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(v0.7.1.9102) lintr

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dr. M.S. (Matthijs) Berends
2019-10-11 17:21:02 +02:00
parent 59af355a89
commit 00cdb498a0
65 changed files with 620 additions and 812 deletions
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15
R/guess_ab_col.R
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@ -83,9 +83,6 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
} else if (any(tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations"))))) {
ab_result <- colnames(x)[tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations")))][1L]
# } else if (any(tolower(colnames(x)) %in% tolower(ab_tradenames(search_string.ab)))) {
# ab_result <- colnames(x)[tolower(colnames(x)) %in% tolower(ab_tradenames(search_string.ab))][1L]
} else {
# sort colnames on length - longest first
cols <- colnames(x[, x %>% colnames() %>% nchar() %>% order() %>% rev()])
@ -128,7 +125,7 @@ get_column_abx <- function(x,
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
# or already have the rsi class (as.rsi)
# and that have no more than 50% invalid values
vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[,c("ab", "atc", "name", "abbreviations", "synonyms")])))
vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[, c("ab", "atc", "name", "abbreviations", "synonyms")])))
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
x_columns <- sapply(colnames(x), function(col, df = x_bak) {
if (toupper(col) %in% vectr_antibiotics |
@ -144,12 +141,12 @@ get_column_abx <- function(x,
df_trans <- data.frame(colnames = colnames(x),
abcode = suppressWarnings(as.ab(colnames(x))))
df_trans <- df_trans[!is.na(df_trans$abcode),]
df_trans <- df_trans[!is.na(df_trans$abcode), ]
x <- as.character(df_trans$colnames)
names(x) <- df_trans$abcode
# add from self-defined dots (...):
# get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
# such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
dots <- list(...)
if (length(dots) > 0) {
newnames <- suppressWarnings(as.ab(names(dots)))
@ -173,12 +170,12 @@ get_column_abx <- function(x,
x <- x[!names(x) %in% names(duplicates)]
if (verbose == TRUE) {
for (i in 1:length(x)) {
for (i in seq_len(length(x))) {
message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE), ").")))
}
} else if (length(duplicates) > 0) {
for (i in 1:length(duplicates)) {
for (i in seq_len(length(duplicates))) {
warning(red(paste0("Using column `", bold(duplicates[i]), "` as input for `", names(x[which(x == duplicates[i])]),
"` (", ab_name(names(x[names(which(x == duplicates))[i]]), tolower = TRUE),
"), although it was matched for multiple antibiotics or columns.")), call. = FALSE)
@ -203,7 +200,7 @@ get_column_abx <- function(x,
mutate(txt = paste0(bold(missing), " (", missing_names, ")")) %>%
arrange(missing_names) %>%
pull(txt)
message(blue('NOTE: Reliability might be improved if these antimicrobial results would be available too:',
message(blue("NOTE: Reliability might be improved if these antimicrobial results would be available too:",
paste(missing_txt, collapse = ", ")))
}
}