mirror of https://github.com/msberends/AMR
(v0.7.1.9058) as.mo() improvement
parent
04d49a62af
commit
7c069145ac
|
|
@ -1,6 +1,6 @@
|
|||
Package: AMR
|
||||
Version: 0.7.1.9057
|
||||
Date: 2019-08-15
|
||||
Version: 0.7.1.9058
|
||||
Date: 2019-08-20
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
person(role = c("aut", "cre"),
|
||||
|
|
|
|||
|
|
@ -233,6 +233,7 @@ importFrom(crayon,bold)
|
|||
importFrom(crayon,green)
|
||||
importFrom(crayon,italic)
|
||||
importFrom(crayon,magenta)
|
||||
importFrom(crayon,make_style)
|
||||
importFrom(crayon,red)
|
||||
importFrom(crayon,silver)
|
||||
importFrom(crayon,strip_style)
|
||||
|
|
|
|||
2
NEWS.md
2
NEWS.md
|
|
@ -1,4 +1,4 @@
|
|||
# AMR 0.7.1.9057
|
||||
# AMR 0.7.1.9058
|
||||
|
||||
### Breaking
|
||||
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
|
||||
|
|
|
|||
|
|
@ -119,7 +119,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
|
|||
#' @rdname eucast_rules
|
||||
#' @export
|
||||
#' @importFrom dplyr %>% select pull mutate_at vars group_by summarise n
|
||||
#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style white red
|
||||
#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style white red make_style
|
||||
#' @importFrom utils menu
|
||||
#' @return The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations.
|
||||
#' @source
|
||||
|
|
@ -197,7 +197,8 @@ eucast_rules <- function(x,
|
|||
q_continue <- menu(choices = c("OK", "Cancel"), graphics = TRUE, title = txt)
|
||||
}
|
||||
if (q_continue %in% c(FALSE, 2)) {
|
||||
return(invisible())
|
||||
message("Cancelled, returning original data")
|
||||
return(x)
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -228,6 +229,8 @@ eucast_rules <- function(x,
|
|||
trimws(format(x, big.mark = big.mark, decimal.mark = decimal.mark))
|
||||
}
|
||||
|
||||
grey <- make_style("grey")
|
||||
|
||||
warned <- FALSE
|
||||
|
||||
txt_error <- function() { cat("", bgRed(white(" ERROR ")), "\n\n") }
|
||||
|
|
@ -235,21 +238,21 @@ eucast_rules <- function(x,
|
|||
txt_ok <- function(no_added, no_changed) {
|
||||
if (warned == FALSE) {
|
||||
if (no_added + no_changed == 0) {
|
||||
cat(green(" (no changes)\n"))
|
||||
cat(pillar::style_subtle(" (no changes)\n"))
|
||||
} else {
|
||||
# opening
|
||||
cat(blue(" ("))
|
||||
cat(grey(" ("))
|
||||
# additions
|
||||
if (no_added > 0) {
|
||||
if (no_added == 1) {
|
||||
cat(blue("1 value added"))
|
||||
cat(green("1 value added"))
|
||||
} else {
|
||||
cat(blue(formatnr(no_added), "values added"))
|
||||
cat(green(formatnr(no_added), "values added"))
|
||||
}
|
||||
}
|
||||
# separator
|
||||
if (no_added > 0 & no_changed > 0) {
|
||||
cat(blue(", "))
|
||||
cat(grey(", "))
|
||||
}
|
||||
# changes
|
||||
if (no_changed > 0) {
|
||||
|
|
@ -260,7 +263,7 @@ eucast_rules <- function(x,
|
|||
}
|
||||
}
|
||||
# closing
|
||||
cat(blue(")\n"))
|
||||
cat(grey(")\n"))
|
||||
}
|
||||
warned <<- FALSE
|
||||
}
|
||||
|
|
@ -770,7 +773,7 @@ eucast_rules <- function(x,
|
|||
verbose_info <- verbose_info %>%
|
||||
arrange(row, rule_group, rule_name, col)
|
||||
|
||||
cat(paste0("\n", silver(strrep("-", options()$width - 1)), "\n"))
