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(v1.7.1.9070) Better WHONET support

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-12-13 10:18:28 +01:00
parent f90e27c1b0
commit 578e7dfee9
74 changed files with 20758 additions and 47402 deletions
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22
R/aa_helper_functions.R
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@ -1096,14 +1096,30 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
}
set_clean_class(pb, new_class = "txtProgressBar")
} else if (n >= n_min) {
pb <- utils::txtProgressBar(max = n, style = 3)
pb$tick <- function() {
pb$up(pb$getVal() + 1)
# rely on the progress package if it is available - it has a more verbose output
progress_bar <- import_fn("progress_bar", "progress", error_on_fail = FALSE)
if (!is.null(progress_bar)) {
# so we use progress::progress_bar
# a close() method was also added, see below this function
pb <- progress_bar$new(format = "[:bar] :percent (:current/:total)",
total = n)
} else {
pb <- utils::txtProgressBar(max = n, style = 3)
pb$tick <- function() {
pb$up(pb$getVal() + 1)
}
}
pb
}
}
#' @method close progress_bar
#' @export
#' @noRd
close.progress_bar <- function(con, ...) {
con$terminate()
}
set_clean_class <- function(x, new_class) {
# return the object with only the new class and no additional attributes where possible
if (is.null(x)) {

2
R/ab.R
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@ -155,7 +155,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x[known_codes_atc],
function(x_) which(vapply(FUN.VALUE = logical(1),
AB_lookup$atc,
function(atc) x_ %in% atc)),
function(atc) x_ %in% atc))[1L],
USE.NAMES = FALSE)]
x_new[known_codes_cid] <- AB_lookup$ab[match(x[known_codes_cid], AB_lookup$cid)]
already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid

2
R/ab_selectors.R
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@ -478,7 +478,7 @@ ab_select_exec <- function(function_name,
sort = FALSE, fn = function_name)
# untreatable drugs
if (only_treatable == TRUE) {
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening"), "ab", drop = TRUE]
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ",

3
R/data.R
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@ -246,13 +246,14 @@
#' - `method`\cr Either `r vector_or(rsi_translation$method)`
#' - `site`\cr Body site, e.g. "Oral" or "Respiratory"
#' - `mo`\cr Microbial ID, see [as.mo()]
#' - `rank_index`\cr Taxonomic rank index of `mo` from 1 (subspecies/infraspecies) to 5 (unknown microorganism)
#' - `ab`\cr Antibiotic ID, see [as.ab()]
#' - `ref_tbl`\cr Info about where the guideline rule can be found
#' - `disk_dose`\cr Dose of the used disk diffusion method
#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
#' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
#' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection AMR Read more on Our Website!
#' @seealso [intrinsic_resistant]

