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(v1.2.0.9011) mo_domain(), improved error handling

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dr. M.S. (Matthijs) Berends
2020-06-22 11:18:40 +02:00
parent e88d7853f5
commit 93a158aebd
49 changed files with 523 additions and 590 deletions
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12
R/mo.R
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@ -350,9 +350,8 @@ exec_as.mo <- function(x,
# defined df to check for
if (!is.null(reference_df)) {
if (!mo_source_isvalid(reference_df)) {
stop("`reference_df` must contain a column `mo` with values from the 'microorganisms' data set.", call. = FALSE)
}
mo_source_isvalid(reference_df)
reference_df <- reference_df %>% filter(!is.na(mo))
# keep only first two columns, second must be mo
if (colnames(reference_df)[1] == "mo") {
@ -1760,9 +1759,8 @@ translate_allow_uncertain <- function(allow_uncertain) {
allow_uncertain[tolower(allow_uncertain) == "none"] <- 0
allow_uncertain[tolower(allow_uncertain) == "all"] <- 3
allow_uncertain <- as.integer(allow_uncertain)
if (!allow_uncertain %in% c(0:3)) {
stop('`allow_uncertain` must be a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0).', call. = FALSE)
}
stop_ifnot(allow_uncertain %in% c(0:3),
'`allow_uncertain` must be a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0)', call = FALSE)
}
allow_uncertain
}
@ -1803,7 +1801,7 @@ parse_and_convert <- function(x) {
tryCatch({
if (!is.null(dim(x))) {
if (NCOL(x) > 2) {
stop("A maximum of two columns is allowed.", call. = FALSE)
stop("a maximum of two columns is allowed", call. = FALSE)
} else if (NCOL(x) == 2) {
# support Tidyverse selection like: df %>% select(colA, colB)
# paste these columns together