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run MICs and disks if detected

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dr. M.S. (Matthijs) Berends 2025-03-14 17:23:24 +01:00
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commit f758ab60f3
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3 changed files with 6 additions and 4 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 2.1.1.9201
Version: 2.1.1.9202
Date: 2025-03-14
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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# AMR 2.1.1.9201
# AMR 2.1.1.9202
*(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://msberends.github.io/AMR/#latest-development-version).)*

6
R/sir.R
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@ -496,9 +496,11 @@ as.sir.default <- function(x,
if (all(x %unlike% "(S|I|R)", na.rm = TRUE)) {
# check if they are actually MICs or disks
if (all_valid_mics(x)) {
warning_("in `as.sir()`: the input seems to contain MIC values. You can transform them with `as.mic()` before running `as.sir()` to interpret them.")
warning_("in `as.sir()`: input values were guessed to be MIC values - preferably transform them with `as.mic()` before running `as.sir()`.")
return(as.sir(as.mic(x), ...))
} else if (all_valid_disks(x)) {
warning_("in `as.sir()`: the input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.sir()` to interpret them.")
warning_("in `as.sir()`: input values were guessed to be disk diffusion values - preferably transform them with `as.disk()` before running `as.sir()`.")
return(as.sir(as.disk(x), ...))
}
}