes(x)$qry)) {
|
||||||
|
cat(paste0(ansi_gray, "This data contains a query. Use qry() to view it.\n", ansi_reset))
|
||||||
|
}
|
||||||
|
cat("\n")
|
||||||
|
}
|
||||||
|
|
||||||
|
# data.table where keys should be printed
|
||||||
|
if (print.keys == TRUE) {
|
||||||
|
printDT(x,
|
||||||
|
class = header,
|
||||||
|
row.names = row.names,
|
||||||
|
print.keys = TRUE,
|
||||||
|
right = right,
|
||||||
|
...
|
||||||
|
)
|
||||||
|
return(invisible())
|
||||||
|
}
|
||||||
|
|
||||||
|
# tibbles give warning when setting column names
|
||||||
|
x <- x %>% base::as.data.frame(stringsAsFactors = FALSE)
|
||||||
|
|
||||||
|
# extra space of 3 chars, right to row name or number
|
||||||
|
if (NROW(x) > 0) {
|
||||||
|
maxrowchars <- rownames(x) %>% nchar() %>% max() + 3
|
||||||
|
rownames(x) <- paste0(rownames(x), strrep(" ", maxrowchars - nchar(rownames(x))))
|
||||||
|
} else {
|
||||||
|
maxrowchars <- 0
|
||||||
|
}
|
||||||
|
|
||||||
|
x.bak <- x
|
||||||
|
|
||||||
|
if (n + 1 < nrow(x)) {
|
||||||
|
# remove in between part, 1 extra for ~~~~ between first and last part
|
||||||
|
rows_list <- c(1:(n / 2 + 1), (nrow(x) - (n / 2) + 1):nrow(x))
|
||||||
|
x <- x %>% filter(row_number() %in% rows_list)
|
||||||
|
rownames(x) <- rownames(x.bak)[rows_list]
|
||||||
|
# set inbetweener between parts
|
||||||
|
rownames(x)[n / 2 + 1] <- strrep("~", maxrowchars)
|
||||||
|
}
|
||||||
|
|
||||||
|
if (header == TRUE) {
|
||||||
|
# add 1 row for classes
|
||||||
|
# class will be marked up per column
|
||||||
|
if (NROW(x.bak) > 0) {
|
||||||
|
rownames.x <- rownames(x)
|
||||||
|
x <- x %>% filter(row_number() == 1) %>% rbind(x, stringsAsFactors = FALSE)
|
||||||
|
rownames(x) <- c('*', rownames.x)
|
||||||
|
}
|
||||||
|
|
||||||
|
# select 1st class per column and abbreviate
|
||||||
|
classes <- x.bak %>%
|
||||||
|
sapply(class) %>%
|
||||||
|
lapply(
|
||||||
|
function(c) {
|
||||||
|
# do print all POSIX classes like "POSct/t"
|
||||||
|
if ('POSIXct' %in% c) {
|
||||||
|
paste0('POS',
|
||||||
|
c %>%
|
||||||
|
gsub('POSIX', '', .) %>%
|
||||||
|
paste0(collapse = '/'))
|
||||||
|
} else {
|
||||||
|
c[[1]]
|
||||||
|
}
|
||||||
|
}) %>%
|
||||||
|
unlist() %>%
|
||||||
|
gsub("character", "chr", ., fixed = TRUE) %>%
|
||||||
|
gsub("complex", "cplx", ., fixed = TRUE) %>%
|
||||||
|
gsub("Date", "Date", ., fixed = TRUE) %>%
|
||||||
|
gsub("double", "dbl", ., fixed = TRUE) %>%
|
||||||
|
gsub("expression", "expr", ., fixed = TRUE) %>%
|
||||||
|
gsub("factor", "fct", ., fixed = TRUE) %>%
|
||||||
|
gsub("IDate", "IDat", ., fixed = TRUE) %>%
|
||||||
|
gsub("integer", "int", ., fixed = TRUE) %>%
|
||||||
|
gsub("integer64", "i64", ., fixed = TRUE) %>%
|
||||||
|
gsub("list", "list", ., fixed = TRUE) %>%
|
||||||
|
gsub("logical", "lgl", ., fixed = TRUE) %>%
|
||||||
|
gsub("numeric", "dbl", ., fixed = TRUE) %>%
|
||||||
|
gsub("ordered", "ord", ., fixed = TRUE) %>%
|
||||||
|
gsub("percent", "pct", ., fixed = TRUE) %>%
|
||||||
|
gsub("single", "sgl", ., fixed = TRUE) %>%
|
||||||
|
paste0("<", ., ">")
|
||||||
|
}
|
||||||
|
|
||||||
|
# markup cols
|
||||||
|
for (i in 1:ncol(x)) {
|
||||||
|
if (all(!class(x[, i]) %in% class(x.bak[, i]))) {
|
||||||
|
