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(v0.9.0) website fixes
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@ -40,12 +40,12 @@
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#'
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#' 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:
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#' ```
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#' | A | B |
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#' --|--------------------|-------------|
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#' 1 | Organisation XYZ | mo |
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#' 2 | lab_mo_ecoli | B_ESCHR_COL |
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#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
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#' 4 | | |
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#' | A | B |
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#' --|--------------------|--------------|
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#' 1 | Organisation XYZ | mo |
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#' 2 | lab_mo_ecoli | B_ESCHR_COLI |
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#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
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#' 4 | | |
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#' ```
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#'
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#' We save it as `"home/me/ourcodes.xlsx"`. Now we have to set it as a source:
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@ -59,7 +59,7 @@
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#' And now we can use it in our functions:
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#' ```
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#' as.mo("lab_mo_ecoli")
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#' \[1\] B_ESCHR_COLI
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#' [1] B_ESCHR_COLI
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#'
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#' mo_genus("lab_mo_kpneumoniae")
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#' [1] "Klebsiella"
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@ -69,7 +69,7 @@
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#' [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
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#' ```
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#'
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#' If we edit the Excel file to, let's say, this:
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#' If we edit the Excel file to, let's say, by adding row 4 like this:
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#' ```
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#' | A | B |
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#' --|--------------------|--------------|
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@ -80,7 +80,7 @@
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#' 5 | | |
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#' ```
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#'
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#' ...any new usage of an MO function in this package will update your data:
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#' ...any new usage of an MO function in this package will update your data file:
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#' ```
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#' as.mo("lab_mo_ecoli")
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#' # Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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@ -90,9 +90,8 @@
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#' [1] "Staphylococcus"
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#' ```
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#'
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#' To remove the reference completely, just use any of these:
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#' To remove the reference data file completely, just use `""` or `NULL` as input for `[set_mo_source()]`:
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#' ```
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#' set_mo_source("")
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#' set_mo_source(NULL)
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#' # Removed mo_source file '~/.mo_source.rds'.
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#' ```
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@ -126,9 +125,7 @@ set_mo_source <- function(path) {
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} else if (path %like% "[.]xlsx?$") {
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# is Excel file (old or new)
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if (!"readxl" %in% utils::installed.packages()) {
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stop("Install the 'readxl' package first.")
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}
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stopifnot_installed_package("readxl")
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df <- readxl::read_excel(path)
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} else if (path %like% "[.]tsv$") {
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@ -219,5 +216,5 @@ mo_source_isvalid <- function(x) {
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if (!"mo" %in% colnames(x)) {
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return(FALSE)
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}
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all(x$mo %in% c("", AMR::microorganisms$mo))
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all(x$mo %in% c("", AMR::microorganisms$mo, AMR::microorganisms.translation$mo_old), na.rm = TRUE)
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}
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