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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

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dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
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6
R/guess_ab_col.R
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@ -23,7 +23,7 @@
#'
#' This tries to find a column name in a data set based on information from the [antibiotics] data set. Also supports WHONET abbreviations.
#' @inheritSection lifecycle Maturing lifecycle
#' @param x a [`data.frame`]
#' @param x a [data.frame]
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
#' @param verbose a logical to indicate whether additional info should be printed
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. **Longer columns names take precendence over shorter column names.**
@ -82,7 +82,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
} else {
# sort colnames on length - longest first
cols <- colnames(x[, x %>% colnames() %>% nchar() %>% order() %>% rev()])
cols <- colnames(x[, x %pm>% colnames() %pm>% nchar() %pm>% order() %pm>% rev()])
df_trans <- data.frame(cols = cols,
abs = suppressWarnings(as.ab(cols)),
stringsAsFactors = FALSE)
@ -147,7 +147,7 @@ get_column_abx <- function(x,
names(x) <- df_trans$abcode
# add from self-defined dots (...):
# such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
# such as get_column_abx(example_isolates %pm>% rename(thisone = AMX), amox = "thisone")
dots <- list(...)
if (length(dots) > 0) {
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))