# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # AUTHORS # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # # LICENCE # # This program is free software; you can redistribute it and/or modify # # it under the terms of the GNU General Public License version 2.0, # # as published by the Free Software Foundation. # # # # This program is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # GNU General Public License for more details. # # ==================================================================== # #' Determine first (weighted) isolates #' #' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. #' @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_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) #' @param col_keyantibiotics column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation. #' @param episode_days episode in days after which a genus/species combination will be determined as 'first isolate' again #' @param testcodes_exclude character vector with test codes that should be excluded (case-insensitive) #' @param icu_exclude logical whether ICU isolates should be excluded #' @param filter_specimen specimen group or type that should be excluded #' @param output_logical return output as \code{logical} (will else be the values \code{0} or \code{1}) #' @param type type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see Details #' @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_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: #' There are two ways to determine whether isolates can be included as first \emph{weighted} isolates which will give generally the same results: \cr #' #' \strong{1. Using} \code{type = "keyantibiotics"} \strong{and parameter} \code{ignore_I} \cr #' Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{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. \cr #' #' \strong{2. Using} \code{type = "points"} \strong{and parameter} \code{points_threshold} \cr #' 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 \code{points_threshold}, an isolate will be (re)selected as a first weighted isolate. #' @keywords isolate isolates first #' @seealso \code{\link{key_antibiotics}} #' @export #' @importFrom dplyr arrange_at lag between row_number filter mutate arrange #' @return A vector to add to table, see Examples. #' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. #' @examples #' # septic_patients is a dataset available in the AMR package. It is true, genuine data. #' ?septic_patients #' #' library(dplyr) #' my_patients <- septic_patients %>% #' mutate(first_isolate = first_isolate(., #' col_date = "date", #' col_patient_id = "patient_id", #' col_mo = "mo")) #' #' # Now let's see if first isolates matter: #' A <- my_patients %>% #' group_by(hospital_id) %>% #' summarise(count = n_rsi(gent), # gentamicin availability #' resistance = portion_IR(gent)) # gentamicin resistance #' #' B <- my_patients %>% #' filter(first_isolate == TRUE) %>% # the 1st isolate filter #' group_by(hospital_id) %>% #' summarise(count = n_rsi(gent), # gentamicin availability #' resistance = portion_IR(gent)) # gentamicin resistance #' #' # Have a look at A and B. #' # B is more reliable because every isolate is only counted once. #' # Gentamicin resitance in hospital D appears to be 5.4% higher than #' # when you (erroneously) would have used all isolates! #' #' ## OTHER EXAMPLES: #' #' \dontrun{ #' #' # set key antibiotics to a new variable #' tbl$keyab <- key_antibiotics(tbl) #' #' tbl$first_isolate <- #' first_isolate(tbl) #' #' tbl$first_isolate_weighed <- #' first_isolate(tbl, #' col_keyantibiotics = 'keyab') #' #' tbl$first_blood_isolate <- #' first_isolate(tbl, #' filter_specimen = 'Blood') #' #' tbl$first_blood_isolate_weighed <- #' first_isolate(tbl, #' filter_specimen = 'Blood', #' col_keyantibiotics = 'keyab') #' #' tbl$first_urine_isolate <- #' first_isolate(tbl, #' filter_specimen = 'Urine') #' #' tbl$first_urine_isolate_weighed <- #' first_isolate(tbl, #' filter_specimen = 'Urine', #' col_keyantibiotics = 'keyab') #' #' tbl$first_resp_isolate <- #' first_isolate(tbl, #' filter_specimen = 'Respiratory') #' #' tbl$first_resp_isolate_weighed <- #' first_isolate(tbl, #' filter_specimen = 'Respiratory', #' col_keyantibiotics = 'keyab') #' } first_isolate <- function(tbl, col_date, col_patient_id, col_mo = NA, col_testcode = NA, col_specimen = NA, col_icu = NA, col_keyantibiotics = NA, episode_days = 365, testcodes_exclude = '', icu_exclude = FALSE, filter_specimen = NA, output_logical = TRUE, type = "keyantibiotics", 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_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 check_columns_existance <- function(column, tblname = tbl) { if (NROW(tblname) <= 1 | NCOL(tblname) <= 1) { stop('Please check tbl for existance.') } if (!is.na(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_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_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_mo) col_genus <- "genus" col_species <- "species" } if (is.na(col_testcode)) { testcodes_exclude <- NA } # remove testcodes if (!is.na(testcodes_exclude[1]) & testcodes_exclude[1] != '' & info == TRUE) { cat('[Criteria] Excluded test codes:\n', toString(testcodes_exclude), '\n') } if (is.na(col_icu)) { icu_exclude <- FALSE } else { tbl <- tbl %>% mutate(col_icu = tbl %>% pull(col_icu) %>% as.logical()) } if (is.na(col_specimen)) { filter_specimen <- '' } # filter on specimen group and keyantibiotics when they are filled in if (!is.na(filter_specimen) & filter_specimen != '') { check_columns_existance(col_specimen, tbl) if (info == TRUE) { cat('[Criteria] Excluded other than specimen group \'', filter_specimen, '\'\n', sep = '') } } else { filter_specimen <- '' } if (col_keyantibiotics %in% c(NA, '')) { col_keyantibiotics <- '' } else { tbl <- tbl %>% mutate(key_ab = tbl %>% pull(col_keyantibiotics)) } if (is.na(testcodes_exclude[1])) { testcodes_exclude <- '' } # create new dataframe with original row index and right sorting tbl <- tbl %>% mutate(first_isolate_row_index = 1:nrow(tbl), date_lab = tbl %>% pull(col_date), patient_id = tbl %>% pull(col_patient_id), species = tbl %>% pull(col_species), genus = tbl %>% pull(col_genus)) %>% mutate(species = if_else(is.na(species) | species == "(no MO)", "", species), genus = if_else(is.na(genus) | genus == "(no MO)", "", genus)) if (filter_specimen == '') { if (icu_exclude == FALSE) { if (info == TRUE & !is.na(col_icu)) { cat('[Criteria] Included isolates from ICU.\n') } tbl <- tbl %>% arrange_at(c(col_patient_id, col_genus, col_species, col_date)) row.start <- 1 row.end <- nrow(tbl) } else { if (info == TRUE) { cat('[Criteria] Excluded isolates from ICU.\n') } tbl <- tbl %>% arrange_at(c(col_icu, col_patient_id, col_genus, col_species, col_date)) suppressWarnings( row.start <- which(tbl %>% pull(col_icu) == FALSE) %>% min(na.rm = TRUE) ) suppressWarnings( row.end <- which(tbl %>% pull(col_icu) == FALSE) %>% max(na.rm = TRUE) ) } } else { # sort on specimen and only analyse these row to save time if (icu_exclude == FALSE) { if (info == TRUE & !is.na(col_icu)) { cat('[Criteria] Included isolates from ICU.\n') } tbl <- tbl %>% arrange_at(c(col_specimen, col_patient_id, col_genus, col_species, col_date)) suppressWarnings( row.start <- which(tbl %>% pull(col_specimen) == filter_specimen) %>% min(na.rm = TRUE) ) suppressWarnings( row.end <- which(tbl %>% pull(col_specimen) == filter_specimen) %>% max(na.rm = TRUE) ) } else { if (info == TRUE) { cat('[Criteria] Excluded isolates from ICU.\n') } tbl <- tbl %>% arrange_at(c(col_icu, col_specimen, col_patient_id, col_genus, col_species, col_date)) suppressWarnings( row.start <- which(tbl %>% pull(col_specimen) == filter_specimen & tbl %>% pull(col_icu) == FALSE) %>% min(na.rm = TRUE) ) suppressWarnings( row.end <- which(tbl %>% pull(col_specimen) == filter_specimen & tbl %>% pull(col_icu) == FALSE) %>% max(na.rm = TRUE) ) } } if (abs(row.start) == Inf | abs(row.end) == Inf) { if (info == TRUE) { message('No isolates found.') } # NA's where genus is unavailable tbl <- tbl %>% mutate(real_first_isolate = if_else(genus == '', NA, FALSE)) if (output_logical == FALSE) { tbl$real_first_isolate <- tbl %>% pull(real_first_isolate) %>% as.integer() } return(tbl %>% pull(real_first_isolate)) } # suppress warnings because dplyr want us to use library(dplyr) when using filter(row_number()) suppressWarnings( scope.size <- tbl %>% filter( row_number() %>% between(row.start, row.end), genus != '') %>% nrow() ) # Analysis of first isolate ---- all_first <- tbl %>% mutate(other_pat_or_mo = if_else(patient_id == lag(patient_id) & genus == lag(genus) & species == lag(species), FALSE, TRUE), days_diff = 0) %>% mutate(days_diff = if_else(other_pat_or_mo == FALSE, (date_lab - lag(date_lab)) + lag(days_diff), 0)) weighted.notice <- '' if (col_keyantibiotics != '') { weighted.notice <- 'weighted ' if (info == TRUE) { if (type == 'keyantibiotics') { cat('[Criteria] Inclusion based on key antibiotics, ') if (ignore_I == FALSE) { cat('not ') } cat('ignoring I.\n') } if (type == 'points') { cat(paste0('[Criteria] Inclusion based on key antibiotics, using points threshold of ' , points_threshold, '.\n')) } } type_param <- type # suppress warnings because dplyr want us to use library(dplyr) when using filter(row_number()) suppressWarnings( all_first <- all_first %>% mutate(key_ab_lag = lag(key_ab)) %>% mutate(key_ab_other = !key_antibiotics_equal(x = key_ab, y = key_ab_lag, type = type_param, ignore_I = ignore_I, points_threshold = points_threshold, info = info)) %>% mutate( real_first_isolate = if_else( between(row_number(), row.start, row.end) & genus != '' & (other_pat_or_mo | days_diff >= episode_days | key_ab_other), TRUE, FALSE)) ) } else { # suppress warnings because dplyr want us to use library(dplyr) when using filter(row_number()) suppressWarnings( all_first <- all_first %>% mutate( real_first_isolate = if_else( between(row_number(), row.start, row.end) & genus != '' & (other_pat_or_mo | days_diff >= episode_days), TRUE, FALSE)) ) } # first one as TRUE all_first[row.start, 'real_first_isolate'] <- TRUE # no tests that should be included, or ICU if (!is.na(col_testcode)) { all_first[which(all_first[, col_testcode] %in% tolower(testcodes_exclude)), 'real_first_isolate'] <- FALSE } if (icu_exclude == TRUE) { all_first[which(all_first[, col_icu] == TRUE), 'real_first_isolate'] <- FALSE } # NA's where genus is unavailable all_first <- all_first %>% mutate(real_first_isolate = if_else(genus %in% c('', '(no MO)', NA), NA, real_first_isolate)) all_first <- all_first %>% arrange(first_isolate_row_index) %>% pull(real_first_isolate) if (info == TRUE) { message(paste0('Found ', all_first %>% sum(na.rm = TRUE), ' first ', weighted.notice, 'isolates (', (all_first %>% sum(na.rm = TRUE) / scope.size) %>% percent(), ' of isolates in scope [where genus was not empty] and ', (all_first %>% sum(na.rm = TRUE) / tbl %>% nrow()) %>% percent(), ' of total)')) } if (output_logical == FALSE) { all_first <- all_first %>% as.integer() } all_first }