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AMR/R/first_isolate.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Determine first (weighted) isolates
#'
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a [`data.frame`] containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class
#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
#' @param col_mo column name of the IDs of the microorganisms (see [as.mo()]), defaults to the first column of class [`mo`]. Values will be coerced using [as.mo()].
#' @param col_testcode column name of the test codes. Use `col_testcode = NULL` to **not** exclude certain test codes (like test codes for screening). In that case `testcodes_exclude` will be ignored.
#' @param col_specimen column name of the specimen type or group
#' @param col_icu column name of the logicals (`TRUE`/`FALSE`) whether a ward or department is an Intensive Care Unit (ICU)
#' @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 column `col_icu`)
#' @param specimen_group value in column `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 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 ... parameters passed on to the [first_isolate()] function
#' @details **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 [(ref)](https://www.ncbi.nlm.nih.gov/pubmed/17304462). 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 *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
#'
#' All isolates with a microbial ID of `NA` will be excluded as first isolate.
#'
#' The functions [filter_first_isolate()] and [filter_first_weighted_isolate()] are helper functions to quickly filter on first isolates. The function [filter_first_isolate()] is essentially equal to one of:
#' ```
#' x %>% filter(first_isolate(., ...))
#' ```
#' The function [filter_first_weighted_isolate()] is essentially equal to:
#' ```
#' x %>%
#' mutate(keyab = key_antibiotics(.)) %>%
#' mutate(only_weighted_firsts = first_isolate(x,
#' col_keyantibiotics = "keyab", ...)) %>%
#' filter(only_weighted_firsts == TRUE) %>%
#' select(-only_weighted_firsts, -keyab)
#' ```
#' @section Key antibiotics:
#' There are two ways to determine whether isolates can be included as first *weighted* isolates which will give generally the same results:
#'
#' 1. Using `type = "keyantibiotics"` and parameter `ignore_I`
#'
#' Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With `ignore_I = FALSE`, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the [key_antibiotics()] function.
#'
#' 2. Using `type = "points"` and parameter `points_threshold`
#'
#' A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds `points_threshold`, which default to `2`, an isolate will be (re)selected as a first weighted isolate.
#' @rdname first_isolate
#' @seealso [key_antibiotics()]
#' @export
#' @return A [`logical`] vector
#' @source Methodology of this function is strictly based on:
#'
#' **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition**, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
#' @inheritSection AMR Read more on our website!
#' @examples
#' # `example_isolates` is a dataset available in the AMR package.
#' # See ?example_isolates.
#'
#' \dontrun{
#' library(dplyr)
#' # Filter on first isolates:
#' example_isolates %>%
#' mutate(first_isolate = first_isolate(.)) %>%
#' filter(first_isolate == TRUE)
#'
#' # Now let's see if first isolates matter:
#' A <- example_isolates %>%
#' group_by(hospital_id) %>%
#' summarise(count = n_rsi(GEN), # gentamicin availability
#' resistance = resistance(GEN)) # gentamicin resistance
#'
#' B <- example_isolates %>%
#' filter_first_weighted_isolate() %>% # the 1st isolate filter
#' group_by(hospital_id) %>%
#' summarise(count = n_rsi(GEN), # gentamicin availability
#' resistance = resistance(GEN)) # gentamicin resistance
#'
#' # Have a look at A and B.
#' # B is more reliable because every isolate is counted only once.
#' # Gentamicin resistance in hospital D appears to be 3.7% higher than
#' # when you (erroneously) would have used all isolates for analysis.
#'
#'
#' ## OTHER EXAMPLES:
#'
#' # Short-hand versions:
#' example_isolates %>%
#' filter_first_isolate()
#'
#' example_isolates %>%
#' filter_first_weighted_isolate()
#'
#'
#' # set key antibiotics to a new variable
#' x$keyab <- key_antibiotics(x)
#'
#' x$first_isolate <- first_isolate(x)
#'
#' x$first_isolate_weighed <- first_isolate(x, col_keyantibiotics = 'keyab')
#'
#' x$first_blood_isolate <- first_isolate(x, specimen_group = "Blood")
#' }
first_isolate <- function(x,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
col_testcode = NULL,
col_specimen = NULL,
col_icu = NULL,
col_keyantibiotics = NULL,
episode_days = 365,
testcodes_exclude = NULL,
icu_exclude = FALSE,
specimen_group = NULL,
type = "keyantibiotics",
ignore_I = TRUE,
points_threshold = 2,
info = interactive(),
include_unknown = FALSE,
...) {
dots <- unlist(list(...))
