mirror of
https://github.com/msberends/AMR.git
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(v2.1.1.9136) console colours, updated Suggests, added as.ab() improvement
This commit is contained in:
parent
700522b466
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22afd918e6
@ -1,6 +1,6 @@
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Package: AMR
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Version: 2.1.1.9135
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Date: 2025-01-28
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Version: 2.1.1.9136
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Date: 2025-01-31
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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@ -36,14 +36,18 @@ Depends: R (>= 3.0.0)
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Suggests:
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cleaner,
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cli,
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crayon,
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curl,
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data.table,
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dplyr,
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ggplot2,
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knitr,
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openxlsx,
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pillar,
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progress,
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readxl,
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rmarkdown,
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rstudioapi,
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rvest,
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skimr,
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testthat,
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3
NEWS.md
3
NEWS.md
@ -1,4 +1,4 @@
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# AMR 2.1.1.9135
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# AMR 2.1.1.9136
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*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
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@ -85,6 +85,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
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* MDRO determination (using `mdro()`)
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* Implemented the new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)
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* Added arguments `esbl`, `carbapenemase`, `mecA`, `mecC`, `vanA`, `vanB` to denote column names or logical values indicating presence of these genes (or production of their proteins)
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* Added console colours support of `sir` class for Positron
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## Other
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* Added Dr. Larisse Bolton as contributor for her fantastic implementation of WISCA in a mathematically solid way
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@ -1,6 +1,6 @@
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Metadata-Version: 2.2
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Name: AMR
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Version: 2.1.1.9135
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Version: 2.1.1.9136
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Summary: A Python wrapper for the AMR R package
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Home-page: https://github.com/msberends/AMR
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Author: Matthijs Berends
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@ -2,7 +2,7 @@ from setuptools import setup, find_packages
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setup(
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name='AMR',
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version='2.1.1.9135',
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version='2.1.1.9136',
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packages=find_packages(),
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install_requires=[
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'rpy2',
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@ -1169,57 +1169,12 @@ message_not_thrown_before <- function(fn, ..., entire_session = FALSE) {
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}
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has_colour <- function() {
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# this is a base R version of crayon::has_color, but disables colours on emacs
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if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") {
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# disable on emacs, which only supports 8 colours
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return(FALSE)
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}
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enabled <- getOption("crayon.enabled")
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if (!is.null(enabled)) {
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return(isTRUE(enabled))
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}
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rstudio_with_ansi_support <- function(x) {
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if (Sys.getenv("RSTUDIO", "") == "") {
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return(FALSE)
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}
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if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.double(cols))) {
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return(TRUE)
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}
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tryCatch(getExportedValue("isAvailable", ns = asNamespace("rstudioapi"))(), error = function(e) {
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return(FALSE)
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}) &&
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tryCatch(getExportedValue("hasFun", ns = asNamespace("rstudioapi"))("getConsoleHasColor"), error = function(e) {
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return(FALSE)
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})
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}
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if (rstudio_with_ansi_support() && sink.number() == 0) {
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return(TRUE)
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}
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if (!isatty(stdout())) {
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return(FALSE)
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}
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if (tolower(Sys.info()["sysname"]) == "windows") {
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if (Sys.getenv("ConEmuANSI") == "ON") {
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return(TRUE)
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}
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if (Sys.getenv("CMDER_ROOT") != "") {
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return(TRUE)
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}
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return(FALSE)
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}
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if ("COLORTERM" %in% names(Sys.getenv())) {
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return(TRUE)
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}
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if (Sys.getenv("TERM") == "dumb") {
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return(FALSE)
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}
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grepl(
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pattern = "^screen|^xterm|^vt100|color|ansi|cygwin|linux",
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x = Sys.getenv("TERM"),
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ignore.case = TRUE,
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perl = TRUE
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)
