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cfta streptococci, codecov.yml

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dr. M.S. (Matthijs) Berends
2019-04-09 14:59:17 +02:00
parent cffb7787d8
commit 461eec9bac
18 changed files with 203 additions and 114 deletions
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35
R/guess_ab_col.R
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@ -26,6 +26,7 @@
#' @param col a character to look for
#' @param verbose a logical to indicate whether additional info should be printed
#' @importFrom dplyr %>% select filter_all any_vars
#' @importFrom crayon blue
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
@ -70,6 +71,9 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
unlist()
if (col %in% tbl_names) {
if (verbose == TRUE) {
message(blue(paste0("NOTE: Using column `", bold(col), "` as input for `", col, "`.")))
}
return(col)
}
ab_result <- antibiotics %>%
@ -77,7 +81,7 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
filter_all(any_vars(tolower(.) == tolower(col))) %>%
filter_all(any_vars(. %in% tbl_names))
if (nrow(ab_result) == 0 & nchar(col) > 4) {
if (nrow(ab_result) == 0 & nchar(col) >= 5) {
# use like when col >= 5 characters
ab_result <- antibiotics %>%
select(atc:trade_name) %>%
@ -87,14 +91,28 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
# WHONET
if (nrow(ab_result) == 0) {
# use like when col >= 5 characters
# use like for any case
ab_result <- antibiotics %>%
select(atc:trade_name) %>%
filter_all(any_vars(tolower(.) == tolower(col))) %>%
filter_all(any_vars(. %in% tbl_names_stripped))
}
if (nrow(ab_result) > 1) {
found_based_on_official_name <- FALSE
if (nrow(ab_result) == 0) {
# check if first part of official name resembles the columns that's been looking for
name <- suppressWarnings(atc_name(col))
if (!is.null(name)) {
ab_result <-
antibiotics %>%
filter(official == name) %>%
pull(official)
ab_result <- tbl_names[tbl_names %like% paste0("^", substr(ab_result, 1, 5))]
found_based_on_official_name <- TRUE
}
}
if (NROW(ab_result) > 1 & found_based_on_official_name == FALSE) {
# looking more and more for reliable hit
ab_result_1 <- ab_result %>% filter(tolower(atc) == tolower(col))
if (nrow(ab_result_1) == 0) {
@ -106,6 +124,9 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
if (nrow(ab_result_1) == 0) {
ab_result_1 <- ab_result %>% filter(tolower(official) == tolower(col))
}
if (nrow(ab_result_1) == 0) {
ab_result_1 <- ab_result %>% filter(tolower(official) == tolower(col))
}
if (nrow(ab_result_1) == 0) {
ab_result_1 <- ab_result[1, ]
}
@ -114,7 +135,7 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
if (length(ab_result) == 0) {
if (verbose == TRUE) {
message('no column found for input "', col, '"')
message('No column found as input for `', col, '`.')
}
return(NULL)
} else {
@ -122,14 +143,14 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
if (length(result) == 0) {
result <- tbl_names[tbl_names_stripped %in% ab_result]
}
if (length(result) == 0) {
if (length(result) == 0 | length(result) > 1) {
if (verbose == TRUE) {
message('no column found for input "', col, '"')
message('No column found as input for `', col, '`.')
}
return(NULL)
}
if (verbose == TRUE) {
message('using column `', result, '` for col "', col, '"')
message(blue(paste0("NOTE: Using column `", bold(result), "` as input for `", col, "`.")))
}
return(result)
}