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count_all and some fixes

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dr. M.S. (Matthijs) Berends
2018-10-12 16:35:18 +02:00
parent e7d937d36e
commit 5b5b95a47b
22 changed files with 232 additions and 246 deletions
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20
R/mo.R
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@ -272,12 +272,14 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
# translate known trivial abbreviations to genus + species ----
if (!is.na(x_trimmed[i])) {
if (toupper(x_trimmed[i]) == 'MRSA'
| toupper(x_trimmed[i]) == 'MSSA'
| toupper(x_trimmed[i]) == 'VISA'
| toupper(x_trimmed[i]) == 'VRSA') {
x[i] <- MOs[mo == 'B_STPHY_AUR', ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) == 'MRSE') {
if (toupper(x_trimmed[i]) == 'MRSE'
| toupper(x_trimmed[i]) == 'MSSE') {
x[i] <- MOs[mo == 'B_STPHY_EPI', ..property][[1]][1L]
next
}
@ -290,6 +292,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x[i] <- MOs[mo == 'B_PDMNS_AER', ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) == 'CRS'
| toupper(x_trimmed[i]) == 'CRSM') {
# co-trim resistant S. maltophilia
x[i] <- MOs[mo == 'B_STNTR_MAL', ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
# peni I, peni R, vanco I, vanco R: S. pneumoniae
x[i] <- MOs[mo == 'B_STRPTC_PNE', ..property][[1]][1L]
@ -578,7 +586,7 @@ 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 (try again with allow_uncertain = TRUE):\n",
warning("These ", length(failures) , " values could not be coerced (try again with allow_uncertain = TRUE): ",
paste('"', unique(failures), '"', sep = "", collapse = ', '),
".",
call. = FALSE)
@ -658,8 +666,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
if (property == "mo") {
class(x) <- "mo"
attr(x, 'package') <- 'AMR'
attr(x, 'ITIS') <- TRUE
} else if (property == "tsn") {
x <- as.integer(x)
}
@ -667,7 +673,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x
}
#' @importFrom dplyr case_when
renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
if (!is.na(ref_old)) {
ref_old <- paste0(" (", ref_old, ")")
@ -687,7 +692,10 @@ renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
#' @noRd
print.mo <- function(x, ...) {
cat("Class 'mo'\n")
print.default(as.character(x), quote = FALSE)
x_names <- names(x)
x <- as.character(x)
names(x) <- x_names
print.default(x, quote = FALSE)
}
#' @exportMethod as.data.frame.mo