mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 19:41:49 +02:00
(v0.7.1.9073) as.mo() self-learning algorithm
This commit is contained in:
26
R/like.R
26
R/like.R
@ -21,7 +21,7 @@
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#' Pattern Matching
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#'
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#' Convenient wrapper around \code{\link[base]{grep}} to match a pattern: \code{a \%like\% b}. It always returns a \code{logical} vector and is always case-insensitive. Also, \code{pattern} (\code{b}) can be as long as \code{x} (\code{a}) to compare items of each index in both vectors.
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#' Convenient wrapper around \code{\link[base]{grep}} to match a pattern: \code{a \%like\% b}. It always returns a \code{logical} vector and is always case-insensitive (use \code{a \%like_case\% b} for case-sensitive matching). Also, \code{pattern} (\code{b}) can be as long as \code{x} (\code{a}) to compare items of each index in both vectors, or can both have the same length to iterate over all cases.
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#' @inheritParams base::grepl
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#' @return A \code{logical} vector
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#' @name like
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@ -53,14 +53,14 @@
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#' left_join_microorganisms() %>%
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#' filter(genus %like% '^ent') %>%
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#' freq(genus, species)
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like <- function(x, pattern) {
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like <- function(x, pattern, ignore.case = TRUE) {
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if (length(pattern) > 1) {
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if (length(x) != length(pattern)) {
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if (length(x) == 1) {
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x <- rep(x, length(pattern))
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}
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# return TRUE for every 'x' that matches any 'pattern', FALSE otherwise
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res <- sapply(pattern, function(pttrn) x %like% pttrn)
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res <- sapply(pattern, function(pttrn) base::grepl(pttrn, x, ignore.case = ignore.case))
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res2 <- as.logical(rowSums(res))
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# get only first item of every hit in pattern
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res2[duplicated(res)] <- FALSE
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@ -71,9 +71,9 @@ like <- function(x, pattern) {
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res <- vector(length = length(pattern))
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for (i in 1:length(res)) {
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if (is.factor(x[i])) {
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res[i] <- as.integer(x[i]) %in% base::grep(pattern[i], levels(x[i]), ignore.case = TRUE)
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res[i] <- as.integer(x[i]) %in% base::grep(pattern[i], levels(x[i]), ignore.case = ignore.case)
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} else {
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res[i] <- base::grepl(pattern[i], x[i], ignore.case = TRUE)
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res[i] <- base::grepl(pattern[i], x[i], ignore.case = ignore.case)
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}
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}
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return(res)
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@ -82,16 +82,24 @@ like <- function(x, pattern) {
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# the regular way how grepl works; just one pattern against one or more x
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if (is.factor(x)) {
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as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE)
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as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = ignore.case)
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} else {
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tryCatch(base::grepl(pattern, x, ignore.case = TRUE),
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tryCatch(base::grepl(pattern, x, ignore.case = ignore.case),
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error = function(e) ifelse(test = grepl("Invalid regexp", e$message),
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# try with perl = TRUE:
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yes = return(base::grepl(pattern, x, ignore.case = TRUE, perl = TRUE)),
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yes = return(base::grepl(pattern, x, ignore.case = ignore.case, perl = TRUE)),
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no = stop(e$message)))
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}
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}
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#' @rdname like
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#' @export
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"%like%" <- like
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"%like%" <- function(x, pattern) {
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like(x, pattern, ignore.case = TRUE)
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}
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#' @rdname like
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#' @export
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"%like_case%" <- function(x, pattern) {
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like(x, pattern, ignore.case = FALSE)
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}
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4
R/misc.R
4
R/misc.R
@ -41,8 +41,8 @@ percent <- function(x, round = 1, force_zero = FALSE, decimal.mark = getOption("
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big.mark <- " "
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}
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}
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x <- percent_clean(x = x, round = round, force_zero = force_zero,
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decimal.mark = decimal.mark, big.mark = big.mark, ...)
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percent_clean(x = x, round = round, force_zero = force_zero,
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decimal.mark = decimal.mark, big.mark = big.mark, ...)