class(x[, i]) <- class(x.bak[, i])
|
||||||
|
}
|
||||||
|
try(x[, i] <- format(x %>% pull(i)), silent = TRUE)
|
||||||
|
|
||||||
|
# replace NAs
|
||||||
|
if (nchar(na) < 2) {
|
||||||
|
# make as long as the text "NA"
|
||||||
|
na <- paste0(na, strrep(" ", 2 - nchar(na)))
|
||||||
|
}
|
||||||
|
try(x[, i] <- gsub("^NA$", na, trimws(x[, i], 'both')), silent = TRUE)
|
||||||
|
# place class into 1st row
|
||||||
|
if (header == TRUE) {
|
||||||
|
x[1, i] <- classes[i]
|
||||||
|
}
|
||||||
|
# dashes between two parts when exceeding nmax
|
||||||
|
maxvalchars <- max(colnames(x)[i] %>% nchar(), x[, i] %>% nchar() %>% max())
|
||||||
|
if (n + 1 < nrow(x.bak)) {
|
||||||
|
x[n / 2 + if_else(header == TRUE, 2, 1), i] <- strrep("~", maxvalchars)
|
||||||
|
}
|
||||||
|
|
||||||
|
# align according to `right` parameter, but only factors and text, but not MICs
|
||||||
|
if (any(x.bak %>% pull(i) %>% class() %in% c('factor', 'character'))
|
||||||
|
& !("mic" %in% (x.bak %>% pull(i) %>% class()))) {
|
||||||
|
vals <- x %>% pull(i) %>% trimws('both')
|
||||||
|
colname <- colnames(x)[i] %>% trimws('both')
|
||||||
|
if (right == FALSE) {
|
||||||
|
vals <- paste0(vals, strrep(" ", maxvalchars - nchar(vals)))
|
||||||
|
colname <- paste0(colname, strrep(" ", maxvalchars - nchar(colname)))
|
||||||
|
} else {
|
||||||
|
vals <- paste0(strrep(" ", maxvalchars - nchar(vals)), vals)
|
||||||
|
colname <- paste0(strrep(" ", maxvalchars - nchar(colname)), colname)
|
||||||
|
}
|
||||||
|
x[, i] <- vals
|
||||||
|
colnames(x)[i] <- colname
|
||||||
|
}
|
||||||
|
|
||||||
|
# add left padding according to `width` parameter
|
||||||
|
# but not in 1st col when row names are off
|
||||||
|
if (row.names == TRUE | i > 1) {
|
||||||
|
x[, i] <- paste0(strrep(" ", width), x[, i])
|
||||||
|
colnames(x)[i] <- paste0(strrep(" ", width), colnames(x)[i])
|
||||||
|
}
|
||||||
|
|
||||||
|
# strip columns that do not fit (3 chars as margin)
|
||||||
|
width_console <- options()$width
|
||||||
|
width_until_col <- x %>%
|
||||||
|
select(1:i) %>%
|
||||||
|
apply(1, paste, collapse = strrep(" ", width + 1)) %>%
|
||||||
|
nchar() %>%
|
||||||
|
max()
|
||||||
|
width_until_col_before <- x %>%
|
||||||
|
select(1:(max(i, 2) - 1)) %>%
|
||||||
|
apply(1, paste, collapse = strrep(" ", width + 1)) %>%
|
||||||
|
nchar() %>%
|
||||||
|
max()
|
||||||
|
extraspace <- maxrowchars + nchar(rownames(x)[length(rownames(x))])
|
||||||
|
width_until_colnames <- colnames(x)[1:i] %>% paste0(collapse = strrep(" ", width + 1)) %>% nchar() + extraspace
|
||||||
|
width_until_colnames_before <- colnames(x)[1:(max(i, 2) - 1)] %>% paste0(collapse = strrep(" ", width + 1)) %>% nchar() + extraspace
|
||||||
|
|
||||||
|
if (i > 1 &
|
||||||
|
(width_until_col > width_console
|
||||||
|
| width_until_colnames > width_console)) {
|
||||||
|
if (width_until_col_before > width_console
|
||||||
|
| width_until_colnames_before > width_console) {
|
||||||
|
x <- x[, 1:(i - 2)]
|
||||||
|
} else {
|
||||||
|
x <- x[, 1:(i - 1)]
|
||||||
|
}
|
||||||
|
break
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# empty table, row name of header should be "*"
|
||||||
|
if (NROW(x.bak) == 0) {
|
||||||
|
rownames(x) <- '* '
