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(v1.6.0.9003) like() fix

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dr. M.S. (Matthijs) Berends 2021-04-16 11:41:05 +02:00
parent d277d58475
commit 00d3e437a8
29 changed files with 78 additions and 62 deletions
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8
.github/workflows/check.yaml vendored
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@ -65,10 +65,10 @@ jobs:
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.3', allowfail: false rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
@ -77,10 +77,10 @@ jobs:
- {os: ubuntu-16.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} # - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} # - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
env: env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.6.0.9002 Version: 1.6.0.9003
Date: 2021-04-12 Date: 2021-04-16
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

5
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.6.0.9002 # AMR 1.6.0.9003
## <small>Last updated: 12 April 2021</small> ## <small>Last updated: 16 April 2021</small>
### New ### New
* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()` * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
@ -13,6 +13,7 @@
* Fix for minor translation errors * Fix for minor translation errors
* Printing of microbial codes in a `data.frame` or `tibble` now gives a warning if the data contains old microbial codes (from a previous AMR package version) * Printing of microbial codes in a `data.frame` or `tibble` now gives a warning if the data contains old microbial codes (from a previous AMR package version)
* `first_isolate()` can now take a vector of values for `col_keyantibiotics` and can have an episode length of `Inf` * `first_isolate()` can now take a vector of values for `col_keyantibiotics` and can have an episode length of `Inf`
* `like()` (and `%like%`) now checks if `pattern` is a *valid* regular expression
* Fixed an installation error on R-3.0 * Fixed an installation error on R-3.0
# AMR 1.6.0 # AMR 1.6.0

16
R/aa_helper_functions.R
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@ -211,10 +211,20 @@ search_type_in_df <- function(x, type, info = TRUE) {
found found
} }
is_possibly_regex <- function(x) { is_valid_regex <- function(x) {
tryCatch(vapply(FUN.VALUE = character(1), strsplit(x, ""), regex_at_all <- tryCatch(vapply(FUN.VALUE = logical(1),
function(y) any(y %in% c("$", "(", ")", "*", "+", "-", ".", "?", "[", "]", "^", "{", "|", "}", "\\"), na.rm = TRUE)), X = strsplit(x, ""),
FUN = function(y) any(y %in% c("$", "(", ")", "*", "+", "-",
".", "?", "[", "]", "^", "{",
"|", "}", "\\"),
na.rm = TRUE)),
error = function(e) rep(TRUE, length(x))) error = function(e) rep(TRUE, length(x)))
regex_valid <- vapply(FUN.VALUE = logical(1),
X = c("[.", "."),
FUN = function(y) !"try-error" %in% class(try(grepl(y, ""),
silent = TRUE)),
USE.NAMES = FALSE)
regex_at_all & regex_valid
} }
stop_ifnot_installed <- function(package) { stop_ifnot_installed <- function(package) {

