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add confidence intervals (fixed #70), remove combine_IR

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-20 16:08:01 +02:00
parent 85e2fbe4a3
commit aa2c0639d0
19 changed files with 248 additions and 144 deletions
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24
R/count.R
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@ -126,7 +126,7 @@ count_resistant <- function(..., only_all_tested = FALSE) {
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
@ -139,7 +139,7 @@ count_susceptible <- function(..., only_all_tested = FALSE) {
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
@ -152,7 +152,7 @@ count_R <- function(..., only_all_tested = FALSE) {
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
@ -168,7 +168,7 @@ count_IR <- function(..., only_all_tested = FALSE) {
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
@ -181,7 +181,7 @@ count_I <- function(..., only_all_tested = FALSE) {
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
@ -194,7 +194,7 @@ count_SI <- function(..., only_all_tested = FALSE) {
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
@ -210,7 +210,7 @@ count_S <- function(..., only_all_tested = FALSE) {
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
@ -223,7 +223,7 @@ count_all <- function(..., only_all_tested = FALSE) {
only_all_tested = only_all_tested,
only_count = TRUE
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc(): ", "", e$message, fixed = TRUE), call = -5)
)
}
@ -236,8 +236,7 @@ n_rsi <- count_all
count_df <- function(data,
translate_ab = "name",
language = get_AMR_locale(),
combine_SI = TRUE,
combine_IR = FALSE) {
combine_SI = TRUE) {
tryCatch(
rsi_calc_df(
type = "count",
@ -245,9 +244,8 @@ count_df <- function(data,
translate_ab = translate_ab,
language = language,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI)
confidence_level = 0.95 # doesn't matter, will be removed
),
error = function(e) stop_(e$message, call = -5)
error = function(e) stop_(gsub("in rsi_calc_df(): ", "", e$message, fixed = TRUE), call = -5)
)
}