|
||||||
|
}
|
||||||
|
|
||||||
|
# and here it is...
|
||||||
|
suppressWarnings(
|
||||||
|
base::print.data.frame(x, row.names = row.names, ...)
|
||||||
|
)
|
||||||
|
|
||||||
|
# print rest of col names when they were stripped
|
||||||
|
if (ncol(x) < ncol(x.bak)) {
|
||||||
|
x.notshown <- x.bak %>% select((ncol(x) + 1):ncol(x.bak))
|
||||||
|
if (ncol(x.notshown) == 1) {
|
||||||
|
cat('...and 1 more column: ')
|
||||||
|
} else {
|
||||||
|
cat('...and', ncol(x.notshown), 'more columns: ')
|
||||||
|
}
|
||||||
|
cat(x.notshown %>%
|
||||||
|
colnames() %>%
|
||||||
|
paste0(' ', ansi_gray, classes[(ncol(x) + 1):ncol(x.bak)], ansi_reset) %>%
|
||||||
|
paste0(collapse = ", "), '\n')
|
||||||
|
}
|
||||||
|
}
|
||||||
98
README.md
98
README.md
@ -90,6 +90,104 @@ after
|
|||||||
# 5 PSEAER R R - - R
|
# 5 PSEAER R R - - R
|
||||||
```
|
```
|
||||||
|
|
||||||
|
### Frequency tables
|
||||||
|
Base R lacks a simple function to create frequency tables. We created such a function that works with almost all data types: `freq()` (or `frequency_tbl()`).
|
||||||
|
```r
|
||||||
|
## Factors sort on item by default:
|
||||||
|
|
||||||
|
freq(septic_patients$hospital_id)
|
||||||
|
# Class: factor
|
||||||
|
# Length: 2000 (of which NA: 0 = 0.0%)
|
||||||
|
# Unique: 5
|
||||||
|
#
|
||||||
|
# Item Count Percent Cum. Count Cum. Percent (Factor Level)
|
||||||
|
# ----- ------ -------- ----------- ------------- ---------------
|
||||||
|
# A 233 11.7% 233 11.7% 1
|
||||||
|
# B 583 29.1% 816 40.8% 2
|
||||||
|
# C 221 11.1% 1037 51.8% 3
|
||||||
|
# D 650 32.5% 1687 84.4% 4
|
||||||
|
# E 313 15.7% 2000 100.0% 5
|
||||||
|
|
||||||
|
|
||||||
|
## This can be changed with the `sort.count` parameter:
|
||||||
|
|
||||||
|
freq(septic_patients$hospital_id, sort.count = TRUE)
|
||||||
|
# Class: factor
|
||||||
|
# Length: 2000 (of which NA: 0 = 0.0%)
|
||||||
|
# Unique: 5
|
||||||
|
#
|
||||||
|
# Item Count Percent Cum. Count Cum. Percent (Factor Level)
|
||||||
|
# ----- ------ -------- ----------- ------------- ---------------
|
||||||
|
# D 650 32.5% 650 32.5% 4
|
||||||
|
# B 583 29.1% 1233 61.7% 2
|
||||||
|
# E 313 15.7% 1546 77.3% 5
|
||||||
|
# A 233 11.7% 1779 88.9% 1
|
||||||
|
# C 221 11.1% 2000 100.0% 3
|
||||||
|
|
||||||
|
|
||||||
|
## Other types, like numbers or dates, sort on count by default:
|
||||||
|
|
||||||
|
> freq(septic_patients$date)
|
||||||
|
# Class: Date
|
||||||
|
# Length: 2000 (of which NA: 0 = 0.0%)
|
