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use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

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dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
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61
R/first_isolate.R
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@ -33,7 +33,7 @@
#' @param x a [data.frame] containing isolates. Can be left blank for automatic determination, see *Examples*.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column 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_mo column name of the names or codes 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 (such as 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). This can also be a [logical] vector with the same length as rows in `x`.
@ -71,17 +71,14 @@
#' | **Isolate-based** | `first_isolate(x, method = "isolate-based")` |
#' | *(= all isolates)* | |
#' | | |
#' | | |
#' | **Patient-based** | `first_isolate(x, method = "patient-based")` |
#' | *(= first isolate per patient)* | |
#' | | |
#' | | |
#' | **Episode-based** | `first_isolate(x, method = "episode-based")`, or: |
#' | *(= first isolate per episode)* | |
#' | - 7-Day interval from initial isolate | - `first_isolate(x, method = "e", episode_days = 7)` |
#' | - 30-Day interval from initial isolate | - `first_isolate(x, method = "e", episode_days = 30)` |
#' | | |
#' | | |
#' | **Phenotype-based** | `first_isolate(x, method = "phenotype-based")`, or: |
#' | *(= first isolate per phenotype)* | |
#' | - Major difference in any antimicrobial result | - `first_isolate(x, type = "points")` |
@ -133,7 +130,7 @@
#' # `example_isolates` is a data set available in the AMR package.
#' # See ?example_isolates.
#'
#' example_isolates[first_isolate(), ]
#' example_isolates[first_isolate(info = TRUE), ]
#' \donttest{
#' # get all first Gram-negatives
#' example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
@ -141,7 +138,7 @@
#' if (require("dplyr")) {
#' # filter on first isolates using dplyr:
#' example_isolates %>%
#' filter(first_isolate())
#' filter(first_isolate(info = TRUE))
#' }
#' if (require("dplyr")) {
#' # short-hand version:
@ -152,7 +149,7 @@
#' # flag the first isolates per group:
#' example_isolates %>%
#' group_by(ward) %>%
#' mutate(first = first_isolate()) %>%
#' mutate(first = first_isolate(info = FALSE)) %>%
#' select(ward, date, patient, mo, first)
#' }
#' }
@ -394,17 +391,17 @@ first_isolate <- function(x = NULL,
} else {
# filtering on specimen and only analyse these rows to save time
x <- x[order(
pm_pull(x, col_specimen),
pull(x, col_specimen),
x$newvar_patient_id,
x$newvar_genus_species,
x$newvar_date
), ]
rownames(x) <- NULL
suppressWarnings(
row.start <- which(x %pm>% pm_pull(col_specimen) == specimen_group) %pm>% min(na.rm = TRUE)
row.start <- which(x %>% pull(col_specimen) == specimen_group) %>% min(na.rm = TRUE)
)
suppressWarnings(
row.end <- which(x %pm>% pm_pull(col_specimen) == specimen_group) %pm>% max(na.rm = TRUE)
row.end <- which(x %>% pull(col_specimen) == specimen_group) %>% max(na.rm = TRUE)
)
}
@ -427,7 +424,7 @@ first_isolate <- function(x = NULL,
}
return(TRUE)
}
if (length(c(row.start:row.end)) == pm_n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
if (length(c(row.start:row.end)) == n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
if (isTRUE(info)) {
message_("=> Found ", font_bold(paste(length(c(row.start:row.end)), "first isolates")),
", as all isolates were different microbial species",
@ -465,7 +462,7 @@ first_isolate <- function(x = NULL,
}
}
x$other_pat_or_mo <- !(x$newvar_patient_id == pm_lag(x$newvar_patient_id) & x$newvar_genus_species == pm_lag(x$newvar_genus_species))
x$other_pat_or_mo <- !(x$newvar_patient_id == lag(x$newvar_patient_id) & x$newvar_genus_species == lag(x$newvar_genus_species))
x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
x$more_than_episode_ago <- unlist(
@ -485,29 +482,21 @@ first_isolate <- function(x = NULL,
# with key antibiotics
x$other_key_ab <- !antimicrobials_equal(
y = x$newvar_key_ab,
z = pm_lag(x$newvar_key_ab),
z = lag(x$newvar_key_ab),
type = type,
ignore_I = ignore_I,
points_threshold = points_threshold
)
x$newvar_first_isolate <- pm_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
)
x$newvar_first_isolate <- x$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$other_key_ab)
} else {
# no key antibiotics
x$newvar_first_isolate <- pm_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$more_than_episode_ago),
TRUE,
FALSE
)
x$newvar_first_isolate <- 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)
}
# first one as TRUE
@ -518,12 +507,14 @@ first_isolate <- function(x = NULL,
}
if (!is.null(col_icu)) {
if (icu_exclude == TRUE) {
message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
add_fn = font_black,
as_note = FALSE
)
if (isTRUE(info)) {
message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
add_fn = font_black,
as_note = FALSE
)
}
x[which(col_icu), "newvar_first_isolate"] <- FALSE
} else {
} else if (isTRUE(info)) {
message_("Including isolates from ICU.",
add_fn = font_black,
as_note = FALSE
@ -532,7 +523,7 @@ first_isolate <- function(x = NULL,
}
decimal.mark <- getOption("OutDec")
big.mark <- ifelse(decimal.mark != ",", ",", ".")
big.mark <- ifelse(decimal.mark != ",", ",", " ")
if (isTRUE(info)) {
# print group name if used in dplyr::group_by()