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bring back antibiogram(), without deps

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-10 16:18:00 +01:00
parent 70a7ba0206
commit bc434db835
42 changed files with 11307 additions and 4734 deletions
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13
R/sir_calc.R
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@ -31,7 +31,8 @@ dots2vars <- function(...) {
# this function is to give more informative output about
# variable names in count_* and proportion_* functions
dots <- substitute(list(...))
as.character(dots)[2:length(dots)]
dots <- as.character(dots)[2:length(dots)]
paste0(dots[dots != "."], collapse = "+")
}
sir_calc <- function(...,
@ -41,7 +42,7 @@ sir_calc <- function(...,
only_all_tested = FALSE,
only_count = FALSE) {
meet_criteria(ab_result, allow_class = c("character", "numeric", "integer"), has_length = c(1, 2, 3))
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
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)
meet_criteria(only_count, allow_class = "logical", has_length = 1)
@ -133,7 +134,7 @@ sir_calc <- function(...,
}
x_transposed <- as.list(as.data.frame(t(x), stringsAsFactors = FALSE))
if (only_all_tested == TRUE) {
if (isTRUE(only_all_tested)) {
# no NAs in any column
y <- apply(
X = as.data.frame(lapply(x, as.integer), stringsAsFactors = FALSE),
@ -224,8 +225,8 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
meet_criteria(type, is_in = c("proportion", "count", "both"), has_length = 1)
meet_criteria(data, allow_class = "data.frame", contains_column_class = "sir")
meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
language <- validate_language(language)
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(combine_SI, allow_class = "logical", has_length = 1)
meet_criteria(confidence_level, allow_class = "numeric", has_length = 1)
@ -236,7 +237,7 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
# select only groups and antibiotics
if (is_null_or_grouped_tbl(data)) {
data_has_groups <- TRUE
groups <- setdiff(names(attributes(data)$groups), ".rows")
groups <- get_group_names(data)
data <- data[, c(groups, colnames(data)[vapply(FUN.VALUE = logical(1), data, is.sir)]), drop = FALSE]
} else {
data_has_groups <- FALSE