P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 18:22:02 +02:00
Code Releases Activity

(v1.6.0.9009) key_antibiotics update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-04-23 16:13:26 +02:00
parent 70b803dbb6
commit 5f9e7bd3ee
20 changed files with 100 additions and 98 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
R/first_isolate.R
View File

@ -42,7 +42,7 @@
#' @param type type to determine weighed isolates; can be `"keyantibiotics"` or `"points"`, see *Details*
#' @param ignore_I logical to indicate whether antibiotic interpretations with `"I"` will be ignored when `type = "keyantibiotics"`, see *Details*
#' @param points_threshold points until the comparison of key antibiotics will lead to inclusion of an isolate when `type = "points"`, see *Details*
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
#' @param info a [logical] to indicate info should be printed, defaults to `TRUE` only in interactive mode
#' @param include_unknown logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
#' @param include_untested_rsi logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `<rsi>` and consequently requires transforming columns with antibiotic results using [as.rsi()] first.
#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], or arguments passed on to [key_antibiotics()] when using [filter_first_weighted_isolate()]
@ -402,7 +402,7 @@ first_isolate <- function(x = NULL,
type = type_param,
ignore_I = ignore_I,
points_threshold = points_threshold,
info = info)
na.rm = TRUE)
# with key antibiotics
x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
x$newvar_row_index_sorted <= row.end &