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AMR
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add column to `as.mic()` and `as.disk()` warnings

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dr. M.S. (Matthijs) Berends 2022-11-28 19:39:52 +01:00
parent 31fb81c382
commit ba51c2d92f
4 changed files with 22 additions and 13 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.2.9053
Date: 2022-11-24
Version: 1.8.2.9054
Date: 2022-11-28
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9053
# AMR 1.8.2.9054
This version will eventually become v2.0! We're happy to reach a new major milestone soon!
@ -69,6 +69,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
* Updated support for all WHONET 2022 microorganism codes
* Antimicrobial interpretation 'SDD' (susceptible dose-dependent, coined by CLSI) will be interpreted as 'I' to comply with EUCAST's 'I' in `as.rsi()`
* Fix for `mo_shortname()` in case of higher taxonomic ranks (order, class, phylum)
* Cleaning columns with `as.rsi()`, `as.mic()`, or `as.disk()` will now show the column name in the warning for invalid results
### Other
* New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions

14
R/disk.R
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@ -118,11 +118,15 @@ as.disk <- function(x, na.rm = FALSE) {
unique() %pm>%
sort() %pm>%
vector_and(quotes = TRUE)
warning_(
"in `as.disk()`: ", na_after - na_before, " results truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ",
list_missing
cur_col <- get_current_column()
warning_("in `as.disk()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ",
list_missing,
call = FALSE
)
}
}

14
R/mic.R
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@ -228,11 +228,15 @@ as.mic <- function(x, na.rm = FALSE) {
unique() %pm>%
sort() %pm>%
vector_and(quotes = TRUE)
warning_("in `as.mic()`: ", na_after - na_before, " results truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid MICs: ",
list_missing,
call = FALSE
cur_col <- get_current_column()
warning_("in `as.mic()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid MICs: ",
list_missing,
call = FALSE
)
}