||||||
|
# Unique: 1662
|
||||||
|
#
|
||||||
|
# Oldest: 2 January 2001
|
||||||
|
# Newest: 18 October 2017 (+6133)
|
||||||
|
#
|
||||||
|
# Item Count Percent Cum. Count Cum. Percent
|
||||||
|
# ----------- ------ -------- ----------- -------------
|
||||||
|
# 2008-12-24 5 0.2% 5 0.2%
|
||||||
|
# 2010-12-10 4 0.2% 9 0.4%
|
||||||
|
# 2011-03-03 4 0.2% 13 0.6%
|
||||||
|
# 2013-06-24 4 0.2% 17 0.8%
|
||||||
|
# 2017-09-01 4 0.2% 21 1.1%
|
||||||
|
# 2002-09-02 3 0.2% 24 1.2%
|
||||||
|
# 2003-10-14 3 0.2% 27 1.4%
|
||||||
|
# 2004-06-25 3 0.2% 30 1.5%
|
||||||
|
# 2004-06-27 3 0.2% 33 1.7%
|
||||||
|
# 2004-10-29 3 0.2% 36 1.8%
|
||||||
|
# 2005-09-27 3 0.2% 39 2.0%
|
||||||
|
# 2006-08-01 3 0.2% 42 2.1%
|
||||||
|
# 2006-10-10 3 0.2% 45 2.2%
|
||||||
|
# 2007-11-16 3 0.2% 48 2.4%
|
||||||
|
# 2008-03-09 3 0.2% 51 2.5%
|
||||||
|
# ... and 1647 more (n = 1949; 97.5%). Use `nmax` to show more rows.
|
||||||
|
|
||||||
|
|
||||||
|
## For numeric values, some extra descriptive statistics will be calculated:
|
||||||
|
|
||||||
|
> freq(runif(n = 10, min = 1, max = 5))
|
||||||
|
# Class: numeric
|
||||||
|
# Length: 10 (of which NA: 0 = 0.0%)
|
||||||
|
# Unique: 10
|
||||||
|
#
|
||||||
|
# Mean: 3
|
||||||
|
# Std. dev.: 0.93 (CV: 0.31)
|
||||||
|
# Five-Num: 1.1 | 2.3 | 3.1 | 3.8 | 4.0 (CQV: 0.25)
|
||||||
|
# Outliers: 0
|
||||||
|
#
|
||||||
|
# Item Count Percent Cum. Count Cum. Percent
|
||||||
|
# --------- ------ -------- ----------- -------------
|
||||||
|
# 1.132033 1 10.0% 1 10.0%
|
||||||
|
# 2.226903 1 10.0% 2 20.0%
|
||||||
|
# 2.280779 1 10.0% 3 30.0%
|
||||||
|
# 2.640898 1 10.0% 4 40.0%
|
||||||
|
# 2.913462 1 10.0% 5 50.0%
|
||||||
|
# 3.364201 1 10.0% 6 60.0%
|
||||||
|
# 3.771975 1 10.0% 7 70.0%
|
||||||
|
# 3.802861 1 10.0% 8 80.0%
|
||||||
|
# 3.803547 1 10.0% 9 90.0%
|
||||||
|
# 3.985691 1 10.0% 10 100.0%
|
||||||
|
#
|
||||||
|
# Warning message:
|
||||||
|
# All observations are unique.
|
||||||
|
```
|
||||||
|
Learn more about this function with:
|
||||||
|
```r
|
||||||
|
?freq
|
||||||
|
```
|
||||||
|
|
||||||
### New classes
|
### New classes
|
||||||
This package contains two new S3 classes: `mic` for MIC values (e.g. from Vitek or Phoenix) and `rsi` for antimicrobial drug interpretations (i.e. S, I and R). Both are actually ordered factors under the hood (an MIC of `2` being higher than `<=1` but lower than `>=32`, and for class `rsi` factors are ordered as `S < I < R`).