17
R/like.R
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@ -28,21 +28,21 @@
#' Convenient wrapper around [grepl()] to match a pattern: `x %like% pattern`. It always returns a [`logical`] vector and is always case-insensitive (use `x %like_case% pattern` for case-sensitive matching). Also, `pattern` can be as long as `x` to compare items of each index in both vectors, or they both can have the same length to iterate over all cases. #' Convenient wrapper around [grepl()] to match a pattern: `x %like% pattern`. It always returns a [`logical`] vector and is always case-insensitive (use `x %like_case% pattern` for case-sensitive matching). Also, `pattern` can be as long as `x` to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
#' @inheritSection lifecycle Stable Lifecycle #' @inheritSection lifecycle Stable Lifecycle
#' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector. #' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
#' @param pattern a character string containing a regular expression (or [character] string for `fixed = TRUE`) to be matched in the given character vector. Coerced by [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. #' @param pattern a character vector containing regular expressions (or a [character] string for `fixed = TRUE`) to be matched in the given character vector. Coerced by [as.character()] to a character string if possible.
#' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching. #' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.
#' @return A [logical] vector #' @return A [logical] vector
#' @name like #' @name like
#' @rdname like #' @rdname like
#' @export #' @export
#' @details #' @details
#' The `%like%` function: #' This `%like%` function:
#' * Is case-insensitive (use `%like_case%` for case-sensitive matching) #' * Is case-insensitive (use `%like_case%` for case-sensitive matching)
#' * Supports multiple patterns #' * Supports multiple patterns
#' * Checks if `pattern` is a regular expression and sets `fixed = TRUE` if not, to greatly improve speed #' * Checks if `pattern` is a valid regular expression and sets `fixed = TRUE` if not, to greatly improve speed (vectorised over `pattern`)
#' * Always uses compatibility with Perl unless `fixed = TRUE`, to greatly improve speed #' * Always uses compatibility with Perl unless `fixed = TRUE`, to greatly improve speed
#' #'
#' Using RStudio? The text `%like%` can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like `Ctrl+Shift+L` or `Cmd+Shift+L` (see `Tools` > `Modify Keyboard Shortcuts...`). #' Using RStudio? The text `%like%` can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like `Ctrl+Shift+L` or `Cmd+Shift+L` (see `Tools` > `Modify Keyboard Shortcuts...`).
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R) #' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R), although altered as explained in *Details*.
#' @seealso [grepl()] #' @seealso [grepl()]
#' @inheritSection AMR Read more on Our Website! #' @inheritSection AMR Read more on Our Website!
#' @examples #' @examples
@ -80,8 +80,9 @@ like <- function(x, pattern, ignore.case = TRUE) {
return(rep(FALSE, length(x))) return(rep(FALSE, length(x)))
} }
# set to fixed if no regex found # set to fixed if no valid regex (vectorised)
fixed <- !any(is_possibly_regex(pattern)) fixed <- !is_valid_regex(pattern)
if (ignore.case == TRUE) { if (ignore.case == TRUE) {
# set here, otherwise if fixed = TRUE, this warning will be thrown: argument `ignore.case = TRUE` will be ignored # set here, otherwise if fixed = TRUE, this warning will be thrown: argument `ignore.case = TRUE` will be ignored
x <- tolower(x) x <- tolower(x)
@ -105,7 +106,9 @@ like <- function(x, pattern, ignore.case = TRUE) {
mapply(FUN = grepl, mapply(FUN = grepl,
x = x, x = x,
pattern = pattern, pattern = pattern,
MoreArgs = list(ignore.case = FALSE, fixed = fixed, perl = !fixed), fixed = fixed,
perl = !fixed,
MoreArgs = list(ignore.case = FALSE),
SIMPLIFY = FALSE, SIMPLIFY = FALSE,
USE.NAMES = FALSE) USE.NAMES = FALSE)
) )

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data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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">1.6.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

6
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>
@ -236,13 +236,13 @@
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small> <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
</div> </div>
<p>Berends MS, Luz CF et al. (2019). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622</p> <p>Berends MS, Luz CF et al. (2021). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622</p>
<pre>@Article{, <pre>@Article{,
title = {AMR - An R Package for Working with Antimicrobial Resistance Data}, title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner}, author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
journal = {bioRxiv}, journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory}, publisher = {Cold Spring Harbor Laboratory},
year = {2019}, year = {2021},
url = {https://doi.org/10.1101/810622}, url = {https://doi.org/10.1101/810622},
}</pre> }</pre>

