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(v1.1.0.9004) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions
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48
R/mo_source.R
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@ -96,7 +96,6 @@
#' set_mo_source(NULL)
#' # Removed mo_source file '~/.mo_source.rds'.
#' ```
#' @importFrom dplyr select everything
#' @export
#' @inheritSection AMR Read more on our website!
set_mo_source <- function(path) {
@ -137,13 +136,13 @@ set_mo_source <- function(path) {
try(
df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
silent = TRUE)
if (!mo_source_isvalid(df)) {
if (!mo_source_isvalid(df, stop_on_error = FALSE)) {
# try tab
try(
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
silent = TRUE)
}
if (!mo_source_isvalid(df)) {
if (!mo_source_isvalid(df, stop_on_error = FALSE)) {
# try pipe
try(
df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
@ -151,9 +150,8 @@ set_mo_source <- function(path) {
}
}
if (!mo_source_isvalid(df)) {
stop("File must contain a column with self-defined values and a reference column `mo` with valid values from the `microorganisms` data set.")
}
# check integrity
mo_source_isvalid(df)
df <- df %>% filter(!is.na(mo))
@ -201,7 +199,7 @@ get_mo_source <- function() {
}
}
mo_source_isvalid <- function(x) {
mo_source_isvalid <- function(x, refer_to_name = "`reference_df`", stop_on_error = TRUE) {
check_dataset_integrity()
@ -212,13 +210,41 @@ mo_source_isvalid <- function(x) {
return(TRUE)
}
if (is.null(x)) {
return(TRUE)
if (stop_on_error == TRUE) {
stop(refer_to_name, " cannot be NULL.", call. = FALSE)
} else {
return(FALSE)
}
}
if (!is.data.frame(x)) {
return(FALSE)
if (stop_on_error == TRUE) {
stop(refer_to_name, " must be a data.frame.", call. = FALSE)
} else {
return(FALSE)
}
}
if (!"mo" %in% colnames(x)) {
return(FALSE)
if (stop_on_error == TRUE) {
stop(refer_to_name, " must contain a column 'mo'.", call. = FALSE)
} else {
return(FALSE)
}
}
all(x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)
if (!all(x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)) {
if (stop_on_error == TRUE) {
invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old)), , drop = FALSE]
if (nrow(invalid) > 1) {
plural <- "s"
} else {
plural <- ""
}
stop("Value", plural, " ", paste0("'", invalid[, 1, drop = TRUE], "'", collapse = ", "),
" found in ", tolower(refer_to_name),
", but with invalid microorganism code", plural, " ", paste0("'", invalid$mo, "'", collapse = ", "), ".",
call. = FALSE)
} else {
return(FALSE)
}
}
TRUE
}