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(v1.5.0.9039) handle first isolates for missing antibiograms

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dr. M.S. (Matthijs) Berends
2021-03-08 02:38:32 +01:00
parent 461793dc34
commit a7c9b4c295
21 changed files with 79 additions and 62 deletions
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17
R/first_isolate.R
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@ -37,13 +37,14 @@
#' @param col_keyantibiotics column name of the key antibiotics to determine first (weighted) isolates, see [key_antibiotics()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use `col_keyantibiotics = FALSE` to prevent this.
#' @param episode_days episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see *Source*.
#' @param testcodes_exclude character vector with test codes that should be excluded (case-insensitive)
#' @param icu_exclude logical whether ICU isolates should be excluded (rows with value `TRUE` in the column set with `col_icu`)
#' @param icu_exclude logical to indicate whether ICU isolates should be excluded (rows with value `TRUE` in the column set with `col_icu`)
#' @param specimen_group value in the column set with `col_specimen` to filter on
#' @param type type to determine weighed isolates; can be `"keyantibiotics"` or `"points"`, see *Details*
#' @param ignore_I logical to determine whether antibiotic interpretations with `"I"` will be ignored when `type = "keyantibiotics"`, 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 print progress
#' @param include_unknown logical to determine 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_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()]
#' @details
#' These functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*.
@ -159,6 +160,7 @@ first_isolate <- function(x = NULL,
points_threshold = 2,
info = interactive(),
include_unknown = FALSE,
include_untested_rsi = TRUE,
...) {
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
@ -188,6 +190,7 @@ first_isolate <- function(x = NULL,
meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(info, allow_class = "logical", has_length = 1)
meet_criteria(include_unknown, allow_class = "logical", has_length = 1)
meet_criteria(include_untested_rsi, allow_class = "logical", has_length = 1)
# remove data.table, grouping from tibbles, etc.
x <- as.data.frame(x, stringsAsFactors = FALSE)
@ -472,6 +475,14 @@ first_isolate <- function(x = NULL,
}
x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
# handle isolates without antibiogram
if (include_untested_rsi == FALSE && any(is.rsi(x))) {
rsi_all_NA <- which(unname(vapply(FUN.VALUE = logical(1),
as.data.frame(t(x[, is.rsi(x), drop = FALSE])),
function(rsi_values) all(is.na(rsi_values)))))
x[rsi_all_NA, "newvar_first_isolate"] <- FALSE
}
# arrange back according to original sorting again
x <- x[order(x$newvar_row_index), ]
rownames(x) <- NULL