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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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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.8.2.9053 Version: 1.8.2.9054
Date: 2022-11-24 Date: 2022-11-28
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by
NEWS.md
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# 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! 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 * 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()` * 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) * 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 ### 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 * 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
R/disk.R
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@@ -118,11 +118,15 @@ as.disk <- function(x, na.rm = FALSE) {
unique() %pm>% unique() %pm>%
sort() %pm>% sort() %pm>%
vector_and(quotes = TRUE) vector_and(quotes = TRUE)
warning_( cur_col <- get_current_column()
"in `as.disk()`: ", na_after - na_before, " results truncated (", warning_("in `as.disk()`: ", na_after - na_before, " result",
round(((na_after - na_before) / length(x)) * 100), ifelse(na_after - na_before > 1, "s", ""),
"%) that were invalid disk zones: ", ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
list_missing " truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ",
list_missing,
call = FALSE
) )
} }
} }
R/mic.R
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@@ -228,11 +228,15 @@ as.mic <- function(x, na.rm = FALSE) {
unique() %pm>% unique() %pm>%
sort() %pm>% sort() %pm>%
vector_and(quotes = TRUE) vector_and(quotes = TRUE)
warning_("in `as.mic()`: ", na_after - na_before, " results truncated (", cur_col <- get_current_column()
round(((na_after - na_before) / length(x)) * 100), warning_("in `as.mic()`: ", na_after - na_before, " result",
"%) that were invalid MICs: ", ifelse(na_after - na_before > 1, "s", ""),
list_missing, ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
call = FALSE " truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid MICs: ",
list_missing,
call = FALSE
) )
} }