|
||||
cat(paste0("\n", grey(strrep("-", options()$width - 1)), "\n"))
|
||||
cat(bold(paste('EUCAST rules', paste0(wouldve, 'affected'),
|
||||
formatnr(n_distinct(verbose_info$row)),
|
||||
'out of', formatnr(nrow(x_original)),
|
||||
|
|
@ -783,7 +786,7 @@ eucast_rules <- function(x,
|
|||
if (n_added == 0) {
|
||||
colour <- cat # is function
|
||||
} else {
|
||||
colour <- blue # is function
|
||||
colour <- green # is function
|
||||
}
|
||||
cat(colour(paste0("=> ", wouldve, "added ",
|
||||
bold(formatnr(verbose_info %>%
|
||||
|
|
@ -828,7 +831,7 @@ eucast_rules <- function(x,
|
|||
cat()
|
||||
cat("\n")
|
||||
}
|
||||
cat(paste0(silver(strrep("-", options()$width - 1)), "\n"))
|
||||
cat(paste0(grey(strrep("-", options()$width - 1)), "\n"))
|
||||
|
||||
if (verbose == FALSE & nrow(verbose_info) > 0) {
|
||||
cat(paste("\nUse", bold("eucast_rules(..., verbose = TRUE)"), "(on your original data) to get a data.frame with all specified edits instead.\n\n"))
|
||||
|
|
|
|||
172
R/mo.R
172
R/mo.R
|
|
@ -314,6 +314,7 @@ exec_as.mo <- function(x,
|
|||
options(mo_uncertainties = NULL)
|
||||
options(mo_renamed = NULL)
|
||||
}
|
||||
options(mo_renamed_last_run = NULL)
|
||||
|
||||
if (NCOL(x) == 2) {
|
||||
# support tidyverse selection like: df %>% select(colA, colB)
|
||||
|
|
@ -336,9 +337,12 @@ exec_as.mo <- function(x,
|
|||
}
|
||||
|
||||
notes <- character(0)
|
||||
uncertainties <- data.frame(input = character(0),
|
||||
uncertainties <- data.frame(uncertainty = integer(0),
|
||||
input = character(0),
|
||||
fullname = character(0),
|
||||
mo = character(0))
|
||||
renamed_to = character(0),
|
||||
mo = character(0),
|
||||
stringsAsFactors = FALSE)
|
||||
failures <- character(0)
|
||||
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
|
||||
|
||||
|
|
@ -488,11 +492,13 @@ exec_as.mo <- function(x,
|
|||
# replace minus by a space
|
||||
x <- gsub("-+", " ", x)
|
||||
# replace hemolytic by haemolytic
|
||||
x <- gsub("ha?emoly", "haemoly", x)
|
||||
x <- gsub("ha?emoly", "haemoly", x, ignore.case = TRUE)
|
||||
# place minus back in streptococci
|
||||
x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x)
|
||||
x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x, ignore.case = TRUE)
|
||||
# remove genus as first word
|
||||
x <- gsub("^Genus ", "", x)
|
||||
x <- gsub("^genus ", "", x, ignore.case = TRUE)
|
||||
# remove 'uncertain' like texts
|
||||
x <- trimws(gsub("(uncertain|susp[ie]c[a-z]+|verdacht)", "", x, ignore.case = TRUE))
|
||||
# allow characters that resemble others = dyslexia_mode ----
|
||||
if (dyslexia_mode == TRUE) {
|
||||
x <- tolower(x)
|
||||
|
|
@ -514,10 +520,11 @@ exec_as.mo <- function(x,
|
|||
x <- gsub("(.)\\1+", "\\1+", x)
|
||||
# allow ending in -en or -us
|
||||
x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, ignore.case = TRUE, perl = TRUE)
|
||||
# if the input is longer than 10 characters, add a [.] between all characters, as some might have forgotten a character
|
||||
# if the input is longer than 10 characters, allow any constant between all characters, as some might have forgotten a character
