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(v2.1.1.9253) parallel computing

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dr. M.S. (Matthijs) Berends
2025-04-26 15:47:00 +02:00
parent abee2a954e
commit 4e7fca3b38
13 changed files with 2311 additions and 44 deletions
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8
R/top_n_microorganisms.R
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@ -32,7 +32,7 @@
#' This function filters a data set to include only the top *n* microorganisms based on a specified property, such as taxonomic family or genus. For example, it can filter a data set to the top 3 species, or to any species in the top 5 genera, or to the top 3 species in each of the top 5 genera.
#' @param x A data frame containing microbial data.
#' @param n An integer specifying the maximum number of unique values of the `property` to include in the output.
#' @param property A character string indicating the microorganism property to use for filtering. Must be one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`. If `NULL`, the raw values from `col_mo` will be used without transformation.
#' @param property A character string indicating the microorganism property to use for filtering. Must be one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`. If `NULL`, the raw values from `col_mo` will be used without transformation. When using `"species"` (default) or `"subpecies"`, the genus will be added to make sure each (sub)species still belongs to the right genus.
#' @param n_for_each An optional integer specifying the maximum number of rows to retain for each value of the selected property. If `NULL`, all rows within the top *n* groups will be included.
#' @param col_mo A character string indicating the column in `x` that contains microorganism names or codes. Defaults to the first column of class [`mo`]. Values will be coerced using [as.mo()].
#' @param ... Additional arguments passed on to [mo_property()] when `property` is not `NULL`.
@ -54,7 +54,7 @@
#' top_n_microorganisms(example_isolates,
#' n = 5, property = "genus", n_for_each = 3
#' )
top_n_microorganisms <- function(x, n, property = "fullname", n_for_each = NULL, col_mo = NULL, ...) {
top_n_microorganisms <- function(x, n, property = "species", n_for_each = NULL, col_mo = NULL, ...) {
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
meet_criteria(n, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE, is_positive = TRUE)
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR::microorganisms))
@ -71,6 +71,10 @@ top_n_microorganisms <- function(x, n, property = "fullname", n_for_each = NULL,
if (is.null(property)) {
x$prop_val <- x[[col_mo]]
} else if (property == "species") {
x$prop_val <- paste(mo_genus(x[[col_mo]], ...), mo_species(x[[col_mo]], ...))
} else if (property == "subspecies") {
x$prop_val <- paste(mo_genus(x[[col_mo]], ...), mo_species(x[[col_mo]], ...), mo_subspecies(x[[col_mo]], ...))
} else {
x$prop_val <- mo_property(x[[col_mo]], property = property, ...)
}