if (length(dots) != 0) {
# backwards compatibility with old parameters
dots.names <- dots %>% names()
if ("filter_specimen" %in% dots.names) {
specimen_group <- dots[which(dots.names == "filter_specimen")]
}
if ("tbl" %in% dots.names) {
x <- dots[which(dots.names == "tbl")]
}
}
if (!is.data.frame(x)) {
stop("`x` must be a data.frame.", call. = FALSE)
}
# remove data.table, grouping from tibbles, etc.
x <- as.data.frame(x, stringsAsFactors = FALSE)
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
}
# -- date
if (is.null(col_date)) {
col_date <- search_type_in_df(x = x, type = "date")
if (is.null(col_date)) {
stop("`col_date` must be set.", call. = FALSE)
}
}
# convert to Date
dates <- as.Date(x[, col_date, drop = TRUE])
dates[is.na(dates)] <- as.Date("1970-01-01")
x[, col_date] <- dates
# -- patient id
if (is.null(col_patient_id)) {
if (all(c("First name", "Last name", "Sex") %in% colnames(x))) {
# WHONET support
x$patient_id <- paste(x$`First name`, x$`Last name`, x$Sex)
col_patient_id <- "patient_id"
message(font_blue(paste0("NOTE: Using combined columns `", font_bold("First name"), "`, `", font_bold("Last name"), "` and `", font_bold("Sex"), "` as input for `col_patient_id`")))
} else {
col_patient_id <- search_type_in_df(x = x, type = "patient_id")
}
if (is.null(col_patient_id)) {
stop("`col_patient_id` must be set.", call. = FALSE)
}
}
# -- key antibiotics
if (is.null(col_keyantibiotics)) {
col_keyantibiotics <- search_type_in_df(x = x, type = "keyantibiotics")
}
if (isFALSE(col_keyantibiotics)) {
col_keyantibiotics <- NULL
}
# -- specimen
if (is.null(col_specimen) & !is.null(specimen_group)) {
col_specimen <- search_type_in_df(x = x, type = "specimen")
}
if (isFALSE(col_specimen)) {
col_specimen <- NULL
}
# check if columns exist
check_columns_existance <- function(column, tblname = x) {
if (NROW(tblname) <= 1 | NCOL(tblname) <= 1) {
stop("Please check tbl for existance.")
}
if (!is.null(column)) {
if (!(column %in% colnames(tblname))) {
stop("Column `", column, "` not found.")
}
}
}
check_columns_existance(col_date)
check_columns_existance(col_patient_id)
check_columns_existance(col_mo)
check_columns_existance(col_testcode)
check_columns_existance(col_icu)
check_columns_existance(col_keyantibiotics)
# create original row index
x$newvar_row_index <- seq_len(nrow(x))
x$newvar_mo <- x %>% pull(col_mo) %>% as.mo()
x$newvar_genus_species <- paste(mo_genus(x$newvar_mo), mo_species(x$newvar_mo))
x$newvar_date <- x %>% pull(col_date)
x$newvar_patient_id <- x %>% pull(col_patient_id)
if (is.null(col_testcode)) {
testcodes_exclude <- NULL
}
# remove testcodes
if (!is.null(testcodes_exclude) & info == TRUE) {
message(font_black(paste0("[Criterion] Exclude test codes: ", toString(paste0("'", testcodes_exclude, "'")))))
}
if (is.null(col_specimen)) {
specimen_group <- NULL
}
# filter on specimen group and keyantibiotics when they are filled in
if (!is.null(specimen_group)) {
check_columns_existance(col_specimen, x)
if (info == TRUE) {
message(font_black(paste0("[Criterion] Exclude other than specimen group '", specimen_group, "'")))
}
}
if (!is.null(col_keyantibiotics)) {
x$newvar_key_ab <- x[, col_keyantibiotics, drop = TRUE]
}
if (is.null(testcodes_exclude)) {
testcodes_exclude <- ""
}
# arrange data to the right sorting
if (is.null(specimen_group)) {
x <- x[order(x$newvar_patient_id,
x$newvar_genus_species,
x$newvar_date), ]
rownames(x) <- NULL
row.start <- 1
row.end <- nrow(x)
} else {
# filtering on specimen and only analyse these rows to save time
x <- x[order(pull(x, col_specimen),
x$newvar_patient_id,
x$newvar_genus_species,
x$newvar_date), ]
rownames(x) <- NULL
suppressWarnings(
row.start <- which(x %>% pull(col_specimen) == specimen_group) %>% min(na.rm = TRUE)
)
suppressWarnings(
row.end <- which(x %>% pull(col_specimen) == specimen_group) %>% max(na.rm = TRUE)
)
}
# no isolates found
if (abs(row.start) == Inf | abs(row.end) == Inf) {
if (info == TRUE) {
message(paste("=> Found", font_bold("no isolates")))
}
return(rep(FALSE, nrow(x)))
}
# did find some isolates - add new index numbers of rows
x$newvar_row_index_sorted <- seq_len(nrow(x))
scope.size <- row.end - row.start + 1
identify_new_year <- function(x, episode_days) {
# I asked on StackOverflow:
# https://stackoverflow.com/questions/42122245/filter-one-row-every-year
if (length(x) == 1) {
return(TRUE)
}
indices <- integer(0)
start <- x[1]
ind <- 1
indices[ind] <- ind
for (i in 2:length(x)) {
if (isTRUE(as.numeric(x[i] - start) >= episode_days)) {
ind <- ind + 1
indices[ind] <- i
start <- x[i]
}
}
result <- rep(FALSE, length(x))
result[indices] <- TRUE