|
This package contains two new S3 classes: `mic` for MIC values (e.g. from Vitek or Phoenix) and `rsi` for antimicrobial drug interpretations (i.e. S, I and R). Both are actually ordered factors under the hood (an MIC of `2` being higher than `<=1` but lower than `>=32`, and for class `rsi` factors are ordered as `S < I < R`).
|
||||||
Both classes have extensions for existing generic functions like `print`, `summary` and `plot`.
|
Both classes have extensions for existing generic functions like `print`, `summary` and `plot`.
|
||||||
|
|||||||
@ -1,5 +1,5 @@
|
|||||||
% Generated by roxygen2: do not edit by hand
|
% Generated by roxygen2: do not edit by hand
|
||||||
% Please edit documentation in R/EUCAST.R
|
% Please edit documentation in R/eucast.R
|
||||||
\name{EUCAST_rules}
|
\name{EUCAST_rules}
|
||||||
\alias{EUCAST_rules}
|
\alias{EUCAST_rules}
|
||||||
\alias{interpretive_reading}
|
\alias{interpretive_reading}
|
||||||
|
|||||||
39
man/MDRO.Rd
Normal file
39
man/MDRO.Rd
Normal file
@ -0,0 +1,39 @@
|
|||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/mdro.R
|
||||||
|
\name{MDRO}
|
||||||
|
\alias{MDRO}
|
||||||
|
\alias{BRMO}
|
||||||
|
\alias{MRGN}
|
||||||
|
\title{Determine multidrug-resistant organisms (MDRO)}
|
||||||
|
\usage{
|
||||||
|
MDRO(tbl, country, col_bactid = "bactid", info = TRUE,
|
||||||
|
aminoglycosides = c("gent", "tobr", "kana"), quinolones = c("cipr",
|
||||||
|
"norf"), carbapenems = c("imip", "mero", "erta"), ceftazidime = "cfta",
|
||||||
|
piperacillin = "pita", trimethoprim_sulfa = "trsu", penicillin = "peni",
|
||||||
|
vancomycin = "vanc")
|
||||||
|
|
||||||
|
BRMO(tbl, country = "nl", ...)
|
||||||
|
|
||||||
|
MRGN(tbl, country = "de", ...)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
|
||||||
|
|
||||||
|
\item{country}{country to determine guidelines. Should be a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
|
||||||
|
|
||||||
|
\item{col_bactid}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$bactid}, see \code{\link{microorganisms}}}
|
||||||
|
|
||||||
|
\item{info}{print progress}
|
||||||
|
|
||||||
|
\item{aminoglycosides, quinolones, carbapenems}{character vector with column names of antibiotics}
|
||||||
|
|
||||||
|
\item{ceftazidime, piperacillin, trimethoprim_sulfa, penicillin, vancomycin}{column names of antibiotics}
|
||||||
|
|
||||||
|
\item{...}{parameters that are passed on to \code{MDR}}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
Ordered factor with values \code{Positive}, \code{Unconfirmed}, \code{Negative}.
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
|
||||||
|
}
|
||||||
71
man/freq.Rd
Normal file
71
man/freq.Rd
Normal file
@ -0,0 +1,71 @@
|
|||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/freq.R
|
||||||
|
\name{freq}
|
||||||
|
\alias{freq}
|
||||||
|
\alias{frequency_tbl}
|
||||||
|
\title{Frequency table}
|
||||||
|
\usage{
|
||||||
|
freq(x, sort.count = TRUE, nmax = 15, na.rm = TRUE, markdown = FALSE,
|
||||||
|
toConsole = TRUE, digits = 2, sep = " ")
|
||||||
|
|
||||||
|
frequency_tbl(x, sort.count = TRUE, nmax = 15, na.rm = TRUE,
|
||||||
|
markdown = FALSE, toConsole = TRUE, digits = 2, sep = " ")
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{x}{data}
|
||||||
|
|
||||||
|
\item{sort.count}{Sort on count. Use \code{FALSE} to sort alphabetically on item.}
|
||||||
|
|
||||||
|
\item{nmax}{number of row to print. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.}
|
||||||
|
|
||||||
|
\item{na.rm}{a logical value indicating whether NA values should be removed from the frequency table. The header will always print the amount of\code{NA}s.}
|
||||||
|
|
||||||
|
\item{markdown}{print table in markdown format (this forces \code{nmax = NA})}
|
||||||
|
|
||||||
|
\item{toConsole}{Print table to the console. Use \code{FALSE} to assign the table to an object.}
|
||||||
|
|
||||||
|
\item{digits}{how many significant digits are to be used for numeric values (not for the items themselves, that depends on \code{\link{getOption}("digits")})}
|
||||||
|
|
||||||
|
\item{sep}{a character string to separate the terms when selecting multiple columns}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Create a frequency table of a vector of data, a single column or a maximum of 9 columns of a data frame. Supports markdown for reports.
