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(v1.2.0.9038) CLSI 2019 fix

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dr. M.S. (Matthijs) Berends
2020-07-29 10:33:47 +02:00
parent 1b65d76cfb
commit 453f7f210b
65 changed files with 211 additions and 514 deletions
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14
R/aa_helper_functions.R
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@ -419,13 +419,7 @@ font_stripstyle <- function(x) {
}
progress_estimated <- function(n = 1, n_min = 0, ...) {
if (n >= n_min & interactive()) {
pb <- utils::txtProgressBar(max = n, style = 3)
pb$tick <- function() {
pb$up(pb$getVal() + 1)
}
pb
} else {
if (!interactive() || n < n_min) {
pb <- list()
pb$tick <- function() {
invisible()
@ -434,6 +428,12 @@ progress_estimated <- function(n = 1, n_min = 0, ...) {
invisible()
}
structure(pb, class = "txtProgressBar")
} else if (n >= n_min) {
pb <- utils::txtProgressBar(max = n, style = 3)
pb$tick <- function() {
pb$up(pb$getVal() + 1)
}
pb
}
}

2
R/rsi.R
View File

@ -37,7 +37,7 @@
#'
#' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline.
#'
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**.
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
#'
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#'