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replaced bactid by mo

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dr. M.S. (Matthijs) Berends
2018-08-31 13:36:19 +02:00
parent 98ff131680
commit 5965d3c794
41 changed files with 786 additions and 411 deletions
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30
R/first_isolate.R
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@ -22,7 +22,7 @@
#' @param tbl a \code{data.frame} containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab)
#' @param col_patient_id column name of the unique IDs of the patients
#' @param col_bactid column name of the unique IDs of the microorganisms: \code{bactid}'s. If this column has another class than \code{"bactid"}, values will be coerced using \code{\link{as.bactid}}.
#' @param col_mo column name of the unique IDs of the microorganisms, see \code{\link{mo}}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.
#' @param col_testcode column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.
#' @param col_specimen column name of the specimen type or group
#' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)
@ -36,8 +36,9 @@
#' @param ignore_I logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details
#' @param points_threshold points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details
#' @param info print progress
#' @param col_genus (deprecated, use \code{col_bactid} instead) column name of the genus of the microorganisms
#' @param col_species (deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms
#' @param col_bactid (deprecated, use \code{col_mo} instead)
#' @param col_genus (deprecated, use \code{col_mo} instead) column name of the genus of the microorganisms
#' @param col_species (deprecated, use \code{col_mo} instead) column name of the species of the microorganisms
#' @details \strong{WHY THIS IS SO IMPORTANT} \cr
#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode \href{https://www.ncbi.nlm.nih.gov/pubmed/17304462}{[1]}. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would be \href{https://en.wikipedia.org/wiki/Selection_bias}{selection bias}.
#' @section Key antibiotics:
@ -63,7 +64,7 @@
#' mutate(first_isolate = first_isolate(.,
#' col_date = "date",
#' col_patient_id = "patient_id",
#' col_bactid = "bactid"))
#' col_mo = "mo"))
#'
#' # Now let's see if first isolates matter:
#' A <- my_patients %>%
@ -126,7 +127,7 @@
first_isolate <- function(tbl,
col_date,
col_patient_id,
col_bactid = NA,
col_mo = NA,
col_testcode = NA,
col_specimen = NA,
col_icu = NA,
@ -140,12 +141,17 @@ first_isolate <- function(tbl,
ignore_I = TRUE,
points_threshold = 2,
info = TRUE,
col_bactid = NA,
col_genus = NA,
col_species = NA) {
if (!is.na(col_bactid)) {
col_mo <- col_bactid
warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
}
# bactid OR genus+species must be available
if (is.na(col_bactid) & (is.na(col_genus) | is.na(col_species))) {
stop('`col_bactid` or both `col_genus` and `col_species` must be available.')
if (is.na(col_mo) & (is.na(col_genus) | is.na(col_species))) {
stop('`col_mo` or both `col_genus` and `col_species` must be available.')
}
# check if columns exist
@ -163,19 +169,19 @@ first_isolate <- function(tbl,
check_columns_existance(col_date)
check_columns_existance(col_patient_id)
check_columns_existance(col_bactid)
check_columns_existance(col_mo)
check_columns_existance(col_genus)
check_columns_existance(col_species)
check_columns_existance(col_testcode)
check_columns_existance(col_icu)
check_columns_existance(col_keyantibiotics)
if (!is.na(col_bactid)) {
if (!tbl %>% pull(col_bactid) %>% is.bactid()) {
warning("Improve integrity of the `", col_bactid, "` column by transforming it with 'as.bactid'.")
if (!is.na(col_mo)) {
if (!tbl %>% pull(col_mo) %>% is.mo()) {
warning("Improve integrity of the `", col_mo, "` column by transforming it with 'as.mo'.")
}
# join to microorganisms data set
tbl <- tbl %>% left_join_microorganisms(by = col_bactid)
tbl <- tbl %>% left_join_microorganisms(by = col_mo)
col_genus <- "genus"
col_species <- "species"
}