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(v0.7.1.9102) lintr

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dr. M.S. (Matthijs) Berends
2019-10-11 17:21:02 +02:00
parent 59af355a89
commit 00cdb498a0
65 changed files with 620 additions and 812 deletions
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208
R/first_isolate.R
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@ -124,39 +124,11 @@
#' # set key antibiotics to a new variable
#' x$keyab <- key_antibiotics(x)
#'
#' x$first_isolate <-
#' first_isolate(x)
#' x$first_isolate <- first_isolate(x)
#'
#' x$first_isolate_weighed <-
#' first_isolate(x,
#' col_keyantibiotics = 'keyab')
#' x$first_isolate_weighed <- first_isolate(x, col_keyantibiotics = 'keyab')
#'
#' x$first_blood_isolate <-
#' first_isolate(x,
#' specimen_group = 'Blood')
#'
#' x$first_blood_isolate_weighed <-
#' first_isolate(x,
#' specimen_group = 'Blood',
#' col_keyantibiotics = 'keyab')
#'
#' x$first_urine_isolate <-
#' first_isolate(x,
#' specimen_group = 'Urine')
#'
#' x$first_urine_isolate_weighed <-
#' first_isolate(x,
#' specimen_group = 'Urine',
#' col_keyantibiotics = 'keyab')
#'
#' x$first_resp_isolate <-
#' first_isolate(x,
#' specimen_group = 'Respiratory')
#'
#' x$first_resp_isolate_weighed <-
#' first_isolate(x,
#' specimen_group = 'Respiratory',
#' col_keyantibiotics = 'keyab')
#' x$first_blood_isolate <- first_isolate(x, specimen_group = "Blood")
#' }
first_isolate <- function(x,
col_date = NULL,
@ -176,23 +148,23 @@ first_isolate <- function(x,
info = TRUE,
include_unknown = FALSE,
...) {
if (!is.data.frame(x)) {
stop("`x` must be a data.frame.", call. = 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 ("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 ("tbl" %in% dots.names) {
x <- dots[which(dots.names == "tbl")]
}
}
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
@ -201,7 +173,7 @@ first_isolate <- function(x,
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")
@ -213,14 +185,14 @@ first_isolate <- function(x,
dates <- x %>% pull(col_date) %>% as.Date()
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", "Identification number") %in% colnames(x))) {
if (all(c("First name", "Last name", "Sex") %in% colnames(x))) {
# WHONET support
x <- x %>% mutate(patient_id = paste(`First name`, `Last name`, Sex))
col_patient_id <- "patient_id"
message(blue(paste0("NOTE: Using combined columns `", bold("First name"), "`, `", bold("Last name"), "` and `", bold("Sex"), "` as input for `col_patient_id`.")))
message(blue(paste0("NOTE: Using combined columns `", bold("First name"), "`, `", bold("Last name"), "` and `", bold("Sex"), "` as input for `col_patient_id`")))
} else {
col_patient_id <- search_type_in_df(x = x, type = "patient_id")
}
@ -228,7 +200,7 @@ first_isolate <- function(x,
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")
@ -236,7 +208,7 @@ first_isolate <- function(x,
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")
@ -244,30 +216,30 @@ first_isolate <- function(x,
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.')
stop("Please check tbl for existance.")
}
if (!is.null(column)) {
if (!(column %in% colnames(tblname))) {
stop('Column `', column, '` not found.')