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
For numeric values, the next values will be calculated and shown into the header:
|
||||||
|
\itemize{
|
||||||
|
\item{Mean, using \code{\link[base]{mean}}}
|
||||||
|
\item{Standard deviation, using \code{\link[stats]{sd}}}
|
||||||
|
\item{Five numbers of Tukey (min, Q1, median, Q3, max), using \code{\link[stats]{fivenum}}}
|
||||||
|
\item{Outliers (count and list), using \code{\link{boxplot.stats}}}
|
||||||
|
\item{Coefficient of variation (CV), the standard deviation divided by the mean}
|
||||||
|
\item{Coefficient of quartile variation (CQV, sometimes called coefficient of dispersion), calculated as \code{(Q3 - Q1) / (Q3 + Q1)} using \code{\link{quantile}} with \code{type = 6} as quantile algorithm to comply with SPSS standards}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
library(dplyr)
|
||||||
|
|
||||||
|
freq(septic_patients$hospital_id)
|
||||||
|
|
||||||
|
septic_patients \%>\%
|
||||||
|
filter(hospital_id == "A") \%>\%
|
||||||
|
select(bactid) \%>\%
|
||||||
|
freq()
|
||||||
|
|
||||||
|
# select multiple columns; they will be pasted together
|
||||||
|
septic_patients \%>\%
|
||||||
|
left_join_microorganisms \%>\%
|
||||||
|
filter(hospital_id == "A") \%>\%
|
||||||
|
select(genus, species) \%>\%
|
||||||
|
freq()
|
||||||
|
|
||||||
|
# save frequency table to an object
|
||||||
|
years <- septic_patients \%>\%
|
||||||
|
mutate(year = format(date, "\%Y")) \%>\%
|
||||||
|
select(year) \%>\%
|
||||||
|
freq(toConsole = FALSE)
|
||||||
|
}
|
||||||
|
\keyword{freq}
|
||||||
|
\keyword{frequency}
|
||||||
|
\keyword{summarise}
|
||||||
|
\keyword{summary}
|
||||||
40
man/like.Rd
Normal file
40
man/like.Rd
Normal file
@ -0,0 +1,40 @@
|
|||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/misc.R
|
||||||
|
\name{like}
|
||||||
|
\alias{like}
|
||||||
|
\alias{\%like\%}
|
||||||
|
\title{Pattern Matching}
|
||||||
|
\source{
|
||||||
|
Inherited from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default.
|
||||||
|
}
|
||||||
|
\usage{
|
||||||
|
x \%like\% pattern
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{x}{a character vector where matches are sought, or an
|
||||||
|
object which can be coerced by \code{as.character} to a character
|
||||||
|
vector. \link{Long vectors} are supported.}
|
||||||
|
|
||||||
|
\item{pattern}{character string containing a \link{regular expression}
|
||||||
|
(or character string for \code{fixed = TRUE}) to be matched
|
||||||
|
in the given character vector. Coerced by
|
||||||
|
\code{\link{as.character}} to a character string if possible. If a
|
||||||
|
character vector of length 2 or more is supplied, the first element
|
||||||
|
is used with a warning. Missing values are allowed except for
|
||||||
|
\code{regexpr} and \code{gregexpr}.}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
A \code{logical} vector
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Convenience function to compare a vector with a pattern, like \code{\link[base]{grep}}. It always returns a \code{logical} vector and is always case-insensitive.