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}
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#' @importFrom crayon blue bold red
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238
R/mo_history.R
238
R/mo_history.R
@ -19,116 +19,152 @@
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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# print successful as.mo coercions to AMR environment
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#' @importFrom dplyr %>% distinct filter
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set_mo_history <- function(x, mo, uncertainty_level, force = FALSE) {
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# disable function for now
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return(base::invisible())
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mo_history_file <- file.path(file.path(system.file(package = "AMR"), "mo_history"), "mo_history.csv")
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# if (base::interactive() | force == TRUE) {
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# mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
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# df <- data.frame(x, mo, stringsAsFactors = FALSE) %>%
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# distinct(x, .keep_all = TRUE) %>%
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# filter(!is.na(x) & !is.na(mo))
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# if (nrow(df) == 0) {
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# return(base::invisible())
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# }
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# x <- toupper(df$x)
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# mo <- df$mo
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# for (i in 1:length(x)) {
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# # save package version too, as both the as.mo() algorithm and the reference data set may change
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# if (NROW(mo_hist[base::which(mo_hist$x == x[i] &
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# mo_hist$uncertainty_level >= uncertainty_level &
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# mo_hist$package_v == utils::packageVersion("AMR")),]) == 0) {
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# tryCatch(
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# assign(x = "mo_history",
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# value = rbind(mo_hist,
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# data.frame(
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# x = x[i],
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# mo = mo[i],
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# uncertainty_level = uncertainty_level,
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# package_v = base::as.character(utils::packageVersion("AMR")),
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# stringsAsFactors = FALSE)),
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# envir = asNamespace("AMR")),
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# error = function(e) invisible())
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# }
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# }
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# }
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# return(base::invisible())
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# print successful as.mo coercions to a options entry
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#' @importFrom dplyr %>% distinct filter
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set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FALSE) {
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if (isTRUE(disable)) {
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return(base::invisible())
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}
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if (base::interactive() | force == TRUE) {
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mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
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df <- data.frame(x, mo, stringsAsFactors = FALSE) %>%
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distinct(x, .keep_all = TRUE) %>%
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filter(!is.na(x) & !is.na(mo))
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if (nrow(df) == 0) {
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return(base::invisible())
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}
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x <- toupper(df$x)
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mo <- df$mo
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for (i in 1:length(x)) {
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# save package version too, as both the as.mo() algorithm and the reference data set may change
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if (NROW(mo_hist[base::which(mo_hist$x == x[i] &
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mo_hist$uncertainty_level >= uncertainty_level &
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mo_hist$package_v == utils::packageVersion("AMR")),]) == 0) {
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# # Not using the file system:
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# tryCatch(options(mo_remembered_results = rbind(mo_hist,
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# data.frame(
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# x = x[i],
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# mo = mo[i],
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# uncertainty_level = uncertainty_level,
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# package_v = base::as.character(utils::packageVersion("AMR")),
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# stringsAsFactors = FALSE))),
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# error = function(e) base::invisible())
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# # don't remember more than 1,000 different input values
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# if (tryCatch(nrow(getOption("mo_remembered_results")), error = function(e) 1001) > 1000) {
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# return(base::invisible())
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# }
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if (is.null(mo_hist)) {
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message(blue(paste0("NOTE: results are saved to ", mo_history_file, ".")))
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}
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tryCatch(write.csv(rbind(mo_hist,
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data.frame(
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x = x[i],
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mo = mo[i],
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uncertainty_level = uncertainty_level,
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package_v = base::as.character(utils::packageVersion("AMR")),
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stringsAsFactors = FALSE)),
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file = mo_history_file, row.names = FALSE),
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error = function(e) base::invisible())
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}
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}
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}
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return(base::invisible())
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}
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get_mo_history <- function(x, uncertainty_level, force = FALSE) {
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# disable function for now
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return(NA)
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get_mo_history <- function(x, uncertainty_level, force = FALSE, disable = FALSE) {
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if (isTRUE(disable)) {
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return(to_class_mo(NA))
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}
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# history <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
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# if (base::is.null(history)) {
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# NA
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# } else {
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# data.frame(x = toupper(x), stringsAsFactors = FALSE) %>%
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# left_join(history, by = "x") %>%
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# pull(mo)
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# }
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history <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
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if (base::is.null(history)) {
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result <- NA
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} else {
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result <- data.frame(x = toupper(x), stringsAsFactors = FALSE) %>%
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left_join(history, by = "x") %>%
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pull(mo)
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}
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to_class_mo(result)
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}
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#' @importFrom dplyr %>% filter distinct
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read_mo_history <- function(uncertainty_level = 2, force = FALSE, unfiltered = FALSE) {
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# disable function for now
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return(NULL)
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read_mo_history <- function(uncertainty_level = 2, force = FALSE, unfiltered = FALSE, disable = FALSE) {
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if (isTRUE(disable)) {
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return(NULL)
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}
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# if ((!base::interactive() & force == FALSE)) {
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# return(NULL)
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# }
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# uncertainty_level_param <- uncertainty_level
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#
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# history <- tryCatch(get("mo_history", envir = asNamespace("AMR")),
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# error = function(e) NULL)
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# if (is.null(history)) {
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# return(NULL)
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# }
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# # Below: filter on current package version.
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# # Even current fullnames may be replaced by new taxonomic names, so new versions of
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# # the Catalogue of Life must not lead to data corruption.
