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(v1.4.0.9007) bugfix
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Package: AMR
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Version: 1.4.0.9006
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Version: 1.4.0.9007
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Date: 2020-10-21
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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3
NEWS.md
3
NEWS.md
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# AMR 1.4.0.9006
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# AMR 1.4.0.9007
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## <small>Last updated: 21 October 2020</small>
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### New
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* Functions `is_gram_negative()` and `is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE`, thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
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* Functions `%not_like%` and `%like_perl%` as wrappers around `%like%`.
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### Changed
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* For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the [`typed`](https://github.com/moodymudskipper/typed) package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.
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@ -144,8 +144,14 @@ first_isolate <- function(x,
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meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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meet_criteria(col_testcode, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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if (isFALSE(col_specimen)) {
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col_specimen <- NULL
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}
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meet_criteria(col_specimen, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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meet_criteria(col_icu, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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if (isFALSE(col_keyantibiotics)) {
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col_keyantibiotics <- NULL
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}
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meet_criteria(col_keyantibiotics, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1)
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meet_criteria(testcodes_exclude, allow_class = "character", allow_NULL = TRUE)
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@ -206,17 +212,11 @@ first_isolate <- function(x,
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if (is.null(col_keyantibiotics)) {
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col_keyantibiotics <- search_type_in_df(x = x, type = "keyantibiotics")
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}
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if (isFALSE(col_keyantibiotics)) {
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col_keyantibiotics <- NULL
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}
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# -- specimen
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if (is.null(col_specimen) & !is.null(specimen_group)) {
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col_specimen <- search_type_in_df(x = x, type = "specimen")
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}
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if (isFALSE(col_specimen)) {
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col_specimen <- NULL
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}
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# check if columns exist
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check_columns_existance <- function(column, tblname = x) {
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18
R/like.R
18
R/like.R
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#' * Tries again with `perl = TRUE` if regex fails
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#'
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#' Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like `Ctrl+Shift+L` or `Cmd+Shift+L` (see `Tools` > `Modify Keyboard Shortcuts...`).
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#'
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#' The `"%not_like%"` and `"%like_perl%"` functions are wrappers around `"%like%"`.
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#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/master/R/like.R)
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#' @seealso [grep()]
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#' @inheritSection AMR Read more on our website!
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@ -146,10 +148,18 @@ like <- function(x, pattern, ignore.case = TRUE) {
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#' @export
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"%like%" <- function(x, pattern) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(pattern, allow_class = "character")
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meet_criteria(pattern, allow_NA = FALSE)
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like(x, pattern, ignore.case = TRUE)
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}
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#' @rdname like
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#' @export
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"%not_like%" <- function(x, pattern) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(pattern, allow_NA = FALSE)
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!like(x, pattern, ignore.case = TRUE)
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}
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#' @rdname like
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#' @export
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"%like_case%" <- function(x, pattern) {
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@ -158,11 +168,13 @@ like <- function(x, pattern, ignore.case = TRUE) {
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like(x, pattern, ignore.case = FALSE)
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}
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# don't export his one, it's just for convenience in eucast_rules()
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# match all Klebsiella and Raoultella, but not K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)"
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#' @rdname like
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#' @export
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"%like_perl%" <- function(x, pattern) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(pattern, allow_NA = FALSE)
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# convenient for e.g. matching all Klebsiella and Raoultella, but not
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# K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)"
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grepl(x = tolower(x),
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pattern = tolower(pattern),
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perl = TRUE,
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1409006" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9006">
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<a href="#amr-1409006" class="anchor"></a>AMR 1.4.0.9006<small> Unreleased </small>
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<div id="amr-1409007" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9007">
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<a href="#amr-1409007" class="anchor"></a>AMR 1.4.0.9007<small> Unreleased </small>
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</h1>
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<div id="last-updated-21-october-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -249,6 +249,7 @@
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<a href="#new" class="anchor"></a>New</h3>
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<ul>
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<li>Functions <code><a href="../reference/mo_property.html">is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code>, thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</li>
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<li>Functions <code>%not_like%</code> and <code>%like_perl%</code> as wrappers around <code><a href="../reference/like.html">%like%</a></code>.</li>
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</ul>
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</div>
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<div id="changed" class="section level3">
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2020-10-21T12:39Z
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last_built: 2020-10-21T13:25Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
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</span>
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</div>
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