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(v1.5.0.9022) mo properties speed improvement

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dr. M.S. (Matthijs) Berends
2021-02-21 22:56:35 +01:00
parent 5ef8cb41a7
commit 062c49fca1
19 changed files with 76 additions and 47 deletions
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25
R/mo.R
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@ -178,13 +178,6 @@ as.mo <- function(x,
return(set_clean_class(x, new_class = c("mo", "character")))
}
if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
& isFALSE(Becker)
& isFALSE(Lancefield), error = function(e) FALSE)) {
# to improve speed, special case for taxonomically correct full names (case-insensitive)
return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
}
# start off with replaced language-specific non-ASCII characters with ASCII characters
x <- parse_and_convert(x)
# replace mo codes used in older package versions
@ -198,6 +191,13 @@ as.mo <- function(x,
x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
& isFALSE(Becker)
& isFALSE(Lancefield), error = function(e) FALSE)) {
# to improve speed, special case for taxonomically correct full names (case-insensitive)
return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
}
if (!is.null(reference_df)
&& check_validity_mo_source(reference_df)
@ -481,11 +481,11 @@ exec_as.mo <- function(x,
# Fill in fullnames and MO codes at once
known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname), property, drop = TRUE]
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
known_codes <- toupper(x_backup) %in% MO_lookup$mo
x[known_codes] <- MO_lookup[match(toupper(x_backup)[known_codes], MO_lookup$mo), property, drop = TRUE]
already_known <- known_names | known_codes
# now only continue where the right taxonomic output is not already known
if (any(!already_known)) {
x_known <- x[already_known]
@ -984,7 +984,6 @@ exec_as.mo <- function(x,
g.x_backup_without_spp %pm>% substr(1, x_length / 2),
".* ",
g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
print(x_split)
found <- lookup(fullname_lower %like_case% x_split,
haystack = data_to_check)
if (!is.na(found)) {
@ -1977,13 +1976,13 @@ parse_and_convert <- function(x) {
if (NCOL(x) > 2) {
stop("a maximum of two columns is allowed", call. = FALSE)
} else if (NCOL(x) == 2) {
# support Tidyverse selection like: df %pm>% select(colA, colB)
# support Tidyverse selection like: df %>% select(colA, colB)
# paste these columns together
x <- as.data.frame(x, stringsAsFactors = FALSE)
colnames(x) <- c("A", "B")
x <- paste(x$A, x$B)
} else {
# support Tidyverse selection like: df %pm>% select(colA)
# support Tidyverse selection like: df %>% select(colA)
x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
}
}
@ -1991,6 +1990,8 @@ parse_and_convert <- function(x) {
parsed <- iconv(x, to = "UTF-8")
parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
parsed <- gsub('"', "", parsed, fixed = TRUE)
parsed <- gsub(" +", " ", parsed, perl = TRUE)
parsed <- trimws(parsed)
}, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
parsed
}