P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 11:51:59 +02:00
Code Releases Activity

(v0.9.0) website fixes

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-11-30 12:01:50 +01:00
parent c9aefd1841
commit 56ce9bf665
21 changed files with 300 additions and 302 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
R/misc.R
View File

@ -117,7 +117,10 @@ search_type_in_df <- function(x, type) {
stopifnot_installed_package <- function(package) {
# no "utils::installed.packages()" since it requires non-staged install since R 3.6.0
# https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
get(".packageName", envir = asNamespace(package))
tryCatch(get(".packageName", envir = asNamespace(package)),
error = function(e) stop("package '", package, "' required but not installed",
' - try to install it with: install.packages("', package, '")',
call. = FALSE))
return(invisible())
}

6
R/mo_property.R
View File

@ -21,7 +21,7 @@
#' Property of a microorganism
#'
#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with [as.mo()], which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. Please see *Examples*.
#' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param property one of the column names of the [microorganisms] data set or `"shortname"`
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
@ -32,7 +32,7 @@
#' - `mo_ref("Chlamydia psittaci")` will return `"Page, 1968"` (with a warning about the renaming)
#' - `mo_ref("Chlamydophila psittaci")` will return `"Everett et al., 1999"` (without a warning)
#'
#' The Gram stain - [mo_gramstain()] - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value `NA`.
#' The Gram stain - [mo_gramstain()] - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`.
#'
#' All output will be [translate]d where possible.
#'
@ -43,7 +43,7 @@
#' @name mo_property
#' @return
#' - An [`integer`] in case of [mo_year()]
#' - A [`list`] in case of [mo_taxonomy()]
#' - A [`list`] in case of [mo_taxonomy()] and [mo_info()]
#' - A named [`character`] in case of [mo_url()]
#' - A [`character`] in all other cases
#' @export

27
R/mo_source.R
View File

@ -40,12 +40,12 @@
#'
#' Imagine this data on a sheet of an Excel file (mo codes were looked up in the `microorganisms` data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
#' ```
#' | A | B |
#' --|--------------------|-------------|
#' 1 | Organisation XYZ | mo |
#' 2 | lab_mo_ecoli | B_ESCHR_COL |
#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
#' 4 | | |
#' | A | B |
#' --|--------------------|--------------|
#' 1 | Organisation XYZ | mo |
#' 2 | lab_mo_ecoli | B_ESCHR_COLI |
#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
#' 4 | | |
#' ```
#'
#' We save it as `"home/me/ourcodes.xlsx"`. Now we have to set it as a source:
@ -59,7 +59,7 @@
#' And now we can use it in our functions:
#' ```
#' as.mo("lab_mo_ecoli")
#' \[1\] B_ESCHR_COLI
#' [1] B_ESCHR_COLI
#'
#' mo_genus("lab_mo_kpneumoniae")
#' [1] "Klebsiella"
@ -69,7 +69,7 @@
#' [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
#' ```
#'
#' If we edit the Excel file to, let's say, this:
#' If we edit the Excel file to, let's say, by adding row 4 like this:
#' ```
#' | A | B |
#' --|--------------------|--------------|
@ -80,7 +80,7 @@
#' 5 | | |
#' ```
#'
#' ...any new usage of an MO function in this package will update your data:
#' ...any new usage of an MO function in this package will update your data file:
#' ```
#' as.mo("lab_mo_ecoli")
#' # Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
@ -90,9 +90,8 @@
#' [1] "Staphylococcus"
#' ```
#'
#' To remove the reference completely, just use any of these:
#' To remove the reference data file completely, just use `""` or `NULL` as input for `[set_mo_source()]`:
#' ```
#' set_mo_source("")
#' set_mo_source(NULL)
#' # Removed mo_source file '~/.mo_source.rds'.
#' ```
@ -126,9 +125,7 @@ set_mo_source <- function(path) {
} else if (path %like% "[.]xlsx?$") {
# is Excel file (old or new)
if (!"readxl" %in% utils::installed.packages()) {
stop("Install the 'readxl' package first.")
}
stopifnot_installed_package("readxl")
df <- readxl::read_excel(path)
} else if (path %like% "[.]tsv$") {
@ -219,5 +216,5 @@ mo_source_isvalid <- function(x) {
if (!"mo" %in% colnames(x)) {
return(FALSE)
}
all(x$mo %in% c("", AMR::microorganisms$mo))
all(x$mo %in% c("", AMR::microorganisms$mo, AMR::microorganisms.translation$mo_old), na.rm = TRUE)
}