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mo_source improvement

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dr. M.S. (Matthijs) Berends
2019-03-01 09:34:04 +01:00
parent 2565b60024
commit c5efb272fd
21 changed files with 324 additions and 294 deletions
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24
R/mo_source.R
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@ -52,15 +52,19 @@
#' # Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#' }
#'
#' It has now created a file "~/.mo_source.rds" with the contents of our Excel file. It it an R specific format with great compression.
#' It has now created a file "~/.mo_source.rds" with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.
#'
#' And now we can use it in our functions:
#' \preformatted{
#' as.mo("lab_mo_ecoli")
#' # B_ESCHR_COL
#' [1] B_ESCHR_COL
#'
#' mo_genus("lab_mo_kpneumoniae")
#' # "Klebsiella"
#' [1] "Klebsiella"
#'
#' # other input values still work too
#' as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
#' [1] B_ESCHR_COL B_ESCHR_COL B_ESCHR_COL
#' }
#'
#' If we edit the Excel file to, let's say, this:
@ -78,10 +82,10 @@
#' \preformatted{
#' as.mo("lab_mo_ecoli")
#' # Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#' # B_ESCHR_COL
#' [1] B_ESCHR_COL
#'
#' mo_genus("lab_Staph_aureus")
#' # "Staphylococcus"
#' [1] "Staphylococcus"
#' }
#'
#' To remove the reference completely, just use any of these:
@ -119,7 +123,9 @@ set_mo_source <- function(path) {
valid <- FALSE
} else if (!"mo" %in% colnames(df)) {
valid <- FALSE
} else if (!all(df$mo %in% AMR::microorganisms$mo)) {
} else if (all(as.data.frame(df)[, 1] == "")) {
valid <- FALSE
} else if (!all(df$mo %in% c("", AMR::microorganisms$mo))) {
valid <- FALSE
} else if (NCOL(df) < 2) {
valid <- FALSE
@ -163,9 +169,11 @@ set_mo_source <- function(path) {
stop("File must contain a column with self-defined values and a reference column `mo` with valid values from the `microorganisms` data set.")
}
# keep only first two columns, second must be mo
if (colnames(df)[1] == "mo") {
# put mo to the end
df <- df %>% select(-"mo", everything(), "mo")
df <- df[, c(2, 1)]
} else {
df <- df[, c(1, 2)]
}
df <- as.data.frame(df, stringAsFactors = FALSE)