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AMR
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(v1.4.0.9007) bugfix

This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-10-21 15:28:48 +02:00
parent 8f868388ce
commit f720c9ba0b
13 changed files with 38 additions and 24 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.4.0.9006
Version: 1.4.0.9007
Date: 2020-10-21
Title: Antimicrobial Resistance Analysis
Authors@R: c(

3
NEWS.md
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@ -1,8 +1,9 @@
# AMR 1.4.0.9006
# AMR 1.4.0.9007
## <small>Last updated: 21 October 2020</small>
### New
* 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.
* Functions `%not_like%` and `%like_perl%` as wrappers around `%like%`.
### Changed
* 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.

14
R/first_isolate.R
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@ -144,8 +144,14 @@ first_isolate <- function(x,
meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
meet_criteria(col_testcode, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
if (isFALSE(col_specimen)) {
col_specimen <- NULL
}
meet_criteria(col_specimen, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
meet_criteria(col_icu, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
if (isFALSE(col_keyantibiotics)) {
col_keyantibiotics <- NULL
}
meet_criteria(col_keyantibiotics, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(testcodes_exclude, allow_class = "character", allow_NULL = TRUE)
@ -206,17 +212,11 @@ first_isolate <- function(x,
if (is.null(col_keyantibiotics)) {
col_keyantibiotics <- search_type_in_df(x = x, type = "keyantibiotics")
}
if (isFALSE(col_keyantibiotics)) {
col_keyantibiotics <- NULL
}
# -- specimen
if (is.null(col_specimen) & !is.null(specimen_group)) {
col_specimen <- search_type_in_df(x = x, type = "specimen")
}
if (isFALSE(col_specimen)) {
col_specimen <- NULL
}
# check if columns exist
check_columns_existance <- function(column, tblname = x) {

18
R/like.R
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@ -42,6 +42,8 @@
#' * Tries again with `perl = TRUE` if regex fails
#'
#' 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...`).
#'
#' The `"%not_like%"` and `"%like_perl%"` functions are wrappers around `"%like%"`.
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/master/R/like.R)
#' @seealso [grep()]
#' @inheritSection AMR Read more on our website!
@ -146,10 +148,18 @@ like <- function(x, pattern, ignore.case = TRUE) {
#' @export
"%like%" <- function(x, pattern) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(pattern, allow_class = "character")
meet_criteria(pattern, allow_NA = FALSE)
like(x, pattern, ignore.case = TRUE)
}
#' @rdname like
#' @export
"%not_like%" <- function(x, pattern) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(pattern, allow_NA = FALSE)
!like(x, pattern, ignore.case = TRUE)
}
#' @rdname like
#' @export
"%like_case%" <- function(x, pattern) {
@ -158,11 +168,13 @@ like <- function(x, pattern, ignore.case = TRUE) {
like(x, pattern, ignore.case = FALSE)
}
# don't export his one, it's just for convenience in eucast_rules()
# match all Klebsiella and Raoultella, but not K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)"
#' @rdname like
#' @export
"%like_perl%" <- function(x, pattern) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(pattern, allow_NA = FALSE)
# convenient for e.g. matching all Klebsiella and Raoultella, but not
# K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)"
grepl(x = tolower(x),
pattern = tolower(pattern),
perl = TRUE,

2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
</span>
</div>

9
docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409006" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9006">
<a href="#amr-1409006" class="anchor"></a>AMR 1.4.0.9006<small> Unreleased </small>
<div id="amr-1409007" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9007">
<a href="#amr-1409007" class="anchor"></a>AMR 1.4.0.9007<small> Unreleased </small>
</h1>
<div id="last-updated-21-october-2020" class="section level2">
<h2 class="hasAnchor">
@ -249,6 +249,7 @@
<a href="#new" class="anchor"></a>New</h3>
<ul>
<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>
<li>Functions <code>%not_like%</code> and <code>%like_perl%</code> as wrappers around <code><a href="../reference/like.html">%like%</a></code>.</li>
</ul>
</div>
<div id="changed" class="section level3">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-10-21T12:39Z
last_built: 2020-10-21T13:25Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
</span>
</div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9007</span>
</span>
</div>