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has_color <- import_fn("has_color", "crayon")
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!is.null(has_color) && isTRUE(has_color())
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}
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# set colours if console has_colour()
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38
R/ab.R
38
R/ab.R
@ -324,7 +324,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# INITIAL SEARCH - More uncertain results ----
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if (loop_time <= 2 && fast_mode == FALSE) {
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# only run on first and second try
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# try by removing all spaces
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if (x[i] %like% " ") {
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found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), loop_time = loop_time + 2))
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@ -333,7 +333,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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next
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}
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}
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# try by removing all spaces and numbers
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if (x[i] %like% " " || x[i] %like% "[0-9]") {
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found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
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@ -342,6 +342,40 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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next
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}
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}
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# reverse a combination, e.g. clavulanic acid/amoxicillin
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if (x[i] %like% " ") {
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split <- strsplit(x[i], " ")[[1]]
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permute <- function(x) {
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if (length(x) == 1) return(list(x))
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result <- vector("list", factorial(length(x)))
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index <- 1
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for (i in seq_along(x)) {
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sub_perms <- permute(x[-i]) # Recursively get permutations of remaining elements
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for (sub in sub_perms) {
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result[[index]] <- c(x[i], sub)
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index <- index + 1
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}
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}
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return(result)
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}
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permutations <- permute(split)
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found_perms <- character(length(permutations))
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for (s in seq_len(length(permutations))) {
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concat <- paste0(permutations[[s]], collapse = " ")
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if (concat %in% AMR_env$AB_lookup$generalised_name) {
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found_perms[s] <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name == concat), "ab", drop = TRUE]
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} else {
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found_perms[s] <- suppressWarnings(as.ab(concat, loop_time = loop_time + 2))
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}
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}
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found_perms <- found_perms[!is.na(found_perms)]
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if (length(found_perms) > 0) {
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found <- found_perms[order(nchar(found_perms), decreasing = TRUE)][1]
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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}
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}
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# transform back from other languages and try again
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x_translated <- paste(
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6
R/mo.R
6
R/mo.R
@ -340,17 +340,17 @@ as.mo <- function(x,
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filtr <- which(MO_lookup_current$full_first %like_case% first_chars)
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} else if (nchar(x_out) == 3) {
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# no space and 3 characters - probably a code such as SAU or ECO
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msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 1)), AMR_env$dots, " ", substr(x_out, 2, 3), AMR_env$dots, "\""))
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msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 1)), AMR_env$ellipsis_icon, " ", substr(x_out, 2, 3), AMR_env$ellipsis_icon, "\""))
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filtr <- which(MO_lookup_current$fullname_lower %like_case% paste0("(^| )", substr(x_out, 1, 1), ".* ", substr(x_out, 2, 3)))
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} else if (nchar(x_out) == 4) {
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# no space and 4 characters - probably a code such as STAU or ESCO
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msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 2)), AMR_env$dots, " ", substr(x_out, 3, 4), AMR_env$dots, "\""))
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msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 2)), AMR_env$ellipsis_icon, " ", substr(x_out, 3, 4), AMR_env$ellipsis_icon, "\""))
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filtr <- which(MO_lookup_current$fullname_lower %like_case% paste0("(^| )", substr(x_out, 1, 2), ".* ", substr(x_out, 3, 4)))
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} else if (nchar(x_out) <= 6) {
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# no space and 5-6 characters - probably a code such as STAAUR or ESCCOL
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first_part <- paste0(substr(x_out, 1, 2), "[a-z]*", substr(x_out, 3, 3))
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second_part <- substr(x_out, 4, nchar(x_out))
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msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", gsub("[a-z]*", AMR_env$dots, totitle(first_part), fixed = TRUE), " ", second_part, AMR_env$dots, "\""))
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msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", gsub("[a-z]*", AMR_env$ellipsis_icon, totitle(first_part), fixed = TRUE), " ", second_part, AMR_env$ellipsis_icon, "\""))
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filtr <- which(MO_lookup_current$fullname_lower %like_case% paste0("(^| )", first_part, ".* ", second_part))
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} else {
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# for genus or species or subspecies
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12
R/zzz.R
12
R/zzz.R
@ -82,15 +82,15 @@ AMR_env$chmatch <- import_fn("chmatch", "data.table", error_on_fail = FALSE)
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AMR_env$chin <- import_fn("%chin%", "data.table", error_on_fail = FALSE)
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# take cli symbols and error function if available
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AMR_env$info_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$info %or% "i"
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AMR_env$bullet_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$bullet %or% "*"
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AMR_env$bullet_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$bullet %or% "*"
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AMR_env$ellipsis_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$ellipsis %or% "..."
