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unit tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-06-22 14:16:25 +02:00
parent 3083828e15
commit c8bda784a6
3 changed files with 8 additions and 6 deletions
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4
R/mo.R
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@@ -267,6 +267,8 @@ as.mo <- function(x,
x_out <- trimws2(gsub(" +", " ", x_out, perl = TRUE))
x_search_cleaned <- x_out
x_out <- tolower(x_out)
# when x_search_cleaned are only capitals (such as in codes), make them lowercase to increase matching score
x_search_cleaned[x_search_cleaned == toupper(x_search_cleaned)] <- x_out[x_search_cleaned == toupper(x_search_cleaned)]
# first check if cleaning led to an exact result, case-insensitive
if (x_out %in% AMR_env$MO_lookup$fullname_lower) {
@@ -334,7 +336,7 @@ as.mo <- function(x,
# correct back for kingdom
minimum_matching_score_current <- minimum_matching_score_current / AMR_env$MO_lookup$kingdom_index[match(mo_to_search, AMR_env$MO_lookup$fullname)]
minimum_matching_score_current <- pmax(minimum_matching_score_current, m)
if (all(m <= 0.55, na.rm = TRUE)) {
if (length(m) > 1 && all(m <= 0.55, na.rm = TRUE)) {
# if the highest score is 0.5, we have nothing serious - 0.5 is the lowest for pathogenic group 1
# make everything NA so the results will get removed below
m[seq_len(length(m))] <- NA_real_