2
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

14
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1609002" class="section level1"> <div id="amr-1609003" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9002"> <h1 class="page-header" data-toc-text="1.6.0.9003">
<a href="#amr-1609002" class="anchor"></a>AMR 1.6.0.9002<small> Unreleased </small> <a href="#amr-1609003" class="anchor"></a>AMR 1.6.0.9003<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-12-april-2021" class="section level2"> <div id="last-updated-16-april-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-12-april-2021" class="anchor"></a><small>Last updated: 12 April 2021</small> <a href="#last-updated-16-april-2021" class="anchor"></a><small>Last updated: 16 April 2021</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -270,6 +270,8 @@
<li> <li>
<code><a href="../reference/first_isolate.html">first_isolate()</a></code> can now take a vector of values for <code>col_keyantibiotics</code> and can have an episode length of <code>Inf</code> <code><a href="../reference/first_isolate.html">first_isolate()</a></code> can now take a vector of values for <code>col_keyantibiotics</code> and can have an episode length of <code>Inf</code>
</li> </li>
<li>
<code><a href="../reference/like.html">like()</a></code> (and <code><a href="../reference/like.html">%like%</a></code>) now checks if <code>pattern</code> is a <em>valid</em> regular expression</li>
<li>Fixed an installation error on R-3.0</li> <li>Fixed an installation error on R-3.0</li>
</ul> </ul>
</div> </div>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-04-12T12:24Z last_built: 2021-04-16T09:40Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

2
docs/reference/first_isolate.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

2
docs/reference/get_episode.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

10
docs/reference/like.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>
@ -257,7 +257,7 @@
</tr> </tr>
<tr> <tr>
<th>pattern</th> <th>pattern</th>
<td><p>a character string containing a regular expression (or <a href='https://rdrr.io/r/base/character.html'>character</a> string for <code>fixed = TRUE</code>) to be matched in the given character vector. Coerced by <code><a href='https://rdrr.io/r/base/character.html'>as.character()</a></code> to a character string if possible. If a <a href='https://rdrr.io/r/base/character.html'>character</a> vector of length 2 or more is supplied, the first element is used with a warning.</p></td> <td><p>a character vector containing regular expressions (or a <a href='https://rdrr.io/r/base/character.html'>character</a> string for <code>fixed = TRUE</code>) to be matched in the given character vector. Coerced by <code><a href='https://rdrr.io/r/base/character.html'>as.character()</a></code> to a character string if possible.</p></td>
</tr> </tr>
<tr> <tr>
<th>ignore.case</th> <th>ignore.case</th>
@ -267,16 +267,16 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R'><code>like</code> function from the <code>data.table</code> package</a></p> <p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R'><code>like</code> function from the <code>data.table</code> package</a>, although altered as explained in <em>Details</em>.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector</p> <p>A <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>%like%</code> function:</p><ul> <p>This <code>%like%</code> function:</p><ul>
<li><p>Is case-insensitive (use <code>%like_case%</code> for case-sensitive matching)</p></li> <li><p>Is case-insensitive (use <code>%like_case%</code> for case-sensitive matching)</p></li>
<li><p>Supports multiple patterns</p></li> <li><p>Supports multiple patterns</p></li>
<li><p>Checks if <code>pattern</code> is a regular expression and sets <code>fixed = TRUE</code> if not, to greatly improve speed</p></li> <li><p>Checks if <code>pattern</code> is a valid regular expression and sets <code>fixed = TRUE</code> if not, to greatly improve speed (vectorised over <code>pattern</code>)</p></li>
<li><p>Always uses compatibility with Perl unless <code>fixed = TRUE</code>, to greatly improve speed</p></li> <li><p>Always uses compatibility with Perl unless <code>fixed = TRUE</code>, to greatly improve speed</p></li>
</ul> </ul>

2
docs/reference/mo_matching_score.html
View File

@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

2
docs/reference/mo_property.html
View File

@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9003</span>
</span> </span>
</div> </div>

6
inst/CITATION
View File

@ -6,9 +6,9 @@ citEntry(
author = "M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner", author = "M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner",
journal = "bioRxiv", journal = "bioRxiv",
publisher = "Cold Spring Harbor Laboratory", publisher = "Cold Spring Harbor Laboratory",
year = 2019, year = 2021,
url = "https://doi.org/10.1101/810622", url = "https://doi.org/10.1101/810622",
textVersion = "Berends MS, Luz CF et al. (2019). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622" textVersion = "Berends MS, Luz CF et al. (2021). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622"
) )
citFooter("The mentioned article is a preprinted version of a manuscript we sent to a journal. Many thanks for using our open-source method to work with microbial and antimicrobial data!") citFooter("This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!")