return(result)
}
# Analysis of first isolate ----
x$other_pat_or_mo <- if_else(x$newvar_patient_id == lag(x$newvar_patient_id) &
x$newvar_genus_species == lag(x$newvar_genus_species),
FALSE,
TRUE)
x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
x$more_than_episode_ago <- unname(unlist(lapply(unique(x$episode_group),
function(g,
df = x,
days = episode_days) {
identify_new_year(x = df[which(df$episode_group == g), "newvar_date"],
episode_days = days)
})))
weighted.notice <- ""
if (!is.null(col_keyantibiotics)) {
weighted.notice <- "weighted "
if (info == TRUE) {
if (type == "keyantibiotics") {
message(font_black(paste0("[Criterion] Base inclusion on key antibiotics, ",
ifelse(ignore_I == FALSE, "not ", ""),
"ignoring I")))
}
if (type == "points") {
message(font_black(paste0("[Criterion] Base inclusion on key antibiotics, using points threshold of "
, points_threshold)))
}
}
type_param <- type
x$other_key_ab <- !key_antibiotics_equal(y = x$newvar_key_ab,
z = lag(x$newvar_key_ab),
type = type_param,
ignore_I = ignore_I,
points_threshold = points_threshold,
info = info)
# with key antibiotics
x$newvar_first_isolate <- if_else(x$newvar_row_index_sorted >= row.start &
x$newvar_row_index_sorted <= row.end &
x$newvar_genus_species != "" &
(x$other_pat_or_mo | x$more_than_episode_ago | x$other_key_ab),
TRUE,
FALSE)
} else {
# no key antibiotics
x$newvar_first_isolate <- if_else(x$newvar_row_index_sorted >= row.start &
x$newvar_row_index_sorted <= row.end &
x$newvar_genus_species != "" &
(x$other_pat_or_mo | x$more_than_episode_ago),
TRUE,
FALSE)
}
# first one as TRUE
x[row.start, "newvar_first_isolate"] <- TRUE
# no tests that should be included, or ICU
if (!is.null(col_testcode)) {
x[which(x[, col_testcode] %in% tolower(testcodes_exclude)), "newvar_first_isolate"] <- FALSE
}
if (!is.null(col_icu)) {
if (icu_exclude == TRUE) {
message(font_black("[Criterion] Exclude isolates from ICU.\n"))
x[which(as.logical(x[, col_icu, drop = TRUE])), "newvar_first_isolate"] <- FALSE
} else {
message(font_black("[Criterion] Include isolates from ICU.\n"))
}
}
decimal.mark <- getOption("OutDec")
big.mark <- ifelse(decimal.mark != ",", ",", ".")
# handle empty microorganisms
if (any(x$newvar_mo == "UNKNOWN", na.rm = TRUE) & info == TRUE) {
message(font_blue(paste0("NOTE: ", ifelse(include_unknown == TRUE, "Included ", "Excluded "),
format(sum(x$newvar_mo == "UNKNOWN"),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'UNKNOWN' (column `", font_bold(col_mo), "`)")))
}
x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
# exclude all NAs
if (any(is.na(x$newvar_mo)) & info == TRUE) {
message(font_blue(paste0("NOTE: Excluded ", format(sum(is.na(x$newvar_mo)),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'NA' (column `", font_bold(col_mo), "`)")))
}
x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
# arrange back according to original sorting again
x <- x[order(x$newvar_row_index), ]
rownames(x) <- NULL
if (info == TRUE) {
n_found <- base::sum(x$newvar_first_isolate, na.rm = TRUE)
p_found_total <- percentage(n_found / nrow(x))
p_found_scope <- percentage(n_found / scope.size)
# mark up number of found
n_found <- base::format(n_found, big.mark = big.mark, decimal.mark = decimal.mark)
if (p_found_total != p_found_scope) {
msg_txt <- paste0("=> Found ",
font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
" (", p_found_scope, " within scope and ", p_found_total, " of total)")
} else {
msg_txt <- paste0("=> Found ",
font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
" (", p_found_total, " of total)")
}
message(font_black(msg_txt))
}
x$newvar_first_isolate
}
#' @rdname first_isolate
#' @export
filter_first_isolate <- function(x,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
...) {
subset(x, first_isolate(x = x,
col_date = col_date,
col_patient_id = col_patient_id,
col_mo = col_mo,
...))
}
#' @rdname first_isolate
#' @export
filter_first_weighted_isolate <- function(x,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
col_keyantibiotics = NULL,
...) {
y <- x
if (is.null(col_keyantibiotics)) {
# first try to look for it
col_keyantibiotics <- search_type_in_df(x = x, type = "keyantibiotics")
# still NULL? Then create it since we are calling filter_first_WEIGHTED_isolate()
if (is.null(col_keyantibiotics)) {
y$keyab <- suppressMessages(key_antibiotics(x,
col_mo = col_mo,
...))
col_keyantibiotics <- "keyab"
}
}
subset(x, first_isolate(x = y,
col_date = col_date,
col_patient_id = col_patient_id,
col_mo = col_mo,
col_keyantibiotics = col_keyantibiotics,
...))
}
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