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fix for as.mo, added also_single_tested

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dr. M.S. (Matthijs) Berends
2018-10-19 13:53:31 +02:00
parent 032c0d51ef
commit 86b03577a7
14 changed files with 128 additions and 66 deletions
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11
R/mo.R
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@ -195,7 +195,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
if (all(x %in% AMR::microorganisms[, property])) {
# already existing mo
} else if (all(x %in% AMR::microorganisms[, "mo"])) {
# existing mo codes
# existing mo codes when not looking for property "mo"
suppressWarnings(
x <- data.frame(mo = x, stringsAsFactors = FALSE) %>%
left_join(AMR::microorganisms, by = "mo") %>%
@ -661,13 +661,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x[x == MOs[mo == 'B_STRPTC_SAL', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRK', ..property][[1]][1L]
}
x_input_unique <- unique(x_input)
# fill in empty values again
x[is.na(x_input_unique) | is.null(x_input_unique) | identical(x_input_unique, "")] <- NA
# comply to x, which is also unique and without empty values
x_input_unique_nonempty <- unique(x_input[!is.na(x_input) & !is.null(x_input) & !identical(x_input, "")])
# left join the found results to the original input values (x_input)
df_found <- data.frame(input = as.character(x_input_unique),
found = x,
df_found <- data.frame(input = as.character(x_input_unique_nonempty),
found = as.character(x),
stringsAsFactors = FALSE)
df_input <- data.frame(input = as.character(x_input),
stringsAsFactors = FALSE)