8
man/like.Rd
View File

@ -6,7 +6,7 @@
\alias{\%like_case\%} \alias{\%like_case\%}
\title{Vectorised Pattern Matching with Keyboard Shortcut} \title{Vectorised Pattern Matching with Keyboard Shortcut}
\source{ \source{
Idea from the \href{https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R}{\code{like} function from the \code{data.table} package} Idea from the \href{https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R}{\code{like} function from the \code{data.table} package}, although altered as explained in \emph{Details}.
} }
\usage{ \usage{
like(x, pattern, ignore.case = TRUE) like(x, pattern, ignore.case = TRUE)
@ -18,7 +18,7 @@ x \%like_case\% pattern
\arguments{ \arguments{
\item{x}{a character vector where matches are sought, or an object which can be coerced by \code{\link[=as.character]{as.character()}} to a character vector.} \item{x}{a character vector where matches are sought, or an object which can be coerced by \code{\link[=as.character]{as.character()}} to a character vector.}
\item{pattern}{a character string containing a regular expression (or \link{character} string for \code{fixed = TRUE}) to be matched in the given character vector. Coerced by \code{\link[=as.character]{as.character()}} to a character string if possible. If a \link{character} vector of length 2 or more is supplied, the first element is used with a warning.} \item{pattern}{a character vector containing regular expressions (or a \link{character} string for \code{fixed = TRUE}) to be matched in the given character vector. Coerced by \code{\link[=as.character]{as.character()}} to a character string if possible.}
\item{ignore.case}{if \code{FALSE}, the pattern matching is \emph{case sensitive} and if \code{TRUE}, case is ignored during matching.} \item{ignore.case}{if \code{FALSE}, the pattern matching is \emph{case sensitive} and if \code{TRUE}, case is ignored during matching.}
} }
@ -29,11 +29,11 @@ A \link{logical} vector
Convenient wrapper around \code{\link[=grepl]{grepl()}} to match a pattern: \code{x \%like\% pattern}. It always returns a \code{\link{logical}} vector and is always case-insensitive (use \code{x \%like_case\% pattern} for case-sensitive matching). Also, \code{pattern} can be as long as \code{x} to compare items of each index in both vectors, or they both can have the same length to iterate over all cases. Convenient wrapper around \code{\link[=grepl]{grepl()}} to match a pattern: \code{x \%like\% pattern}. It always returns a \code{\link{logical}} vector and is always case-insensitive (use \code{x \%like_case\% pattern} for case-sensitive matching). Also, \code{pattern} can be as long as \code{x} to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
} }
\details{ \details{
The \verb{\%like\%} function: This \verb{\%like\%} function:
\itemize{ \itemize{
\item Is case-insensitive (use \verb{\%like_case\%} for case-sensitive matching) \item Is case-insensitive (use \verb{\%like_case\%} for case-sensitive matching)
\item Supports multiple patterns \item Supports multiple patterns
\item Checks if \code{pattern} is a regular expression and sets \code{fixed = TRUE} if not, to greatly improve speed \item Checks if \code{pattern} is a valid regular expression and sets \code{fixed = TRUE} if not, to greatly improve speed (vectorised over \code{pattern})
\item Always uses compatibility with Perl unless \code{fixed = TRUE}, to greatly improve speed \item Always uses compatibility with Perl unless \code{fixed = TRUE}, to greatly improve speed
} }

2
tests/testthat/test-eucast_rules.R
View File

@ -38,7 +38,7 @@ test_that("EUCAST rules work", {
"reference.version", "reference.version",
"note")) "note"))
MOs_mentioned <- unique(eucast_rules_file$this_value) MOs_mentioned <- unique(eucast_rules_file$this_value)
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_possibly_regex(MOs_mentioned)], ",", fixed = TRUE)))) MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned))) MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
expect_length(MOs_mentioned[MOs_test != MOs_mentioned], 0) expect_length(MOs_mentioned[MOs_test != MOs_mentioned], 0)