P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 07:51:57 +02:00
Code Releases Activity

(v1.4.0.9044) mo tibble printing, mo_shortname() fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-24 23:29:10 +01:00
parent 128ebcfd62
commit df37584189
96 changed files with 1039 additions and 2847 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
R/mo_source.R
View File

@ -25,9 +25,9 @@
#' User-defined reference data set for microorganisms
#'
#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()].
#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all [`mo_*`][mo_property()] functions (such as [mo_genus()] and [mo_gramstain()]).
#'
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package.
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.
#' @inheritSection lifecycle Stable lifecycle
#' @param path location of your reference file, see Details. Can be `""`, `NULL` or `FALSE` to delete the reference file.
#' @param destination destination of the compressed data file, default to the user's home directory.
@ -103,7 +103,7 @@
#' ```
#' as.mo("lab_mo_ecoli")
#' #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
#' #> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
#' #> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
#' #> "Organisation XYZ" and "mo"
#' #> Class <mo>
#' #> [1] B_ESCHR_COLI
@ -119,7 +119,7 @@
#' #> Removed mo_source file '/Users/me/mo_source.rds'
#' ```
#'
#' If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of [as.mo()].
#' If the original file (in the previous case an Excel file) is moved or deleted, the `mo_source.rds` file will be removed upon the next use of [as.mo()] or any [`mo_*`][mo_property()] function.
#' @export
#' @inheritSection AMR Read more on our website!
set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_source.rds")) {