P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 05:41:59 +02:00
Code Releases Activity

new SDD and N for as.sir()

Browse Source
This commit is contained in:
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
Download Patch File Download Diff File Expand all files Collapse all files

120
R/count.R
View File

@ -143,66 +143,11 @@ count_susceptible <- function(..., only_all_tested = FALSE) {
)
}
#' @rdname count
#' @export
count_R <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = "R",
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
#' @rdname count
#' @export
count_IR <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" being resistant. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("I", "R"),
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
#' @rdname count
#' @export
count_I <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = "I",
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
#' @rdname count
#' @export
count_SI <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("S", "I"),
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
#' @rdname count
#' @export
count_S <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_S", entire_session = TRUE)) {
message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" and \"SDD\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
@ -214,12 +159,73 @@ count_S <- function(..., only_all_tested = FALSE) {
)
}
#' @rdname count
#' @export
count_SI <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_SI", entire_session = TRUE)) {
message_("Note that `count_SI()` will also count dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("S", "SDD", "I"),
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
#' @rdname count
#' @export
count_I <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_I", entire_session = TRUE)) {
message_("Note that `count_I()` will also count dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("I", "SDD"),
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
#' @rdname count
#' @export
count_IR <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" and \"SDD\" being resistant. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("I", "SDD", "R"),
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
#' @rdname count
#' @export
count_R <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = "R",
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
#' @rdname count
#' @export
count_all <- function(..., only_all_tested = FALSE) {
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
),