61
R/mo.R
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@ -469,7 +469,7 @@ exec_as.mo <- function(x,
x_backup_untouched <- x
x <- strip_whitespace(x, dyslexia_mode)
# translate 'unknown' names back to English
if (any(x %like% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
if (any(tolower(x) %like_case% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
trns <- subset(TRANSLATIONS, pattern %like% "unknown")
langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
for (l in langs) {
@ -493,6 +493,11 @@ exec_as.mo <- function(x,
x_backup[x %like_case% "^(fungus|fungi)$"] <- "(unknown fungus)" # will otherwise become the kingdom
x_backup[x_backup_untouched == "Fungi"] <- "Fungi" # is literally the kingdom
# remove spp and species
x_backup <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x_backup, perl = TRUE)
x_backup <- gsub("( spp?.?| ss |subsp.?|subspecies|biovar|serovar|species)", "", x_backup, perl = TRUE)
x_backup <- strip_whitespace(x_backup, dyslexia_mode)
# Fill in fullnames and MO codes directly
known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
@ -503,23 +508,19 @@ exec_as.mo <- function(x,
microorganisms.codes$code), "mo", drop = TRUE],
MO_lookup$mo), property, drop = TRUE]
already_known <- known_names | known_codes_mo | known_codes_lis
# now only continue where the right taxonomic output is not already known
if (any(!already_known)) {
x_known <- x[already_known]
# remove spp and species
x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x)
x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x)
x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x, perl = TRUE) # when ending in SPE instead of SPP and preceded by 2-4 characters
x <- strip_whitespace(x, dyslexia_mode)
# when ending in SPE instead of SPP and preceded by 2-4 characters
x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x, perl = TRUE)
x_backup_without_spp <- x
x_species <- paste(x, "species")
# translate to English for supported languages of mo_property
x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x, perl = TRUE)
# no groups and complexes as ending
x <- gsub("(complex|group)$", "", x, perl = TRUE)
x <- gsub("(complex|group|serotype|serovar|serogroup)[^a-zA-Z]*$", "", x, perl = TRUE)
x <- gsub("(^|[^a-z])((an)?aero+b)[a-z]*", "", x, perl = TRUE)
x <- gsub("^atyp[a-z]*", "", x, perl = TRUE)
x <- gsub("(vergroen)[a-z]*", "viridans", x, perl = TRUE)
@ -546,12 +547,12 @@ exec_as.mo <- function(x,
# allow characters that resemble others = dyslexia_mode ----
if (dyslexia_mode == TRUE) {
x <- tolower(x)
x <- gsub("[iy]+", "[iy]+", x)
x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x)
x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x)
x <- gsub("(th|ht|t)+", "(th|ht|t)+", x)
x <- gsub("a+", "a+", x)
x <- gsub("u+", "u+", x)
x <- gsub("[iy]+", "[iy]+", x, perl = TRUE)
x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x, perl = TRUE)
x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x, perl = TRUE)
x <- gsub("(th|ht|t)+", "(th|ht|t)+", x, perl = TRUE)
x <- gsub("a+", "a+", x, perl = TRUE)
x <- gsub("u+", "u+", x, perl = TRUE)
# allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica, -ia and -a (needs perl for the negative backward lookup):
x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
@ -561,9 +562,9 @@ exec_as.mo <- function(x,
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
x <- gsub("(\\[iy\\]\\+a\\+)(?![a-z])",
"([iy]*a+|[iy]+a*)", x, perl = TRUE)
x <- gsub("e+", "e+", x)
x <- gsub("o+", "o+", x)
x <- gsub("(.)\\1+", "\\1+", x)
x <- gsub("e+", "e+", x, perl = TRUE)
x <- gsub("o+", "o+", x, perl = TRUE)
x <- gsub("(.)\\1+", "\\1+", x, perl = TRUE)
# allow multiplication of all other consonants
x <- gsub("([bdgjlnrw]+)", "\\1+", x, perl = TRUE)
# allow ending in -en or -us
@ -575,6 +576,8 @@ exec_as.mo <- function(x,
# allow au and ou after all above regex implementations
x <- gsub("a+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE)
x <- gsub("o+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE)
# correct for a forgotten Latin ae instead of e
x <- gsub("e+", "a*e+", x, fixed = TRUE)
}
x <- strip_whitespace(x, dyslexia_mode)
# make sure to remove regex overkill (will lead to errors)
@ -582,10 +585,9 @@ exec_as.mo <- function(x,
x <- gsub("?+", "?", x, fixed = TRUE)
x_trimmed <- x
x_trimmed_species <- paste(x_trimmed, "species")
x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed, perl = TRUE)
# remove last part from "-" or "/"
x_trimmed_without_group <- gsub("(.*)[-/].*", "\\1", x_trimmed_without_group)
x_trimmed_without_group <- gsub("(.*)[-/].*", "\\1", x_trimmed_without_group, perl = TRUE)
# replace space and dot by regex sign
x_withspaces <- gsub("[ .]+", ".* ", x, perl = TRUE)
x <- gsub("[ .]+", ".*", x, perl = TRUE)
@ -598,14 +600,12 @@ exec_as.mo <- function(x,
if (isTRUE(debug)) {
cat(paste0(font_blue("x"), ' "', x, '"\n'))
cat(paste0(font_blue("x_species"), ' "', x_species, '"\n'))
cat(paste0(font_blue("x_withspaces_start_only"), ' "', x_withspaces_start_only, '"\n'))
cat(paste0(font_blue("x_withspaces_end_only"), ' "', x_withspaces_end_only, '"\n'))
cat(paste0(font_blue("x_withspaces_start_end"), ' "', x_withspaces_start_end, '"\n'))
cat(paste0(font_blue("x_backup"), ' "', x_backup, '"\n'))
cat(paste0(font_blue("x_backup_without_spp"), ' "', x_backup_without_spp, '"\n'))
cat(paste0(font_blue("x_trimmed"), ' "', x_trimmed, '"\n'))
cat(paste0(font_blue("x_trimmed_species"), ' "', x_trimmed_species, '"\n'))
cat(paste0(font_blue("x_trimmed_without_group"), ' "', x_trimmed_without_group, '"\n'))
}
@ -914,20 +914,12 @@ exec_as.mo <- function(x,
d.x_withspaces_start_end,
e.x_withspaces_start_only,
f.x_withspaces_end_only,
g.x_backup_without_spp,
h.x_species,
i.x_trimmed_species) {
g.x_backup_without_spp) {
# FIRST TRY FULLNAMES AND CODES ----
# if only genus is available, return only genus
if (all(c(x[i], b.x_trimmed) %unlike_case% " ")) {
found <- lookup(fullname_lower %in% c(h.x_species, i.x_trimmed_species),
haystack = data_to_check)
if (!is.na(found)) {
x[i] <- found[1L]
return(x[i])
}
if (nchar(g.x_backup_without_spp) >= 6) {
found <- lookup(fullname_lower %like_case% paste0("^", unregex(g.x_backup_without_spp), "[a-z]+"),
haystack = data_to_check)
@ -1425,14 +1417,11 @@ exec_as.mo <- function(x,
d.x_withspaces_start_end = x_withspaces_start_end[i],
e.x_withspaces_start_only = x_withspaces_start_only[i],
f.x_withspaces_end_only = x_withspaces_end_only[i],
g.x_backup_without_spp = x_backup_without_spp[i],
h.x_species = x_species[i],
i.x_trimmed_species = x_trimmed_species[i])
g.x_backup_without_spp = x_backup_without_spp[i])
if (!empty_result(x[i])) {
next
}
# no results found: make them UNKNOWN ----
x[i] <- lookup(mo == "UNKNOWN", uncertainty = -1)
if (initial_search == TRUE) {

