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(v0.9.0) website fixes

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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
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27
R/mo_source.R
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@ -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)
}