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AMR_env$info_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$info %or% "i"
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AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %or% "*"
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AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
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AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
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AMR_env$dots <- import_fn("symbol", "cli", error_on_fail = FALSE)$ellipsis %or% "..."
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AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %or% "*"
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AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
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.onLoad <- function(lib, pkg) {
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# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
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# without the need to depend on other packages. This was suggested by the
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@ -1,6 +1,6 @@
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This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
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First and foremost, you are trained on version 2.1.1.9135. Remember this whenever someone asks which AMR package version you’re at.
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First and foremost, you are trained on version 2.1.1.9136. Remember this whenever someone asks which AMR package version you’re at.
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Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens.
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----------------------------------------------------------------------------------------------------
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@ -34,10 +34,17 @@
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import_functions <- c(
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"%chin%" = "data.table",
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"anti_join" = "dplyr",
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"as.data.table" = "data.table",
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"as_tibble" = "tibble",
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"chmatch" = "data.table",
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"cli_abort" = "cli",
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"cur_column" = "dplyr",
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"cur_group" = "dplyr",
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"document_position" = "rstudioapi",
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"document_range" = "rstudioapi",
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"full_join" = "dplyr",
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"getActiveDocumentContext" = "rstudioapi",
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"has_color" = "crayon",
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"has_internet" = "curl",
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"html_attr" = "rvest",
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"html_children" = "rvest",
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@ -48,26 +55,28 @@ import_functions <- c(
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"inner_join" = "dplyr",
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"insertText" = "rstudioapi",
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"left_join" = "dplyr",
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"modifyRange" = "rstudioapi",
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"new_pillar_shaft_simple" = "pillar",
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"progress_bar" = "progress",
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"read_html" = "xml2",
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"right_join" = "dplyr",
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"semi_join" = "dplyr",
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"showQuestion" = "rstudioapi"
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"showQuestion" = "rstudioapi",
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"symbol" = "cli",
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"tibble" = "tibble",
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"write.xlsx" = "openxlsx"
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)
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# functions that are called directly with ::
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call_functions <- c(
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# cleaner
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"freq" = "cleaner",
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"freq.default" = "cleaner",
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"percentage" = "cleaner",
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# cli
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"symbol" = "cli",
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"ansi_has_hyperlink_support" = "cli",
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# rstudioapi (RStudio)
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"isAvailable" = "rstudioapi",
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"versionInfo" = "rstudioapi",
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# readxl
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"read_excel" = "readxl",
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# curl
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"has_internet" = "curl",
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# ggplot2
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"aes" = "ggplot2",
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"arrow" = "ggplot2",
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@ -77,6 +86,8 @@ call_functions <- c(
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"element_text" = "ggplot2",
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"expand_limits" = "ggplot2",
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"facet_wrap" = "ggplot2",
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"fortify" = "ggplot2",
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"geom_col" = "ggplot2",
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"geom_errorbar" = "ggplot2",
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"geom_path" = "ggplot2",
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"geom_point" = "ggplot2",
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@ -85,10 +96,10 @@ call_functions <- c(
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"geom_text" = "ggplot2",