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 new dataframe with original row index
x <- x %>%
mutate(newvar_row_index = 1:nrow(x),
mutate(newvar_row_index = seq_len(nrow(x)),
newvar_mo = x %>% pull(col_mo) %>% as.mo(),
newvar_genus_species = paste(mo_genus(newvar_mo), mo_species(newvar_mo)),
newvar_date = x %>% pull(col_date),
@ -278,41 +250,41 @@ first_isolate <- function(x,
}
# remove testcodes
if (!is.null(testcodes_exclude) & info == TRUE) {
cat('[Criterion] Excluded test codes:\n', toString(testcodes_exclude), '\n')
message(blue(paste0("[Criterion] Excluded test codes: ", toString(testcodes_exclude))))
}
if (is.null(col_icu)) {
icu_exclude <- FALSE
} else {
x <- x %>%
mutate(col_icu = x %>% pull(col_icu) %>% as.logical())
}
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) {
cat('[Criterion] Excluded other than specimen group \'', specimen_group, '\'\n', sep = '')
message(blue(paste0("[Criterion] Excluded other than specimen group '", specimen_group, "'")))
}
}
if (!is.null(col_keyantibiotics)) {
x <- x %>% mutate(key_ab = x %>% pull(col_keyantibiotics))
}
if (is.null(testcodes_exclude)) {
testcodes_exclude <- ''
testcodes_exclude <- ""
}
# arrange data to the right sorting
if (is.null(specimen_group)) {
# not filtering on specimen
if (icu_exclude == FALSE) {
if (info == TRUE & !is.null(col_icu)) {
cat('[Criterion] Included isolates from ICU.\n')
message(blue("[Criterion] Included isolates from ICU"))
}
x <- x %>%
arrange(newvar_patient_id,
@ -322,14 +294,14 @@ first_isolate <- function(x,
row.end <- nrow(x)
} else {
if (info == TRUE) {
cat('[Criterion] Excluded isolates from ICU.\n')
message(blue("[Criterion] Excluded isolates from ICU"))
}
x <- x %>%
arrange_at(c(col_icu,
"newvar_patient_id",
"newvar_genus_species",
"newvar_date"))
suppressWarnings(
row.start <- which(x %>% pull(col_icu) == FALSE) %>% min(na.rm = TRUE)
)
@ -337,12 +309,12 @@ first_isolate <- function(x,
row.end <- which(x %>% pull(col_icu) == FALSE) %>% max(na.rm = TRUE)
)
}
} else {
# filtering on specimen and only analyse these row to save time
if (icu_exclude == FALSE) {
if (info == TRUE & !is.null(col_icu)) {
cat('[Criterion] Included isolates from ICU.\n')
message(blue("[Criterion] Included isolates from ICU.\n"))
}
x <- x %>%
arrange_at(c(col_specimen,
@ -357,7 +329,7 @@ first_isolate <- function(x,
)
} else {
if (info == TRUE) {
cat('[Criterion] Excluded isolates from ICU.\n')
message(blue("[Criterion] Excluded isolates from ICU"))
}
x <- x %>%
arrange_at(c(col_icu,
@ -366,17 +338,19 @@ first_isolate <- function(x,
"newvar_genus_species",
"newvar_date"))
suppressWarnings(
row.start <- which(x %>% pull(col_specimen) == specimen_group
& x %>% pull(col_icu) == FALSE) %>% min(na.rm = TRUE)
row.start <- min(which(x %>% pull(col_specimen) == specimen_group
& x %>% pull(col_icu) == FALSE),
na.rm = TRUE)
)
suppressWarnings(
row.end <- which(x %>% pull(col_specimen) == specimen_group
& x %>% pull(col_icu) == FALSE) %>% max(na.rm = TRUE)
row.end <- max(which(x %>% pull(col_specimen) == specimen_group &
x %>% pull(col_icu) == FALSE),
na.rm = TRUE)
)
}
}
# no isolates found
if (abs(row.start) == Inf | abs(row.end) == Inf) {
if (info == TRUE) {
@ -386,21 +360,11 @@ first_isolate <- function(x,
}
# did find some isolates - add new index numbers of rows
x <- x %>% mutate(newvar_row_index_sorted = 1:nrow(.))
# suppress warnings because dplyr wants us to use library(dplyr) when using filter(row_number())
#suppressWarnings(
scope.size <- row.end - row.start + 1
# x %>%
# filter(
# row_number() %>% between(row.start,
# row.end),
# newvar_genus != "",
# newvar_species != "") %>%
# nrow()
# )
identify_new_year = function(x, episode_days) {
x <- x %>% mutate(newvar_row_index_sorted = seq_len(nrow(.)))
