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read.4D improvements

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-15 12:42:35 +01:00
parent 5cb8f3cf72
commit fab64e6728
10 changed files with 89 additions and 51 deletions
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16
R/mo.R
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@ -181,7 +181,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x[is.null(x)] <- NA
# support tidyverse selection like: df %>% select(colA)
if (!is.vector(x)) {
if (!is.vector(x) & !is.null(dim(x))) {
x <- pull(x, 1)
}
}
@ -360,9 +360,15 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
# next
}
if (x_backup[i] %in% AMR::microorganisms.umcg[, 1]) {
ref_certe <- AMR::microorganisms.umcg[AMR::microorganisms.umcg[, 1] == x_backup[i], 2]
ref_mo <- AMR::microorganisms.certe[AMR::microorganisms.certe[, 1] == ref_certe, 2]
x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
mo_umcg <- AMR::microorganisms.umcg[AMR::microorganisms.umcg[, 1] == x_backup[i], 2]
mo_found <- AMR::microorganisms.certe[AMR::microorganisms.certe[, 1] == mo_umcg, 2]
if (length(mo_found) == 0) {
# not found
x[i] <- NA_character_
failures <- c(failures, x_backup[i])
} else {
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
}
next
}
if (x_backup[i] %in% reference_df[, 1]) {
@ -575,7 +581,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
failures <- failures[!failures %in% c(NA, NULL, NaN)]
if (length(failures) > 0) {
warning("These ", length(failures) , " values could not be coerced: ",
warning("These ", length(failures) , " values could not be coerced to a valid MO code: ",
paste('"', unique(failures), '"', sep = "", collapse = ', '),
".",
call. = FALSE)