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(v2.1.1.9249) unit test

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dr. M.S. (Matthijs) Berends 2025-04-20 17:49:47 +02:00
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DESCRIPTION
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Package: AMR
Version: 2.1.1.9248
Version: 2.1.1.9249
Date: 2025-04-20
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# AMR 2.1.1.9248
# AMR 2.1.1.9249
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*

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R/sir.R
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#'
#' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor] containing the levels `S`, `SDD`, `I`, `R`, `NI`.
#'
#' Breakpoints are currently implemented from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*. All breakpoints used for interpretation are available in our [clinical_breakpoints] data set.
#' Breakpoints are currently implemented from EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`, see *Details*. All breakpoints used for interpretation are available in our [clinical_breakpoints] data set.
#' @rdname as.sir
#' @param x Vector of values (for class [`mic`]: MIC values in mg/L, for class [`disk`]: a disk diffusion radius in millimetres).
#' @param mo A vector (or column name) with [character]s that can be coerced to valid microorganism codes with [as.mo()], can be left empty to determine it automatically.

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man/as.sir.Rd
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@ -144,7 +144,7 @@ Ordered \link{factor} with new class \code{sir}
\description{
Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. \code{\link[=as.sir]{as.sir()}} transforms the input to a new class \code{\link{sir}}, which is an ordered \link{factor} containing the levels \code{S}, \code{SDD}, \code{I}, \code{R}, \code{NI}.
Breakpoints are currently implemented from EUCAST (2011-2025) and CLSI (2011-2025), see \emph{Details}. All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see \emph{Details}. All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
}
\details{
\emph{Note: The clinical breakpoints in this package were validated through, and imported from, \href{https://whonet.org}{WHONET}. The public use of this \code{AMR} package has been endorsed by both CLSI and EUCAST. See \link{clinical_breakpoints} for more information.}

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tests/testthat/test-sir.R
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@ -129,7 +129,7 @@ test_that("test-sir.R", {
# allow for guideline length > 1
expect_equal(
AMR:::get_guideline(c("CLSI", "CLSI", "CLSI2023", "EUCAST", "EUCAST2020"), AMR::clinical_breakpoints),
c("CLSI 2024", "CLSI 2024", "CLSI 2023", "EUCAST 2024", "EUCAST 2020")
c("CLSI 2025", "CLSI 2025", "CLSI 2023", "EUCAST 2025", "EUCAST 2020")
)
# these are used in the script