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
library(dplyr)
|
||||||
|
# get unique occurences of bacteria whose name start with 'Ent'
|
||||||
|
septic_patients \%>\%
|
||||||
|
left_join_microorganisms() \%>\%
|
||||||
|
filter(fullname \%like\% '^Ent') \%>\%
|
||||||
|
pull(fullname) \%>\%
|
||||||
|
unique()
|
||||||
|
}
|
||||||
@ -1,5 +1,5 @@
|
|||||||
% Generated by roxygen2: do not edit by hand
|
% Generated by roxygen2: do not edit by hand
|
||||||
% Please edit documentation in R/EUCAST.R
|
% Please edit documentation in R/eucast.R
|
||||||
\name{mo_property}
|
\name{mo_property}
|
||||||
\alias{mo_property}
|
\alias{mo_property}
|
||||||
\title{Poperties of a microorganism}
|
\title{Poperties of a microorganism}
|
||||||
|
|||||||
55
man/print.Rd
Normal file
55
man/print.Rd
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/print.R
|
||||||
|
\name{print}
|
||||||
|
\alias{print}
|
||||||
|
\alias{print.tbl_df}
|
||||||
|
\alias{print.tbl}
|
||||||
|
\alias{print.data.table}
|
||||||
|
\title{Printing Data Tables and Tibbles}
|
||||||
|
\usage{
|
||||||
|
\method{print}{tbl_df}(x, nmax = 10, header = TRUE, row.names = TRUE,
|
||||||
|
right = FALSE, width = 1, na = "<NA>", ...)
|
||||||
|
|
||||||
|
\method{print}{tbl}(x, ...)
|
||||||
|
|
||||||
|
\method{print}{data.table}(x, nmax = 10, header = TRUE, row.names = TRUE,
|
||||||
|
print.keys = FALSE, right = FALSE, width = 1, na = "<NA>", ...)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{x}{object of class \code{data.frame}.}
|
||||||
|
|
||||||
|
\item{nmax}{amount of rows to print in total. When the total amount of rows exceeds this limit, the first and last \code{nmax / 2} rows will be printed. Use \code{nmax = NA} to print all rows.}
|
||||||
|
|
||||||
|
\item{header}{print header with information about data size and tibble grouping}
|
||||||
|
|
||||||
|
\item{row.names}{logical (or character vector), indicating whether (or
|
||||||
|
what) row names should be printed.}
|
||||||
|
|
||||||
|
\item{right}{logical, indicating whether or not strings should be
|
||||||
|
right-aligned. The default is right-alignment.}
|
||||||
|
|
||||||
|
\item{width}{amount of white spaces to keep between columns, must be at least 1}
|
||||||
|
|
||||||
|
\item{na}{value to print instead of NA}
|
||||||
|
|
||||||
|
\item{...}{optional arguments to \code{print} or \code{plot} methods.}
|
||||||
|
|
||||||
|
\item{print.keys}{print keys for \code{data.table}}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Print a data table or tibble. It prints: \cr- The \strong{first and last rows} like \code{data.table}s are printed by the \code{data.table} package,\cr- A \strong{header} and \strong{left aligned text} like \code{tibble}s are printed by the \code{tibble} package with info about grouped variables,\cr- \strong{Unchanged values} and \strong{support for row names} like \code{data.frame}s are printed by the \code{base} package.