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#
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# if (unfiltered == FALSE) {
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# history <- history %>%
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# filter(package_v == as.character(utils::packageVersion("AMR")),
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# # only take unknowns if uncertainty_level_param is higher
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# ((mo == "UNKNOWN" & uncertainty_level_param == uncertainty_level) |
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# (mo != "UNKNOWN" & uncertainty_level_param >= uncertainty_level))) %>%
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# arrange(desc(uncertainty_level)) %>%
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# distinct(x, mo, .keep_all = TRUE)
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# }
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#
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# if (nrow(history) == 0) {
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# NULL
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# } else {
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# history
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# }
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if ((!base::interactive() & force == FALSE)) {
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return(NULL)
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}
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uncertainty_level_param <- uncertainty_level
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# # Not using the file system:
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# history <- tryCatch(getOption("mo_remembered_results"),
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# error = function(e) NULL)
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history <- tryCatch(read.csv(mo_history_file, stringsAsFactors = FALSE),
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warning = function(w) invisible(),
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error = function(e) NULL)
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if (is.null(history)) {
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return(NULL)
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}
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# Below: filter on current package version.
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# Even current fullnames may be replaced by new taxonomic names, so new versions of
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# the Catalogue of Life must not lead to data corruption.
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if (unfiltered == FALSE) {
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history <- history %>%
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filter(package_v == as.character(utils::packageVersion("AMR")),
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# only take unknowns if uncertainty_level_param is higher
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((mo == "UNKNOWN" & uncertainty_level_param == uncertainty_level) |
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(mo != "UNKNOWN" & uncertainty_level_param >= uncertainty_level))) %>%
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arrange(desc(uncertainty_level)) %>%
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distinct(x, mo, .keep_all = TRUE)
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}
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if (nrow(history) == 0) {
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NULL
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} else {
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history
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}
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}
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# @rdname as.mo
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# @importFrom crayon red
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# @importFrom utils menu
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# @export
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clean_mo_history <- function(...) {
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# if (!is.null(read_mo_history())) {
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# if (interactive() & !isTRUE(list(...)$force)) {
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# q <- menu(title = paste("This will remove all",
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# format(nrow(read_mo_history(999, unfiltered = TRUE)), big.mark = ","),
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# "microbial IDs determined previously in this session. Are you sure?"),
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# choices = c("Yes", "No"),
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# graphics = FALSE)
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# if (q != 1) {
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# return(invisible())
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# }
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# }
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# tryCatch(
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# assign(x = "mo_history",
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# value = NULL,
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# envir = asNamespace("AMR")),
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# error = function(e) invisible())
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# cat(red("History removed."))
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# }
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#' @rdname as.mo
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#' @importFrom crayon red
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#' @importFrom utils menu
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#' @export
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clear_mo_history <- function(...) {
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if (!is.null(read_mo_history())) {
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if (interactive() & !isTRUE(list(...)$force)) {
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q <- menu(title = paste("This will clear all",
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format(nrow(read_mo_history(999, unfiltered = TRUE)), big.mark = ","),
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"previously determined microbial IDs. Are you sure?"),
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choices = c("Yes", "No"),
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graphics = FALSE)
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if (q != 1) {
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return(invisible())
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}
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}
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# # Not using the file system:
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# success <- tryCatch(options(mo_remembered_results = NULL),
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# error = function(e) FALSE)
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success <- create_blank_mo_history()
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if (!isFALSE(success)) {
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cat(red(paste("File", mo_history_file, "cleared.")))
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}
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}
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}
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create_blank_mo_history <- function() {
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tryCatch(
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write.csv(x = data.frame(x = character(0),
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mo = character(0),
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uncertainty_level = integer(0),
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package_v = character(0),
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stringsAsFactors = FALSE),
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file = mo_history_file),
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warning = function(w) invisible(),
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error = function(e) TRUE)
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}
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@ -408,7 +408,7 @@ mo_validate <- function(x, property, ...) {
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if (!"AMR" %in% base::.packages()) {
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require("AMR")
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# check onLoad() in R/zzz.R: data tables are created there.
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# check .onLoad() in R/zzz.R: data tables are created there.
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}
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# try to catch an error when inputting an invalid parameter
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6
R/zzz.R
6
R/zzz.R
@ -26,7 +26,8 @@
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# register data
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microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
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microorganisms.oldDT$fullname_lower <- tolower(microorganisms.oldDT$fullname)
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# for fullname_lower: keep only dots, letters, numbers, slashes, spaces and dashes
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microorganisms.oldDT$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(microorganisms.oldDT$fullname))
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setkey(microorganisms.oldDT, col_id, fullname)
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assign(x = "microorganismsDT",
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@ -81,7 +82,8 @@
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#' @importFrom data.table as.data.table setkey
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make_DT <- function() {
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microorganismsDT <- as.data.table(AMR::microorganisms)
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microorganismsDT$fullname_lower <- tolower(microorganismsDT$fullname)
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# for fullname_lower: keep only dots, letters, numbers, slashes, spaces and dashes
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microorganismsDT$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(microorganismsDT$fullname))
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setkey(microorganismsDT,
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prevalence,
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kingdom,
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