|
||||
# this will allow "Pasteurella damatis" to be correctly read as "Pasteurella dagmatis".
|
||||
x[nchar(x_backup_without_spp) > 10] <- gsub("([a-z])([a-z])", "\\1.*\\2", x[nchar(x_backup_without_spp) > 10], ignore.case = TRUE)
|
||||
x[nchar(x_backup_without_spp) > 10] <- gsub("[+]", "+.*", x[nchar(x_backup_without_spp) > 10])
|
||||
constants <- paste(letters[!letters %in% c("a", "e", "i", "o", "u")], collapse = "")
|
||||
#x[nchar(x_backup_without_spp) > 10] <- gsub("([a-z])([a-z])", paste0("\\1[", constants, "]?\\2"), x[nchar(x_backup_without_spp) > 10], ignore.case = TRUE)
|
||||
x[nchar(x_backup_without_spp) > 10] <- gsub("[+]", paste0("+[", constants, "]?"), x[nchar(x_backup_without_spp) > 10])
|
||||
}
|
||||
x <- strip_whitespace(x)
|
||||
|
||||
|
|
@ -825,10 +832,9 @@ exec_as.mo <- function(x,
|
|||
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
|
||||
}
|
||||
uncertainties <- rbind(uncertainties,
|
||||
data.frame(uncertainty = 1,
|
||||
data.frame(uncertainty_level = 1,
|
||||
input = x_backup_without_spp[i],
|
||||
fullname = microorganismsDT[mo == "B_SLMNL_ENT", fullname][[1]],
|
||||
mo = "B_SLMNL_ENT"))
|
||||
result_mo = "B_SLMNL_ENT"))
|
||||
}
|
||||
next
|
||||
}
|
||||
|
|
@ -1051,6 +1057,7 @@ exec_as.mo <- function(x,
|
|||
} else {
|
||||
x[i] <- microorganismsDT[col_id == found[1, col_id_new], ..property][[1]]
|
||||
}
|
||||
options(mo_renamed_last_run = found[1, fullname])
|
||||
was_renamed(name_old = found[1, fullname],
|
||||
name_new = microorganismsDT[col_id == found[1, col_id_new], fullname],
|
||||
ref_old = found[1, ref],
|
||||
|
|
@ -1081,7 +1088,7 @@ exec_as.mo <- function(x,
|
|||
|
||||
# (1) look again for old taxonomic names, now for G. species ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 1] (1) look again for old taxonomic names, now for G. species\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (1) look again for old taxonomic names, now for G. species\n")
|
||||
}
|
||||
if (isTRUE(debug)) {
|
||||
message("Running '", c.x_withspaces_start_end, "' and '", d.x_withspaces_start_only, "'")
|
||||
|
|
@ -1102,11 +1109,11 @@ exec_as.mo <- function(x,
|
|||
ref_old = found[1, ref],
|
||||
ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
|
||||
mo = microorganismsDT[col_id == found[1, col_id_new], mo])
|
||||
options(mo_renamed_last_run = found[1, fullname])
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = found[1, fullname],
|
||||
mo = paste("CoL", found[1, col_id])))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = microorganismsDT[col_id == found[1, col_id_new], mo]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(x, property), 1, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1116,7 +1123,7 @@ exec_as.mo <- function(x,
|
|||
# (2) Try with misspelled input ----
|
||||
# just rerun with dyslexia_mode = TRUE will used the extensive regex part above
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 1] (2) Try with misspelled input\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (2) Try with misspelled input\n")
|
||||
}
|
||||
if (isTRUE(debug)) {
|
||||
message("Running '", a.x_backup, "'")
|
||||
|
|
@ -1131,10 +1138,9 @@ exec_as.mo <- function(x,
|
|||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 1, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1148,7 +1154,7 @@ exec_as.mo <- function(x,
|
|||
|
||||
# (3) look for genus only, part of name ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 2] (3) look for genus only, part of name\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n")
|
||||
}
|
||||
if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like% " ") {
|
||||
if (!grepl("^[A-Z][a-z]+", b.x_trimmed, ignore.case = FALSE)) {
|
||||
|
|
@ -1160,10 +1166,9 @@ exec_as.mo <- function(x,
|
|||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found[1L], fullname][[1]],
|
||||
mo = found[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(x, property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1174,7 +1179,7 @@ exec_as.mo <- function(x,
|
|||
|
||||
# (4) strip values between brackets ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 2] (4) strip values between brackets\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (4) strip values between brackets\n")
|
||||
}
|
||||
a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup)
|
||||
a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped))
|
||||
|
|
@ -1191,10 +1196,9 @@ exec_as.mo <- function(x,
|
|||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1203,7 +1207,7 @@ exec_as.mo <- function(x,
|
|||
|
||||