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) {
@ -421,7 +385,7 @@ first_isolate <- function(x,
result[indices] <- TRUE
return(result)
}
# Analysis of first isolate ----
all_first <- x %>%
mutate(other_pat_or_mo = if_else(newvar_patient_id == lag(newvar_patient_id)
@ -433,21 +397,19 @@ first_isolate <- function(x,
mutate(more_than_episode_ago = identify_new_year(x = newvar_date,
episode_days = episode_days)) %>%
ungroup()
weighted.notice <- ''
weighted.notice <- ""
if (!is.null(col_keyantibiotics)) {
weighted.notice <- 'weighted '
weighted.notice <- "weighted "
if (info == TRUE) {
if (type == 'keyantibiotics') {
cat('[Criterion] Inclusion based on key antibiotics, ')
if (ignore_I == FALSE) {
cat('not ')
}
cat('ignoring I.\n')
if (type == "keyantibiotics") {
message(blue(paste0("[Criterion] Inclusion based on key antibiotics, ",
ifelse(ignore_I == FALSE, "not ", ""),
"ignoring I")))
}
if (type == 'points') {
cat(paste0('[Criterion] Inclusion based on key antibiotics, using points threshold of '
, points_threshold, '.\n'))
if (type == "points") {
message(blue(paste0("[Criterion] Inclusion based on key antibiotics, using points threshold of "
, points_threshold)))
}
}
type_param <- type
@ -473,24 +435,24 @@ first_isolate <- function(x,
# no key antibiotics
all_first <- all_first %>%
mutate(
real_first_isolate =
if_else(
newvar_row_index_sorted %>% between(row.start, row.end)
& newvar_genus_species != ""
& (other_pat_or_mo | more_than_episode_ago),
TRUE,
FALSE))
real_first_isolate =
if_else(
newvar_row_index_sorted %>% between(row.start, row.end)
& newvar_genus_species != ""
& (other_pat_or_mo | more_than_episode_ago),
TRUE,
FALSE))
}
# first one as TRUE
all_first[row.start, 'real_first_isolate'] <- TRUE
all_first[row.start, "real_first_isolate"] <- TRUE
# no tests that should be included, or ICU
if (!is.null(col_testcode)) {
all_first[which(all_first[, col_testcode] %in% tolower(testcodes_exclude)), 'real_first_isolate'] <- FALSE
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
all_first[which(all_first[, col_icu] == TRUE), "real_first_isolate"] <- FALSE
}
decimal.mark <- getOption("OutDec")
@ -498,26 +460,20 @@ first_isolate <- function(x,
# handle empty microorganisms
if (any(all_first$newvar_mo == "UNKNOWN", na.rm = TRUE) & info == TRUE) {
if (include_unknown == TRUE) {
message(blue(paste0("NOTE: Included ", format(sum(all_first$newvar_mo == "UNKNOWN"),
decimal.mark = decimal.mark, big.mark = big.mark),
' isolates with a microbial ID "UNKNOWN" (column `', bold(col_mo), '`).')))
} else {
message(blue(paste0("NOTE: Excluded ", format(sum(all_first$newvar_mo == "UNKNOWN"),
decimal.mark = decimal.mark, big.mark = big.mark),
' isolates with a microbial ID "UNKNOWN" (column `', bold(col_mo), '`).')))
}
message(blue(paste0("NOTE: ", ifelse(include_unknown == TRUE, "Included ", "Excluded "),
format(sum(all_first$newvar_mo == "UNKNOWN"),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'UNKNOWN' (column `", bold(col_mo), "`)")))
}
all_first[which(all_first$newvar_mo == "UNKNOWN"), 'real_first_isolate'] <- include_unknown
all_first[which(all_first$newvar_mo == "UNKNOWN"), "real_first_isolate"] <- include_unknown
# exclude all NAs
if (any(is.na(all_first$newvar_mo)) & info == TRUE) {
message(blue(paste0("NOTE: Excluded ", format(sum(is.na(all_first$newvar_mo)),
decimal.mark = decimal.mark, big.mark = big.mark),
' isolates with a microbial ID "NA" (column `', bold(col_mo), '`).')))
" isolates with a microbial ID 'NA' (column `", bold(col_mo), "`)")))
}
all_first[which(is.na(all_first$newvar_mo)), 'real_first_isolate'] <- FALSE
all_first[which(is.na(all_first$newvar_mo)), "real_first_isolate"] <- FALSE
# arrange back according to original sorting again
all_first <- all_first %>%
@ -541,9 +497,9 @@ first_isolate <- function(x,
}
base::message(msg_txt)
}
all_first
}
#' @rdname first_isolate
@ -580,5 +536,5 @@ filter_first_weighted_isolate <- function(x,
col_mo = col_mo,
col_keyantibiotics = "keyab",
...))
x[which(tbl_keyab$firsts == TRUE),]
x[which(tbl_keyab$firsts == TRUE), ]
}