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(v2.1.1.9060) SDD results now in as.sir()

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dr. M.S. (Matthijs) Berends
2024-06-19 15:08:23 +02:00
parent 0c3d81f32e
commit c67d003e9e
17 changed files with 34127 additions and 34129 deletions
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1
R/data.R
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@ -283,6 +283,7 @@
#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
#' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
#' - `is_SDD`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to `r sum(clinical_breakpoints$is_SDD)` breakpoints.
#' @details
#' ### Different types of breakpoints
#' Supported types of breakpoints are `r vector_and(clinical_breakpoints$type, quote = FALSE)`. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.

13
R/sir.R
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@ -1033,13 +1033,14 @@ as_sir_method <- function(method_short,
stop_("No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.sir.", call = FALSE)
}
ab.bak <- ab
ab.bak <- trimws2(ab)
ab <- suppressWarnings(as.ab(ab))
if (!is.null(list(...)$mo.bak)) {
mo.bak <- list(...)$mo.bak
} else {
mo.bak <- mo
}
mo.bak <- trimws2(mo.bak)
# be sure to take current taxonomy, as the 'clinical_breakpoints' data set only contains current taxonomy
mo <- suppressWarnings(suppressMessages(as.mo(mo, keep_synonyms = FALSE, info = FALSE)))
if (all(is.na(ab))) {
@ -1352,8 +1353,9 @@ as_sir_method <- function(method_short,
values <= breakpoints_current$breakpoint_S ~ as.sir("S"),
guideline_coerced %like% "EUCAST" & values > breakpoints_current$breakpoint_R ~ as.sir("R"),
guideline_coerced %like% "CLSI" & values >= breakpoints_current$breakpoint_R ~ as.sir("R"),
# return "I" when breakpoints are in the middle
!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) ~ as.sir("I"),
# return "I" or "SDD" when breakpoints are in the middle
!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == TRUE ~ as.sir("SDD"),
# and NA otherwise
TRUE ~ NA_sir_
)
@ -1363,8 +1365,9 @@ as_sir_method <- function(method_short,
as.double(values) >= as.double(breakpoints_current$breakpoint_S) ~ as.sir("S"),
guideline_coerced %like% "EUCAST" & as.double(values) < as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
guideline_coerced %like% "CLSI" & as.double(values) <= as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
# return "I" when breakpoints are in the middle
!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) ~ as.sir("I"),
# return "I" or "SDD" when breakpoints are in the middle
!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == TRUE ~ as.sir("SDD"),
# and NA otherwise
TRUE ~ NA_sir_
)