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(v0.7.1.9030) eucast_rules() fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-08 15:52:07 +02:00
parent f67c739892
commit 22a206ffd8
70 changed files with 470 additions and 420 deletions
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17
R/eucast_rules.R
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@ -416,10 +416,12 @@ eucast_rules <- function(x,
},
error = function(e) {
txt_error()
stop(paste0("Error in row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
'... while writing value "', to,
stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
ifelse(length(rows) > 10, "...", ""),
' while writing value "', to,
'" to column(s) `', paste(cols, collapse = "`, `"),
"` (data class:", paste(class(x_original), collapse = "/"), "):\n", e$message), call. = FALSE)
"` (data class: ", paste(class(x_original), collapse = "/"), "):\n", e$message),
call. = FALSE)
}
)
@ -520,6 +522,9 @@ eucast_rules <- function(x,
x <- trimws(unlist(strsplit(x, ",", fixed = TRUE)))
y <- character(0)
for (i in 1:length(x)) {
if (is.function(get(x[i]))) {
stop("Column ", x[i], " is also a function. Please create an issue on github.com/msberends/AMR/issues.")
}
y <- c(y, tryCatch(get(x[i]), error = function(e) ""))
}
y[y != "" & y %in% colnames(df)]
@ -736,7 +741,7 @@ eucast_rules <- function(x,
mutate(plural = ifelse(n > 1, "s", ""),
txt = paste0(formatnr(n), " test result", plural, " added as ", new)) %>%
pull(txt) %>%
paste(" *", ., collapse = "\n") %>%
paste(" -", ., collapse = "\n") %>%
cat()
}
@ -765,7 +770,7 @@ eucast_rules <- function(x,
mutate(plural = ifelse(n > 1, "s", ""),
txt = paste0(formatnr(n), " test result", plural, " changed from ", old, " to ", new)) %>%
pull(txt) %>%
paste(" *", ., collapse = "\n") %>%
paste(" -", ., collapse = "\n") %>%
cat()
cat("\n")
}
@ -774,7 +779,7 @@ eucast_rules <- function(x,
if (verbose == FALSE & nrow(verbose_info) > 0) {
cat(paste("\nUse", bold("eucast_rules(..., verbose = TRUE)"), "(on your original data) to get a data.frame with all specified edits instead.\n\n"))
} else if (verbose == TRUE) {
cat(paste(red("\nUsed 'Verbose mode' (verbose = TRUE)"), ", which returns a data.frame with all specified edits.\nUse", bold("verbose = FALSE"), "to apply the rules on your data.\n\n"))
cat(paste0("\nUsed 'Verbose mode' (", bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", bold("verbose = FALSE"), " to apply the rules on your data.\n\n"))
}
}