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Try to support older R versions
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NEWS.md
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NEWS.md
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## 0.2.0
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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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* 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 [this link](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E). 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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- Support for older R versions, only R 3.1.0 and later is needed
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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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* Support for older R versions, only R 3.1.0 and later is needed
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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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* 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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# 0.1.1
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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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# 0.1.0
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* First submission to CRAN.
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14
R/misc.R
14
R/misc.R
@ -112,11 +112,23 @@ size_humanreadable <- function(bytes, decimals = 1) {
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out
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}
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# Support for older R versions --------------------------------------------
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# strrep is only available in R 3.3 and later
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# and we want to support R 3.2 too, so:
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strrep <- function(x, times) {
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for (i in 1:length(x)) {
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x[i] <- paste(rep(x[i], times[i]), collapse = "")
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}
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x
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}
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# trimws is only available in R 3.2 and later
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trimws <- function(x, which = "both") {
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if (which %in% c("left", "both", "l", "b")) {
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x <- gsub('^ {1,255}', '', x)
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}
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if (which %in% c("right", "both", "r", "b")) {
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x <- gsub(' {1,255}$', '', x)
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}
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x
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}
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@ -10,6 +10,8 @@ This R package contains functions to make microbiological, epidemiological data
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With AMR you can also apply EUCAST rules to isolates, identify first isolates of every patient, translate antibiotic codes from the lab (like `"AMOX"`) or the [WHO](https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no) (like `"J01CA04"`) to trivial names (like `"amoxicillin"`), or predict antimicrobial resistance for the nextcoming years with the `rsi_predict` function.
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With the `MDRO` function (abbreviation of mutli-drug resistant organisms), you can check your isolates for exceptional resistance with country-specific guidelines. Currently guidelines for Germany and the Netherlands are supported. Please suggest addition of your own country here: [https://github.com/msberends/AMR/issues](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E).
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For regular AMR analysis, the `rsi` function can be used. This function als works with the `dplyr` package (e.g. in conjunction with `summarise`) to calculate the resistance percentages of different antibiotic columns of a table.
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This package contains an example data set `septic_patients`, consisting of 2000 isolates from anonymised septic patients between 2001 and 2017.
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@ -14,3 +14,14 @@ test_that("percentages works", {
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expect_equal(percent(0.1234), "12.3%")
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})
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test_that("size format works", {
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expect_equal(size_humanreadable(123456), "121 kB")
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})
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test_that("functions missing in older R versions work", {
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expect_equal(strrep("A", 5), "AAAAA")
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expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
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expect_equal(trimws(" test "), "test")
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expect_equal(trimws(" test ", "l"), "test ")
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expect_equal(trimws(" test ", "r"), " test")
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})
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