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(v1.3.0.9031) matching score update

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dr. M.S. (Matthijs) Berends
2020-09-26 16:51:17 +02:00
parent 050a9a04fb
commit 22f6ceb3e4
19 changed files with 85 additions and 81 deletions
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16
R/mo.R
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@ -301,7 +301,7 @@ exec_as.mo <- function(x,
initial = initial_search,
uncertainty = actual_uncertainty,
input_actual = actual_input) {
if (!is.null(input_actual)) {
input <- input_actual
} else {
@ -318,7 +318,7 @@ exec_as.mo <- function(x,
if (NROW(res_df) > 1 & uncertainty != -1) {
# sort the findings on matching score
scores <- mo_matching_score(x = input,
fullname = res_df[, "fullname", drop = TRUE])
n = res_df[, "fullname", drop = TRUE])
res_df <- res_df[order(scores, decreasing = TRUE), , drop = FALSE]
}
res <- as.character(res_df[, column, drop = TRUE])
@ -442,7 +442,7 @@ exec_as.mo <- function(x,
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
x <- MO_lookup[match(tolower(x), MO_lookup$fullname_lower), property, drop = TRUE]
} else if (all(x %in% reference_data_to_use$fullname)) {
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
@ -1544,7 +1544,7 @@ exec_as.mo <- function(x,
# this will save the uncertain items as attribute, so they can be bound to `uncertainties` in the uncertain_fn() function
x <- structure(x, uncertainties = uncertainties)
}
if (old_mo_warning == TRUE & property != "mo") {
warning("The input contained old microorganism IDs from previous versions of this package.\nPlease use `as.mo()` on these old IDs to transform them to the new format.\nSUPPORT FOR THIS WILL BE DROPPED IN A FUTURE VERSION.", call. = FALSE)
@ -1639,7 +1639,7 @@ freq.mo <- function(x, ...) {
")"),
`No. of genera` = pm_n_distinct(mo_genus(x_noNA, language = NULL)),
`No. of species` = pm_n_distinct(paste(mo_genus(x_noNA, language = NULL),
mo_species(x_noNA, language = NULL)))))
mo_species(x_noNA, language = NULL)))))
}
#' @method print mo
@ -1773,7 +1773,7 @@ print.mo_uncertainties <- function(x, ...) {
if (x[i, ]$candidates != "") {
candidates <- unlist(strsplit(x[i, ]$candidates, ", ", fixed = TRUE))
scores <- mo_matching_score(x = x[i, ]$input,
fullname = candidates)
n = candidates)
# sort on descending scores
candidates <- candidates[order(1 - scores)]
n_candidates <- length(candidates)
@ -1799,8 +1799,8 @@ print.mo_uncertainties <- function(x, ...) {
ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""),
" (", x[i, ]$mo,
", matching score = ", trimws(percentage(mo_matching_score(x = x[i, ]$input,
fullname = x[i, ]$fullname),
digits = 1)),
n = x[i, ]$fullname),
digits = 1)),
") "),
uncertainty_interpretation,
candidates),