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(v1.4.0.9015) bugfix

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dr. M.S. (Matthijs) Berends
2020-11-10 16:35:56 +01:00
parent dd5a0319ef
commit 15c732703d
35 changed files with 224 additions and 161 deletions
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41
R/mo.R
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@ -173,7 +173,7 @@ as.mo <- function(x,
& isFALSE(Becker)
& isFALSE(Lancefield), error = function(e) FALSE)) {
# don't look into valid MO codes, just return them
# is.mo() won't work - codes might change between package versions
# is.mo() won't work - MO codes might change between package versions
return(to_class_mo(x))
}
@ -1393,9 +1393,10 @@ exec_as.mo <- function(x,
"You can also use your own reference data, e.g.:\n",
' as.mo("mycode", reference_df = data.frame(own = "mycode", mo = "B_ESCHR_COLI"))\n',
' mo_name("mycode", reference_df = data.frame(own = "mycode", mo = "B_ESCHR_COLI"))\n')
warning(font_red(paste0("\n", msg)),
call. = FALSE,
immediate. = TRUE) # thus will always be shown, even if >= warnings
warning_(paste0("\n", msg),
add_fn = font_red,
call = FALSE,
immediate = TRUE) # thus will always be shown, even if >= warnings
}
# handling uncertainties ----
if (NROW(uncertainties) > 0 & initial_search == TRUE) {
@ -1420,13 +1421,13 @@ exec_as.mo <- function(x,
post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
font_italic(paste("S.",
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
collapse = ", ")),
".",
call. = FALSE,
immediate. = TRUE)
warning_("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
font_italic(paste("S.",
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
collapse = ", ")),
".",
call = FALSE,
immediate = TRUE)
}
# 'MO_CONS' and 'MO_COPS' are <mo> vectors created in R/zzz.R
@ -1903,13 +1904,14 @@ replace_old_mo_codes <- function(x, property) {
mo_new <- microorganisms.translation$mo_new[matched]
# assign on places where a match was found
x[which(!is.na(matched))] <- mo_new[which(!is.na(matched))]
n_matched <- length(matched[!is.na(matched)])
if (property != "mo") {
message_(font_blue("NOTE: The input contained old microbial codes (from previous package versions). Please update your MO codes with as.mo()."))
} else {
if (length(matched) == 1) {
message_(font_blue("NOTE: 1 old microbial code (from previous package versions) was updated to a current used code."))
if (n_matched == 1) {
message_(font_blue("NOTE: 1 old microbial code (from previous package versions) was updated to a current used MO code."))
} else {
message_(font_blue("NOTE:", length(matched), "old microbial codes (from previous package versions) were updated to current used codes."))
message_(font_blue("NOTE:", n_matched, "old microbial codes (from previous package versions) were updated to current used MO codes."))
}
}
}
@ -1940,13 +1942,14 @@ repair_reference_df <- function(reference_df) {
} else {
reference_df <- reference_df %pm>% pm_select(1, "mo")
}
# some microbial codes might be old
reference_df[, 2] <- as.mo(reference_df[, 2, drop = TRUE])
# remove factors, just keep characters
suppressWarnings(
reference_df[] <- lapply(reference_df, as.character)
)
colnames(reference_df)[1] <- "x"
reference_df[, "x"] <- as.character(reference_df[, "x", drop = TRUE])
reference_df[, "mo"] <- as.character(reference_df[, "mo", drop = TRUE])
# some microbial codes might be old
reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE])
reference_df
}