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This commit is contained in:
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions

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@ -95,20 +95,17 @@
#' # dplyr -------------------------------------------------------------------
#' \donttest{
#' if (require("dplyr")) {
#'
#' # get AMR for all aminoglycosides e.g., per ward:
#' example_isolates %>%
#' group_by(ward) %>%
#' summarise(across(aminoglycosides(), resistance))
#' }
#' if (require("dplyr")) {
#'
#' # You can combine selectors with '&' to be more specific:
#' example_isolates %>%
#' select(penicillins() & administrable_per_os())
#' }
#' if (require("dplyr")) {
#'
#' # get AMR for only drugs that matter - no intrinsic resistance:
#' example_isolates %>%
#' filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
@ -116,7 +113,6 @@
#' summarise(across(not_intrinsic_resistant(), resistance))
#' }
#' if (require("dplyr")) {
#'
#' # get susceptibility for antibiotics whose name contains "trim":
#' example_isolates %>%
#' filter(first_isolate()) %>%
@ -124,19 +120,16 @@
#' summarise(across(ab_selector(name %like% "trim"), susceptibility))
#' }
#' if (require("dplyr")) {
#'
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
#' example_isolates %>%
#' select(carbapenems())
#' }
#' if (require("dplyr")) {
#'
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
#' example_isolates %>%
#' select(mo, aminoglycosides())
#' }
#' if (require("dplyr")) {
#'
#' # any() and all() work in dplyr's filter() too:
#' example_isolates %>%
#' filter(
@ -145,25 +138,21 @@
#' )
#' }
#' if (require("dplyr")) {
#'
#' # also works with c():
#' example_isolates %>%
#' filter(any(c(carbapenems(), aminoglycosides()) == "R"))
#' }
#' if (require("dplyr")) {
#'
#' # not setting any/all will automatically apply all():
#' example_isolates %>%
#' filter(aminoglycosides() == "R")
#' }
#' if (require("dplyr")) {
#'
#' # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
#' example_isolates %>%
#' select(mo, ab_class("mycobact"))
#' }
#' if (require("dplyr")) {
#'
#' # get bug/drug combinations for only glycopeptides in Gram-positives:
#' example_isolates %>%
#' filter(mo_is_gram_positive()) %>%
@ -179,7 +168,6 @@
#' select(penicillins()) # only the 'J01CA01' column will be selected
#' }
#' if (require("dplyr")) {
#'
#' # with recent versions of dplyr this is all equal:
#' x <- example_isolates[carbapenems() == "R", ]
#' y <- example_isolates %>% filter(carbapenems() == "R")
@ -433,14 +421,16 @@ administrable_per_os <- function(only_sir_columns = FALSE, ...) {
ab_group = "administrable_per_os",
examples = paste0(
" (such as ",
vector_or(ab_name(sample(agents_all,
size = min(5, length(agents_all)),
replace = FALSE
),
tolower = TRUE,
language = NULL
),
quotes = FALSE
vector_or(
ab_name(
sample(agents_all,
size = min(5, length(agents_all)),
replace = FALSE
),
tolower = TRUE,
language = NULL
),
quotes = FALSE
),
")"
)
@ -491,20 +481,21 @@ not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, ver
sort = FALSE, fn = "not_intrinsic_resistant"
)
# intrinsic vars
vars_df_R <- tryCatch(sapply(
eucast_rules(vars_df,
col_mo = col_mo,
version_expertrules = version_expertrules,
rules = "expert",
info = FALSE
vars_df_R <- tryCatch(
sapply(
eucast_rules(vars_df,
col_mo = col_mo,
version_expertrules = version_expertrules,
rules = "expert",
info = FALSE
),
function(col) {
tryCatch(!any(is.na(col)) && all(col == "R"),
error = function(e) FALSE
)
}
),
function(col) {
tryCatch(!any(is.na(col)) && all(col == "R"),
error = function(e) FALSE
)
}
),
error = function(e) stop_("in not_intrinsic_resistant(): ", e$message, call = FALSE)
error = function(e) stop_("in not_intrinsic_resistant(): ", e$message, call = FALSE)
)
agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])]
@ -549,12 +540,13 @@ ab_select_exec <- function(function_name,
if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
warning_(
"in `", function_name, "()`: some drugs were ignored since they cannot be used for treating patients: ",
vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
language = NULL,
tolower = TRUE
),
quotes = FALSE,
sort = TRUE
vector_and(
ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
language = NULL,
tolower = TRUE
),
quotes = FALSE,
sort = TRUE
), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
"This warning will be shown once per session."
)
@ -593,11 +585,12 @@ ab_select_exec <- function(function_name,
}
ab_group <- function_name
}
examples <- paste0(" (such as ", vector_or(ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE),
tolower = TRUE,
language = NULL
),
quotes = FALSE
examples <- paste0(" (such as ", vector_or(
ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE),
tolower = TRUE,
language = NULL
),
quotes = FALSE
), ")")
} else {
# this for the 'manual' ab_class() function
@ -821,11 +814,12 @@ find_ab_names <- function(ab_group, n = 3) {
if (length(drugs) == 0) {
return("??")
}
vector_or(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
tolower = TRUE,
language = NULL
),
quotes = FALSE
vector_or(
ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
tolower = TRUE,
language = NULL
),
quotes = FALSE
)
}