# (5) inverse input ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 2] (5) inverse input\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (5) inverse input\n")
|
||||
}
|
||||
a.x_backup_inversed <- paste(rev(unlist(strsplit(a.x_backup, split = " "))), collapse = " ")
|
||||
if (isTRUE(debug)) {
|
||||
|
|
@ -1219,10 +1223,9 @@ exec_as.mo <- function(x,
|
|||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1231,7 +1234,7 @@ exec_as.mo <- function(x,
|
|||
|
||||
# (6) try to strip off half an element from end and check the remains ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 2] (6) try to strip off half an element from end and check the remains\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (6) try to strip off half an element from end and check the remains\n")
|
||||
}
|
||||
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
|
||||
if (length(x_strip) > 1) {
|
||||
|
|
@ -1254,10 +1257,9 @@ exec_as.mo <- function(x,
|
|||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1268,7 +1270,7 @@ exec_as.mo <- function(x,
|
|||
}
|
||||
# (7) try to strip off one element from end and check the remains ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 2] (7) try to strip off one element from end and check the remains\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (7) try to strip off one element from end and check the remains\n")
|
||||
}
|
||||
if (length(x_strip) > 1) {
|
||||
for (i in 1:(length(x_strip) - 1)) {
|
||||
|
|
@ -1287,10 +1289,9 @@ exec_as.mo <- function(x,
|
|||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1301,17 +1302,16 @@ exec_as.mo <- function(x,
|
|||
}
|
||||
# (8) check for unknown yeasts/fungi ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 2] (8) check for unknown yeasts/fungi\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (8) check for unknown yeasts/fungi\n")
|
||||
}
|
||||
if (b.x_trimmed %like% "yeast") {
|
||||
found <- "F_YEAST"
|
||||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1322,10 +1322,9 @@ exec_as.mo <- function(x,
|
|||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1333,7 +1332,7 @@ exec_as.mo <- function(x,
|
|||
}
|
||||
# (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 2] (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n")
|
||||
}
|
||||
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
|
||||
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
|
||||
|
|
@ -1354,10 +1353,9 @@ exec_as.mo <- function(x,
|
|||
# uncertainty level 2 only if searched part contains a space (otherwise it will be found with lvl 3)
|
||||
if (x_strip_collapsed %like% " ") {
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1374,7 +1372,7 @@ exec_as.mo <- function(x,
|
|||
|
||||
# (10) try to strip off one element from start and check the remains (any text size) ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 3] (10) try to strip off one element from start and check the remains (any text size)\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (10) try to strip off one element from start and check the remains (any text size)\n")
|
||||
}
|
||||
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
|
||||
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
|
||||
|
|
@ -1393,10 +1391,9 @@ exec_as.mo <- function(x,
|
|||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 3, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1407,7 +1404,7 @@ exec_as.mo <- function(x,
|
|||
# (11) try to strip off one element from end and check the remains (any text size) ----
|
||||
# (this is in fact 7 but without nchar limit of >=6)
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 3] (11) try to strip off one element from end and check the remains (any text size)\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (11) try to strip off one element from end and check the remains (any text size)\n")
|
||||
}
|
||||
if (length(x_strip) > 1) {
|
||||
for (i in 1:(length(x_strip) - 1)) {
|
||||
|
|
@ -1425,10 +1422,9 @@ exec_as.mo <- function(x,
|
|||
found_result <- found
|
||||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1439,7 +1435,7 @@ exec_as.mo <- function(x,
|
|||
|
||||
# (12) part of a name (very unlikely match) ----
|
||||
if (isTRUE(debug)) {
|
||||
cat("\n[UNCERTAINLY LEVEL 3] (12) part of a name (very unlikely match)\n")
|
||||
cat("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (12) part of a name (very unlikely match)\n")
|
||||
}
|
||||
if (isTRUE(debug)) {
|
||||
message("Running '", f.x_withspaces_end_only, "'")
|
||||
|
|
@ -1450,10 +1446,9 @@ exec_as.mo <- function(x,
|
|||
if (!empty_result(found_result) & nchar(g.x_backup_without_spp) >= 6) {
|
||||
