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(v0.9.0.9003) as.mo() speedup for fullnames

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dr. M.S. (Matthijs) Berends
2019-12-20 15:05:58 +01:00
parent f7eb6e4107
commit 2db2a2458a
21 changed files with 209 additions and 204 deletions
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34
R/mo.R
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@ -25,10 +25,10 @@
#' @param x a character vector or a [`data.frame`] with one or two columns
#' @param Becker a logical to indicate whether *Staphylococci* should be categorised into coagulase-negative *Staphylococci* ("CoNS") and coagulase-positive *Staphylococci* ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2). Note that this does not include species that were newly named after these publications, like *S. caeli*.
#'
#' This excludes *Staphylococcus aureus* at default, use `Becker = "all"` to also categorise *S. aureus* as "CoPS".
#' This excludes *Staphylococcus aureus* at default, use `Becker = "all"` to also categorise *S. aureus* as "CoPS".
#' @param Lancefield a logical to indicate whether beta-haemolytic *Streptococci* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (3). These *Streptococci* will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L.
#'
#' This excludes *Enterococci* at default (who are in group D), use `Lancefield = "all"` to also categorise all *Enterococci* as group D.
#' This excludes *Enterococci* at default (who are in group D), use `Lancefield = "all"` to also categorise all *Enterococci* as group D.
#' @param allow_uncertain a number between `0` (or `"none"`) and `3` (or `"all"`), or `TRUE` (= `2`) or `FALSE` (= `0`) to indicate whether the input should be checked for less probable results, please see *Details*
#' @param reference_df a [`data.frame`] to use for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
#' @param ... other parameters passed on to functions
@ -228,19 +228,7 @@ as.mo <- function(x,
& isFALSE(Lancefield)) {
# check previously found results
y <- mo_hist
} else if (all(tolower(x) %in% microorganismsDT$fullname_lower)
& isFALSE(Becker)
& isFALSE(Lancefield)) {
# we need special treatment for very prevalent full names, they are likely! (case insensitive)
# e.g. as.mo("Staphylococcus aureus")
y <- data.frame(fullname_lower = tolower(x),
stringsAsFactors = FALSE) %>%
left_join(microorganismsDT, by = "fullname_lower") %>%
pull(mo)
# don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
} else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
y <- mo_validate(x = x, property = "mo",
@ -249,7 +237,6 @@ as.mo <- function(x,
...)
}
to_class_mo(y)
}
@ -283,7 +270,7 @@ exec_as.mo <- function(x,
initial_search = TRUE,
dyslexia_mode = FALSE,
force_mo_history = FALSE,
disable_mo_history = FALSE,
disable_mo_history = getOption("AMR_disable_mo_history", FALSE),
debug = FALSE,
reference_data_to_use = microorganismsDT) {
@ -433,18 +420,7 @@ exec_as.mo <- function(x,
} else if (all(tolower(x) %in% reference_data_to_use$fullname_lower)) {
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
y <- reference_data_to_use[prevalence == 1][data.table(fullname_lower = tolower(x)), on = "fullname_lower", ..property][[1]]
if (any(is.na(y))) {
y[is.na(y)] <- reference_data_to_use[prevalence == 2][data.table(fullname_lower = tolower(x[is.na(y)])),
on = "fullname_lower",
..property][[1]]
}
if (any(is.na(y))) {
y[is.na(y)] <- reference_data_to_use[prevalence == 3][data.table(fullname_lower = tolower(x[is.na(y)])),
on = "fullname_lower",
..property][[1]]
}
x <- y
x <- reference_data_to_use[data.table(fullname_lower = tolower(x)), on = "fullname_lower", ..property][[1]]
} else if (all(toupper(x) %in% AMR::microorganisms.codes$code)) {
# commonly used MO codes