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"ggplot" = "ggplot2",
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"labs" = "ggplot2",
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"layer" = "ggplot2",
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"position_dodge2" = "ggplot2",
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"position_fill" = "ggplot2",
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"scale_colour_discrete" = "ggplot2",
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"scale_discrete_manual" = "ggplot2",
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"scale_fill_discrete" = "ggplot2",
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"scale_fill_manual" = "ggplot2",
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"scale_x_discrete" = "ggplot2",
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@ -99,51 +110,61 @@ call_functions <- c(
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"unit" = "ggplot2",
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"xlab" = "ggplot2",
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"ylab" = "ggplot2",
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"vec_arith" = "vctrs"
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)
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if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
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call_functions <- c(call_functions,
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# skimr
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"inline_hist" = "skimr",
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"sfl" = "skimr"
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)
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}
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extended_functions <- c(
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"freq" = "cleaner",
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"autoplot" = "ggplot2",
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# knitr
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"asis_output" = "knitr",
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"kable" = "knitr",
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"knit_print" = "knitr",
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"opts_chunk" = "knitr",
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"rmarkdown" = "knitr",
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# pillar
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"pillar_shaft" = "pillar",
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"get_skimmers" = "skimr",
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"tbl_format_footer" = "pillar",
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"tbl_sum" = "pillar",
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"type_sum" = "pillar",
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# readxl
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"read_excel" = "readxl",
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# rmarkdown
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"html_vignette" = "rmarkdown",
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# skimr
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"get_skimmers" = "skimr",
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"inline_hist" = "skimr",
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"sfl" = "skimr",
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# tibble
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"tibble" = "tibble",
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# vctrs
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"vec_arith" = "vctrs",
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"vec_cast" = "vctrs",
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"vec_math" = "vctrs",
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"vec_ptype2" = "vctrs"
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"vec_ptype2" = "vctrs",
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"vec_ptype_abbr" = "vctrs",
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"vec_ptype_full" = "vctrs"
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)
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import_functions <- c(import_functions, call_functions, extended_functions)
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import_functions <- c(import_functions, call_functions)
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suggests <- desc::desc(".")$get_deps()
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suggests <- suggests[which(suggests$type == "Suggests"), ]$package
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for (i in seq_len(length(import_functions))) {
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fn <- names(import_functions)[i]
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pkg <- unname(import_functions[i])
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expect_true(pkg %in% suggests,
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info = paste0("package `", pkg, "` is not in Suggests"))
|
||||
# function should exist in foreign pkg namespace
|
||||
if (AMR:::pkg_is_available(pkg,
|
||||
also_load = FALSE,
|
||||
min_version = if (pkg == "dplyr") "1.0.0" else NULL
|
||||
also_load = FALSE,
|
||||
min_version = if (pkg == "dplyr") "1.0.0" else NULL
|
||||
)) {
|
||||
expect_true(!is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
|
||||
info = paste0("does not exist (anymore): function `", pkg, "::", fn, "()`")
|
||||
)
|
||||
info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`"))
|
||||
} else if (pkg != "rstudioapi") {
|
||||
warning("Package '", pkg, "' does not exist anymore")
|
||||
warning("Package '", pkg, "' not available")
|
||||
}
|
||||
}
|
||||
|
||||
if (AMR:::pkg_is_available("cli")) {
|
||||
expect_true(!is.null(cli::symbol$info))
|
||||
}
|
||||
if (AMR:::pkg_is_available("cli")) {
|
||||
}
|
||||
if (AMR:::pkg_is_available("cli")) {
|
||||
expect_true(!is.null(cli::symbol$ellipsis))
|
||||
expect_true(!is.null(cli::symbol$bullet) && is.character(cli::symbol$bullet) && length(cli::symbol$bullet) == 1)
|
||||
expect_true(!is.null(cli::symbol$ellipsis) && is.character(cli::symbol$ellipsis) && length(cli::symbol$ellipsis) == 1)
|
||||
expect_true(!is.null(cli::symbol$info) && is.character(cli::symbol$info) && length(cli::symbol$info) == 1)
|
||||
expect_true(!is.null(cli::symbol$sup_1) && is.character(cli::symbol$sup_1) && length(cli::symbol$sup_1) == 1)
|
||||
}
|
||||
if (AMR:::pkg_is_available("ggplot2")) {
|
||||
# the scale_*_mic() functions rely on these
|
||||
@ -152,5 +173,3 @@ if (AMR:::pkg_is_available("ggplot2")) {
|
||||
expect_true(is.function(ggplot2::scale_colour_discrete()$transform))
|
||||
expect_true(is.function(ggplot2::scale_fill_discrete()$transform))
|
||||
}
|
||||
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user