1
R/plot.R
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@ -146,6 +146,7 @@ plot.mic <- function(x,
legend_txt <- c(legend_txt, "Resistant")
legend_col <- c(legend_col, colours_RSI[1])
}
legend("top",
x.intersp = 0.5,
legend = translate_AMR(legend_txt, language = language),

15
R/rsi.R
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@ -836,11 +836,11 @@ exec_as.rsi <- function(method,
get_record <- get_record %pm>%
# be as specific as possible (i.e. prefer species over genus):
# pm_desc(uti) = TRUE on top and FALSE on bottom
pm_arrange(pm_desc(uti), pm_desc(nchar(mo))) # 'uti' is a column in data set 'rsi_translation'
pm_arrange(pm_desc(uti), rank_index) # 'uti' is a column in data set 'rsi_translation'
} else {
get_record <- get_record %pm>%
pm_filter(uti == FALSE) %pm>% # 'uti' is a column in rsi_translation
pm_arrange(pm_desc(nchar(mo)))
pm_arrange(rank_index)
}
get_record <- get_record[1L, , drop = FALSE]
@ -851,21 +851,16 @@ exec_as.rsi <- function(method,
} else if (method == "mic") {
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
# start interpreting: EUCAST uses <= S and > R, CLSI uses <=S and >= R
# these basically call `<=.mic()` and `>=.mic()`:
x[i] <= get_record$breakpoint_S ~ "S",
guideline_coerced %like% "EUCAST" & x[i] > get_record$breakpoint_R ~ "R",
guideline_coerced %like% "CLSI" & x[i] >= get_record$breakpoint_R ~ "R",
x[i] >= get_record$breakpoint_R ~ "R",
# return "I" when not match the bottom or top
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
# and NA otherwise
TRUE ~ NA_character_)
} else if (method == "disk") {
new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
# start interpreting: EUCAST uses >= S and < R, CLSI uses >=S and <= R
guideline_coerced %like% "EUCAST" &
isTRUE(as.double(x[i]) < as.double(get_record$breakpoint_R)) ~ "R",
guideline_coerced %like% "CLSI" &
isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
# return "I" when not match the bottom or top
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
# and NA otherwise

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R/sysdata.rda
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