found <- microorganismsDT[mo == found_result[1L], ..property][[1]]
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
data.frame(uncertainty = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
|
||||
mo = found_result[1L]))
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result[1L]))
|
||||
if (initial_search == TRUE) {
|
||||
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 3, force = force_mo_history)
|
||||
}
|
||||
|
|
@ -1654,6 +1649,29 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
|
|||
options(mo_renamed = total[order(names(total))])
|
||||
}
|
||||
|
||||
format_uncertainty_as_df <- function(uncertainty_level,
|
||||
input,
|
||||
result_mo) {
|
||||
if (!is.null(getOption("mo_renamed_last_run", default = NULL))) {
|
||||
# was found as a renamed mo
|
||||
df <- data.frame(uncertainty = uncertainty_level,
|
||||
input = input,
|
||||
fullname = getOption("mo_renamed_last_run"),
|
||||
renamed_to = microorganismsDT[mo == result_mo, fullname][[1]],
|
||||
mo = result_mo,
|
||||
stringsAsFactors = FALSE)
|
||||
options(mo_renamed_last_run = NULL)
|
||||
} else {
|
||||
df <- data.frame(uncertainty = uncertainty_level,
|
||||
input = input,
|
||||
fullname = microorganismsDT[mo == result_mo, fullname][[1]],
|
||||
renamed_to = NA_character_,
|
||||
mo = result_mo,
|
||||
stringsAsFactors = FALSE)
|
||||
}
|
||||
df
|
||||
}
|
||||
|
||||
#' @exportMethod print.mo
|
||||
#' @export
|
||||
#' @noRd
|
||||
|
|
@ -1805,7 +1823,9 @@ print.mo_uncertainties <- function(x, ...) {
|
|||
}
|
||||
msg <- paste(msg,
|
||||
paste0(colour2(paste0(" [", x[i, "uncertainty"], "] ")), ' "', x[i, "input"], '" -> ',
|
||||
colour1(paste0(italic(x[i, "fullname"]), " (", x[i, "mo"], ")"))),
|
||||
colour1(paste0(italic(x[i, "fullname"]),
|
||||
ifelse(!is.na(x[i, "renamed_to"]), paste(", renamed to", italic(x[i, "renamed_to"])), ""),
|
||||
" (", x[i, "mo"], ")"))),
|
||||
sep = "\n")
|
||||
}
|
||||
cat(msg)
|
||||
|
|
|
|||
10
R/rsi_calc.R
10
R/rsi_calc.R
|
|
@ -21,6 +21,8 @@
|
|||
|
||||
#' @importFrom rlang enquos as_label
|
||||
dots2vars <- function(...) {
|
||||
# this function is to give more informative output about
|
||||
# variable names in count_* and portion_* functions
|
||||
paste(
|
||||
unlist(
|
||||
lapply(enquos(...),
|
||||
|
|
@ -109,20 +111,14 @@ rsi_calc <- function(...,
|
|||
x[, i] <- suppressWarnings(x %>% pull(i) %>% as.rsi()) # warning will be given later
|
||||
print_warning <- TRUE
|
||||
}
|
||||
#x[, i] <- x %>% pull(i)
|
||||
}
|
||||
if (length(rsi_integrity_check) > 0) {
|
||||
# this will give a warning for invalid results, of all input columns (so only 1 warning)
|
||||
rsi_integrity_check <- as.rsi(rsi_integrity_check)
|
||||
}
|
||||
|
||||
# THE CHANCE THAT AT LEAST ONE RESULT IS ab_result
|
||||
#numerator <- x %>% filter_all(any_vars(. %in% ab_result)) %>% nrow()
|
||||
if (only_all_tested == TRUE) {
|
||||
# THE NUMBER OF ISOLATES WHERE *ALL* ABx ARE S/I/R
|
||||
# x_filtered <- x %>% filter_all(all_vars(!is.na(.)))
|
||||
# numerator <- x_filtered %>% filter_all(any_vars(. %in% ab_result)) %>% nrow()
|
||||
# denominator <- x_filtered %>% nrow()
|
||||
x <- apply(X = x %>% mutate_all(as.integer),
|
||||
MARGIN = 1,
|
||||
FUN = base::min)
|
||||
|
|
@ -159,7 +155,7 @@ rsi_calc <- function(...,
|
|||
if (data_vars != "") {
|
||||
data_vars <- paste(" for", data_vars)
|
||||
}
|
||||
warning("Introducing NA: only ", denominator, " results available", data_vars, " (minimum set to ", minimum, ").", call. = FALSE)
|
||||
warning("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` was set to ", minimum, ").", call. = FALSE)
|
||||
fraction <- NA
|
||||
} else {
|
||||
fraction <- numerator / denominator
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -42,7 +42,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -225,9 +225,9 @@
|
|||
|
||||
</div>
|
||||
|
||||
<div id="amr-0-7-1-9057" class="section level1">
|
||||
<div id="amr-0-7-1-9058" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0-7-1-9057" class="anchor"></a>AMR 0.7.1.9057<small> Unreleased </small>
|
||||
<a href="#amr-0-7-1-9058" class="anchor"></a>AMR 0.7.1.9058<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="breaking" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
|
|
@ -1238,7 +1238,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-0-7-1-9057">0.7.1.9057</a></li>
|
||||
<li><a href="#amr-0-7-1-9058">0.7.1.9058</a></li>
|
||||
<li><a href="#amr-0-7-1">0.7.1</a></li>
|
||||
<li><a href="#amr-0-7-0">0.7.0</a></li>
|
||||
<li><a href="#amr-0-6-1">0.6.1</a></li>
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue