mirror of
https://github.com/msberends/AMR.git
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218 lines
8.5 KiB
R
218 lines
8.5 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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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 a options entry
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#' @importFrom dplyr %>% distinct filter
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#' @importFrom utils write.csv
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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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# don't save codes that are in a code data set already
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mo <- mo[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
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x <- x[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
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warning_new_write <- FALSE
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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 seq_len(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_version == 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_version = 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) & interactive()) {
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warning_new_write <- TRUE
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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_version = base::as.character(utils::packageVersion("AMR")),
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stringsAsFactors = FALSE)),
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row.names = FALSE,
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file = mo_history_file()),
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error = function(e) {
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warning_new_write <- FALSE; base::invisible()
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})
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}
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}
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}
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if (warning_new_write == TRUE) {
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message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
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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, 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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result <- NA
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} else {
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result <- data.frame(x = as.character(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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#' @importFrom utils read.csv
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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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# # 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_version == 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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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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#' @importFrom utils write.csv
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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_version = character(0),
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stringsAsFactors = FALSE),
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row.names = 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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# Borrowed all below code from the extrafont package,
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# https://github.com/wch/extrafont/blob/254c3f99b02f11adb59affbda699a92aec8624f5/R/utils.r
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inst_path <- function() {
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envname <- environmentName(parent.env(environment()))
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# If installed in package, envname == "AMR"
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# If loaded with load_all, envname == "package:AMR"
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# (This is kind of strange)
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if (envname == "AMR") {
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system.file(package = "AMR")
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} else {
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srcfile <- attr(attr(inst_path, "srcref"), "srcfile")
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file.path(dirname(dirname(srcfile$filename)), "inst")
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}
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}
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# Get the path where extrafontdb is installed
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db_path <- function() {
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system.file(package = "AMR")
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}
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# fonttable file
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mo_history_file <- function() {
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file.path(mo_history_path(), "mo_history.csv")
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}
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# Path of fontmap directory
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mo_history_path <- function() {
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file.path(db_path(), "mo_history")
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}
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