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fix for as.mo and freq

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dr. M.S. (Matthijs) Berends
2018-11-30 12:05:59 +01:00
parent 9ddf6dc530
commit 31e977937d
7 changed files with 43 additions and 24 deletions
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2
R/freq.R
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@ -337,7 +337,7 @@ frequency_tbl <- function(x,
header_txt <- header_txt %>% paste0(markdown_line, '\nLongest: ', x %>% base::nchar() %>% base::max(na.rm = TRUE))
}
if (NROW(x) > 0 & any(class(x) == "difftime")) {
if (NROW(x) > 0 & any(class(x) == "difftime") & !is.hms(x)) {
header_txt <- header_txt %>% paste0('\n')
header_txt <- header_txt %>% paste(markdown_line, '\nUnits: ', attributes(x)$units)
x <- as.double(x)

40
R/mo.R
View File

@ -192,7 +192,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x_input <- x
# only check the uniques, which is way faster
x <- unique(x)
# remove empty values (to later fill them in again)
# remove empty values (to later fill them in again with NAs)
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
# defined df to check for
@ -270,27 +270,24 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
# check if search term was like "A. species", then return first genus found with ^A
if (x_backup[i] %like% "species" | x_backup[i] %like% "spp[.]?") {
# get mo code of first hit
found <- microorganismsDT[fullname %like% x_withspaces_start[i], mo][[1]]
mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
found <- microorganismsDT[mo == mo_code, ..property][[1]]
# return first genus that begins with x_trimmed, e.g. when "E. spp."
found <- microorganismsDT[fullname %like% x_withspaces_start[i], mo]
if (length(found) > 0) {
x[i] <- found[1L]
next
} else {
# fewer than 3 chars, add as failure
x[i] <- NA_character_
failures <- c(failures, x_backup[i])
next
mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
found <- microorganismsDT[mo == mo_code, ..property][[1]]
# return first genus that begins with x_trimmed, e.g. when "E. spp."
if (length(found) > 0) {
x[i] <- found[1L]
next
}
}
} else {
# fewer than 3 chars, add as failure
x[i] <- NA_character_
failures <- c(failures, x_backup[i])
next
}
# fewer than 3 chars and not looked for species, add as failure
x[i] <- NA_character_
failures <- c(failures, x_backup[i])
next
}
# translate known trivial abbreviations to genus + species ----
if (!is.na(x_trimmed[i])) {
if (toupper(x_trimmed[i]) == 'MRSA'
@ -377,9 +374,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
}
# TRY OTHER SOURCES ----
if (toupper(x_backup[i]) %in% microorganisms.certe[, 1]) {
mo_found <- microorganisms.certe[toupper(x_backup[i]) == microorganisms.certe[, 1], 2][1L]
if (length(mo_found) > 0) {
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
next
}
}
if (x_backup[i] %in% microorganisms.umcg[, 1]) {
mo_umcg <- microorganisms.umcg[microorganisms.umcg[, 1] == x_backup[i], 2]
mo_found <- microorganisms.certe[microorganisms.certe[, 1] == mo_umcg, 2]
mo_found <- microorganisms.certe[microorganisms.certe[, 1] == mo_umcg, 2][1L]
if (length(mo_found) == 0) {
# not found
x[i] <- NA_character_