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(v1.5.0.9015) unit test fix, grouped first isolates

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dr. M.S. (Matthijs) Berends
2021-02-04 16:48:16 +01:00
parent 2eca8c3f01
commit 8fda473e49
44 changed files with 239 additions and 168 deletions
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12
R/mo.R
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@ -1418,7 +1418,7 @@ exec_as.mo <- function(x,
" (covering ", percentage(total_failures / total_n),
") could not be coerced and ", plural[3], " considered 'unknown'")
if (pm_n_distinct(failures) <= 10) {
msg <- paste0(msg, ": ", paste('"', unique(failures), '"', sep = "", collapse = ", "))
msg <- paste0(msg, ": ", vector_and(failures, quotes = TRUE))
}
msg <- paste0(msg,
".\nUse mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` argument if needed (see ?as.mo).\n",
@ -1450,7 +1450,7 @@ exec_as.mo <- function(x,
# - Becker et al. 2014, PMID 25278577
# - Becker et al. 2019, PMID 30872103
# - Becker et al. 2020, PMID 32056452
post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers (otherwise uncomment below)
post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers (otherwise uncomment the section below)
# nolint start
# if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
@ -1796,7 +1796,6 @@ print.mo_uncertainties <- function(x, ...) {
return(NULL)
}
message_("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See ?mo_matching_score.", as_note = FALSE)
cat("\n")
msg <- ""
for (i in seq_len(nrow(x))) {
@ -1807,7 +1806,7 @@ print.mo_uncertainties <- function(x, ...) {
candidates <- candidates[order(1 - scores)]
scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3))
n_candidates <- length(candidates)
candidates <- paste0(candidates, " (", scores_formatted[order(1 - scores)], ")", collapse = ", ")
candidates <- vector_and(paste0(candidates, " (", scores_formatted[order(1 - scores)], ")"), quotes = FALSE)
# align with input after arrow
candidates <- paste0("\n",
strwrap(paste0("Also matched",
@ -1987,9 +1986,8 @@ replace_ignore_pattern <- function(x, ignore_pattern) {
ignore_cases <- x %like% ignore_pattern
if (sum(ignore_cases) > 0) {
message_("The following input was ignored by `ignore_pattern = \"", ignore_pattern, "\"`: ",
paste0("'", sort(unique(x[x %like% ignore_pattern])), "'", collapse = ", "),
collapse = ", ")
x[x %like% ignore_pattern] <- NA_character_
vector_and(x[ignore_cases], quotes = TRUE))
x[ignore_cases] <- NA_character_
}
}
x