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
# still showing all values unchanged:
|
||||||
|
library(dplyr)
|
||||||
|
starwars
|
||||||
|
print(starwars, width = 3)
|
||||||
|
|
||||||
|
# compare the significance notation of this
|
||||||
|
starwars \%>\% select(birth_year)
|
||||||
|
# with this
|
||||||
|
tibble:::print.tbl_df(starwars \%>\% select(birth_year))
|
||||||
|
|
||||||
|
# supports info about groups (look at header)
|
||||||
|
starwars \%>\% group_by(homeworld, gender)
|
||||||
|
}
|
||||||
@ -1,4 +1,4 @@
|
|||||||
context("EUCAST.R")
|
context("eucast.R")
|
||||||
|
|
||||||
test_that("EUCAST rules work", {
|
test_that("EUCAST rules work", {
|
||||||
a <- data.frame(bactid = c("KLEPNE", # Klebsiella pneumoniae
|
a <- data.frame(bactid = c("KLEPNE", # Klebsiella pneumoniae
|
||||||
|
|||||||
26
tests/testthat/test-freq.R
Normal file
26
tests/testthat/test-freq.R
Normal file
@ -0,0 +1,26 @@
|
|||||||
|
context("freq.R")
|
||||||
|
|
||||||
|
test_that("frequency table works", {
|
||||||
|
expect_equal(nrow(freq(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5), toConsole = FALSE)), 5)
|
||||||
|
expect_equal(nrow(frequency_tbl(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5), toConsole = FALSE)), 5)
|
||||||
|
|
||||||
|
# date column of septic_patients should contain 1662 unique dates
|
||||||
|
expect_equal(nrow(freq(septic_patients$date, toConsole = FALSE)), 1662)
|
||||||
|
expect_equal(nrow(freq(septic_patients$date, toConsole = FALSE)),
|
||||||
|
length(unique(septic_patients$date)))
|
||||||
|
|
||||||
|
expect_output(freq(septic_patients$age))
|
||||||
|
expect_output(freq(septic_patients$date))
|
||||||
|
expect_output(freq(septic_patients$hospital_id))
|
||||||
|
|
||||||
|
library(dplyr)
|
||||||
|
expect_output(septic_patients %>% select(1:2) %>% freq())
|
||||||
|
expect_output(septic_patients %>% select(1:3) %>% freq())
|
||||||
|
expect_output(septic_patients %>% select(1:4) %>% freq())
|
||||||
|
expect_output(septic_patients %>% select(1:5) %>% freq())
|
||||||
|
expect_output(septic_patients %>% select(1:6) %>% freq())
|
||||||
|
expect_output(septic_patients %>% select(1:7) %>% freq())
|
||||||
|
expect_output(septic_patients %>% select(1:8) %>% freq())
|
||||||
|
expect_output(septic_patients %>% select(1:9) %>% freq())
|
||||||
|
})
|
||||||
|
|
||||||
16
tests/testthat/test-mdro.R
Normal file
16
tests/testthat/test-mdro.R
Normal file
@ -0,0 +1,16 @@
|
|||||||
|
context("mdro.R")
|
||||||
|
|
||||||
|
|
||||||
|
test_that("MDRO works", {
|
||||||
|
library(dplyr)
|
||||||
|
outcome <- MDRO(septic_patients, "nl", info = FALSE)
|
||||||
|
|
||||||
|
# check class
|
||||||
|
expect_equal(outcome %>% class(), c('ordered', 'factor'))
|
||||||
|
|
||||||
|
# septic_patients should have these finding using Dutch guidelines
|
||||||
|
expect_equal(outcome %>% freq(toConsole = FALSE) %>% pull(Count), c(1152, 824, 3, 21))
|
||||||
|
|
||||||
|
expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))
|
||||||
|
|
||||||
|
})
|
||||||
@ -10,5 +10,7 @@ test_that("`like` works", {
|
|||||||
test_that("percentages works", {
|
test_that("percentages works", {
|
||||||
expect_equal(percent(0.25), "25%")
|
expect_equal(percent(0.25), "25%")
|
||||||
expect_equal(percent(0.5), "50%")
|
expect_equal(percent(0.5), "50%")
|
||||||
|
expect_equal(percent(0.500, force_zero = TRUE), "50.0%")
|
||||||
expect_equal(percent(0.1234), "12.3%")
|
expect_equal(percent(0.1234), "12.3%")
|
||||||
})
|
})
|
||||||
|
|
||||||
|
|||||||
8
tests/testthat/test-print.R
Normal file
8
tests/testthat/test-print.R
Normal file
@ -0,0 +1,8 @@
|
|||||||
|
context("print.R")
|
||||||
|
|
||||||
|
|
||||||
|
test_that("tibble printing works", {
|
||||||
|
library(dplyr)
|
||||||
|
expect_output(print(starwars))
|
||||||
|
expect_output(print(septic_patients))
|
||||||
|
})
|
||||||
Loading…
Reference in New Issue
Block a user