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new SDD and N for as.sir()

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dr. M.S. (Matthijs) Berends
2024-05-20 15:27:04 +02:00
parent b68f47d985
commit 08a27922a8
28 changed files with 225 additions and 172 deletions
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23
R/proportion.R
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@ -48,7 +48,7 @@
#' @details
#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms.
#'
#' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()].
#' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()]. Since AMR v3.0, [proportion_SI()] and [proportion_I()] include dose-dependent susceptibility ('SDD').
#'
#' Use [sir_confidence_interval()] to calculate the confidence interval, which relies on [binom.test()], i.e., the Clopper-Pearson method. This function returns a vector of length 2 at default for antimicrobial *resistance*. Change the `side` argument to "left"/"min" or "right"/"max" to return a single value, and change the `ab_result` argument to e.g. `c("S", "I")` to test for antimicrobial *susceptibility*, see Examples.
#'
@ -247,7 +247,7 @@ susceptibility <- function(...,
only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("S", "I"),
ab_result = c("S", "SDD", "I"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@ -267,7 +267,7 @@ sir_confidence_interval <- function(...,
confidence_level = 0.95,
side = "both",
collapse = FALSE) {
meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = c(1, 2, 3), is_in = c("S", "I", "R"))
meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = c(1:5), is_in = c("S", "SDD", "I", "R", "N"))
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
meet_criteria(as_percent, allow_class = "logical", has_length = 1)
meet_criteria(only_all_tested, allow_class = "logical", has_length = 1)
@ -285,7 +285,7 @@ sir_confidence_interval <- function(...,
)
n <- tryCatch(
sir_calc(...,
ab_result = c("S", "I", "R"),
ab_result = c("S", "SDD", "I", "R", "N"),
only_all_tested = only_all_tested,
only_count = TRUE
),
@ -351,9 +351,12 @@ proportion_IR <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
if (message_not_thrown_before("proportion_IR", entire_session = TRUE)) {
message_("Note that `proportion_IR()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("I", "R"),
ab_result = c("I", "SDD", "R"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@ -369,9 +372,12 @@ proportion_I <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
if (message_not_thrown_before("proportion_I", entire_session = TRUE)) {
message_("Note that `proportion_I()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = "I",
ab_result = c("I", "SDD"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@ -387,9 +393,12 @@ proportion_SI <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
if (message_not_thrown_before("proportion_SI", entire_session = TRUE)) {
message_("Note that `proportion_SI()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("S", "I"),
ab_result = c("S", "I", "SDD"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,