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add all options to documentation

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dr. M.S. (Matthijs) Berends
2023-01-23 20:07:57 +01:00
parent 19fd0ef121
commit eef00069fd
31 changed files with 207 additions and 104 deletions
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11
R/custom_antimicrobials.R
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@@ -35,20 +35,20 @@
#'
#' There are two ways to automate this process:
#'
#' **Method 1:** Save the antimicrobials to a local or remote file (can even be the internet). To use this method:
#' **Method 1:** Using the 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 `AMR_custom_ab` \R option: `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 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 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 antibiotic drug codes:
#' # Add custom antimicrobial codes:
#' options(AMR_custom_ab = "~/my_custom_ab.rds")
#' ```
#'
#' Upon package load, this file will be loaded and run through the [add_custom_antimicrobials()] function.
#'
#' **Method 2:** Save the antimicrobial additions directly to your `.Rprofile` file. An important downside is that this requires to load the `AMR` package at every start-up. To use this method:
#' **Method 2:** Loading the antimicrobial additions directly from your `.Rprofile` file. An important downside is that this requires the `AMR` package to be installed or else this method will fail. To use this method:
#'
#' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`.
#'
@@ -56,8 +56,7 @@
#'
#' ```r
#' # Add custom antibiotic drug codes:
#' library(AMR)
#' add_custom_antimicrobials(
#' AMR::add_custom_antimicrobials(
#' data.frame(ab = "TESTAB",
#' name = "Test Antibiotic",
#' group = "Test Group")