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dr. M.S. (Matthijs) Berends
2023-01-19 12:54:53 +01:00
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commit 593d740b84
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R/custom_microorganisms.R Normal file → Executable file
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@ -37,11 +37,11 @@
#'
#' There are two ways to automate this process:
#'
#' **Method 1:** Save the microorganisms to a local or remote file (can even be the internet). To use this method:
#' **Method 1:** Using the [option `AMR_custom_mo`][AMR-options], which is the preferred method. To use this method:
#'
#' 1. Create a data set in the structure of the [microorganisms] data set (containing at the very least column "genus") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
#'
#' 2. Set the file location to the `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.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 `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.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 microorganism codes:
@ -50,7 +50,7 @@
#'
#' Upon package load, this file will be loaded and run through the [add_custom_microorganisms()] function.
#'
#' **Method 2:** Save the microorganism 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 microorganism 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")`.
#'
@ -58,8 +58,7 @@
#'
#' ```r
#' # Add custom antibiotic drug codes:
#' library(AMR)
#' add_custom_microorganisms(
#' AMR::add_custom_microorganisms(
#' data.frame(genus = "Enterobacter",
#' species = "asburiae/cloacae")
#' )
@ -71,7 +70,6 @@
#' @export
#' @examples
#' \donttest{
#'
#' # a combination of species is not formal taxonomy, so
#' # this will result in only "Enterobacter asburiae":
#' mo_name("Enterobacter asburiae/cloacae")
@ -102,13 +100,15 @@
#'
#' # the function tries to be forgiving:
#' add_custom_microorganisms(
#' data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
#' data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
#' SPECIES = "SPECIES")
#' )
#' mo_name("ESCHERICHIA / KLEBSIELLA")
#' mo_rank("ESCHERICHIA / KLEBSIELLA")
#' mo_name("BACTEROIDES / PARABACTEROIDES")
#' mo_rank("BACTEROIDES / PARABACTEROIDES")
#'
#' # taxonomy still works, although a slashline genus was given as input:
#' mo_family("Escherichia/Klebsiella")
#' mo_family("Bacteroides/Parabacteroides")
#'
#'
#' # for groups and complexes, set them as species or subspecies:
#' add_custom_microorganisms(
@ -208,8 +208,10 @@ add_custom_microorganisms <- function(x) {
x$family[which(x$family == "" & genus_to_check != "")] <- AMR_env$MO_lookup$family[match(genus_to_check[which(x$family == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
# fill in other columns that are used in internal algorithms
x$prevalence <- NA_real_
x$prevalence[which(genus_to_check != "")] <- AMR_env$MO_lookup$prevalence[match(genus_to_check[which(genus_to_check != "")], AMR_env$MO_lookup$genus)]
x$prevalence[is.na(x$prevalence)] <- 1.25
x$status <- "accepted"
x$prevalence <- 1
x$ref <- paste("Self-added,", format(Sys.Date(), "%Y"))
x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(genus_to_check, AMR_env$MO_lookup$genus)]
# complete missing kingdom index, so mo_matching_score() will not return NA