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(v2.1.1.9079) fix for uti in as.sir()

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dr. M.S. (Matthijs) Berends
2024-09-24 15:34:12 +02:00
parent 127892430d
commit 1ca40e8d67
32 changed files with 98 additions and 109 deletions
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R/custom_antimicrobials.R
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@@ -35,11 +35,11 @@
#'
#' There are two ways to circumvent this and automate the process of adding antimicrobials:
#'
#' **Method 1:** Using the [package option][AMR-options] [`AMR_custom_ab`][AMR-options], which is the preferred method. To use this method:
#' **Method 1:** Using the package option [`AMR_custom_ab`][AMR-options], which is the preferred method. To use this method:
#'
#' 1. Create a data set in the structure of the [antibiotics] data set (containing at the very least columns "ab" and "name") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_ab.rds"`, or any remote location.
#'
#' 2. Set the file location to the [package option][AMR-options] [`AMR_custom_ab`][AMR-options]: `options(AMR_custom_ab = "~/my_custom_ab.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
#' 2. Set the file location to the package option [`AMR_custom_ab`][AMR-options]: `options(AMR_custom_ab = "~/my_custom_ab.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
#'
#' ```r
#' # Add custom antimicrobial codes: