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fix documentation
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.8.2.9004
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Date: 2022-10-05
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Version: 1.8.2.9006
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Date: 2022-10-06
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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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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9004
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# AMR 1.8.2.9006
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -1174,6 +1174,7 @@ font_stripstyle <- function(x) {
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progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
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if (print == FALSE || n < n_min) {
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# create fake/empty object
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pb <- list()
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pb$tick <- function() {
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invisible()
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@ -1183,16 +1184,17 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
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}
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set_clean_class(pb, new_class = "txtProgressBar")
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} else if (n >= n_min) {
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# rely on the progress package if it is available - it has a more verbose output
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# use `progress`, which also has a timer
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progress_bar <- import_fn("progress_bar", "progress", error_on_fail = FALSE)
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if (!is.null(progress_bar)) {
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# so we use progress::progress_bar
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# a close() method was also added, see below this function
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pb <- progress_bar$new(
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format = "[:bar] :percent (:current/:total)",
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format = "(:spin) [:bar] :percent (:current/:total,:eta)",
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total = n
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)
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} else {
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# use base R
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pb <- utils::txtProgressBar(max = n, style = 3)
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pb$tick <- function() {
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pb$up(pb$getVal() + 1)
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@ -1206,6 +1208,7 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
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#' @export
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#' @noRd
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close.progress_bar <- function(con, ...) {
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# for progress::progress_bar$new()
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con$terminate()
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}
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11
R/mo.R
11
R/mo.R
@ -113,9 +113,8 @@
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#' "staaur",
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#' "S. aureus",
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#' "S aureus",
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#' "Staphylococcus aureus",
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#' "Staphylococcus aureus (MRSA,",
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#' "Zthafilokkoockus oureuz", # handles incorrect spelling
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#' "Sthafilokkockus aureus", # handles incorrect spelling
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#' "Staphylococcus aureus (MRSA)",
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#' "MRSA", # Methicillin Resistant S. aureus
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#' "VISA", # Vancomycin Intermediate S. aureus
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#' "VRSA", # Vancomycin Resistant S. aureus
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@ -822,6 +821,7 @@ print.mo_uncertainties <- function(x, ...) {
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txt <- paste(txt,
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paste0(
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paste0(
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"", strrep(font_grey("-"), times = options()$width), "\n",
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'"', x[i, ]$original_input, '"',
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" -> ",
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paste0(
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@ -844,7 +844,10 @@ print.mo_uncertainties <- function(x, ...) {
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candidates,
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sep = "\n"
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)
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txt <- paste0(gsub("\n\n", "\n", txt), "\n\n")
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txt <- gsub("[\n]+", "\n", txt)
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# remove first and last break
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txt <- gsub("(^[\n]|[\n]$)", "", txt)
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txt <- paste0("\n", txt, "\n")
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}
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cat(txt)
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}
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@ -98,6 +98,7 @@
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#' mo_authors("Klebsiella pneumoniae")
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#' mo_year("Klebsiella pneumoniae")
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#' mo_lpsn("Klebsiella pneumoniae")
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#' mo_gbif("Klebsiella pneumoniae")
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#'
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#' # abbreviations known in the field -----------------------------------------
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#' mo_genus("MRSA")
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@ -109,20 +110,15 @@
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#' mo_species("EHEC")
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#'
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#' # known subspecies ---------------------------------------------------------
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#' mo_name("doylei")
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#' mo_genus("doylei")
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#' mo_species("doylei")
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#' mo_subspecies("doylei")
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#'
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#' mo_fullname("K. pneu rh")
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#' mo_shortname("K. pneu rh")
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#'
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#' \donttest{
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#' # Becker classification, see ?as.mo ----------------------------------------
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#' mo_fullname("S. epi")
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#' mo_fullname("S. epi", Becker = TRUE)
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#' mo_shortname("S. epi")
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#' mo_shortname("S. epi", Becker = TRUE)
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#' mo_fullname("Staph. epi")
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#' mo_fullname("Staph. epi", Becker = TRUE)
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#' mo_shortname("Staph. epi")
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#' mo_shortname("Staph. epi", Becker = TRUE)
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#'
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#' # Lancefield classification, see ?as.mo ------------------------------------
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#' mo_fullname("S. pyo")
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@ -132,23 +128,19 @@
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#'
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#'
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#' # language support --------------------------------------------------------
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#' mo_gramstain("Klebsiella pneumoniae", language = "de")
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#' mo_gramstain("Klebsiella pneumoniae", language = "nl")
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#' mo_gramstain("Klebsiella pneumoniae", language = "es")
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#' mo_gramstain("Klebsiella pneumoniae", language = "de") # German
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#' mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
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#' mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
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#' mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
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#' mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
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#'
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#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official
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#' mo_kingdom("Klebsiella pneumoniae")
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#' mo_type("Klebsiella pneumoniae")
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#' mo_type("Klebsiella pneumoniae")
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#' mo_type("Klebsiella pneumoniae", language = "nl")
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#'
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "de"
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#' )
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "nl"
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#' )
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#' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
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#' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk")
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#'
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#'
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#' # other --------------------------------------------------------------------
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@ -158,10 +150,13 @@
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#' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' filter(mo_is_gram_positive())
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#'
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#' filter(mo_is_gram_positive()) %>%
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#' count(mo_genus(), count = TRUE)
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#' }
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' filter(mo_is_intrinsic_resistant(ab = "vanco"))
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#' filter(mo_is_intrinsic_resistant(ab = "vanco")) %>%
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#' count(mo_genus(), count = TRUE)
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#' }
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#'
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#'
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expect_identical(
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suppressWarnings(as.character(
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as.mo(c(
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"stau",
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"stau", # WHONET code
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"STAU",
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"staaur",
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"S. aureus",
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"S aureus",
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"Sthafilokkockus aureus",
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"Staphylococcus aureus",
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"MRSA",
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"VISA"
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), minimum_matching_score = 0)
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"Sthafilokkockus aureus", # handles incorrect spelling
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"Staphylococcus aureus (MRSA)",
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"MRSA", # Methicillin Resistant S. aureus
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"VISA", # Vancomycin Intermediate S. aureus
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"VRSA", # Vancomycin Resistant S. aureus
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115329001 # SNOMED CT code
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))
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)),
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rep("B_STPHY_AURS", 9)
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rep("B_STPHY_AURS", 11)
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)
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expect_identical(
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as.character(
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"staaur",
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"S. aureus",
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"S aureus",
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"Staphylococcus aureus",
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"Staphylococcus aureus (MRSA,",
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"Zthafilokkoockus oureuz", # handles incorrect spelling
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"Sthafilokkockus aureus", # handles incorrect spelling
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"Staphylococcus aureus (MRSA)",
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"MRSA", # Methicillin Resistant S. aureus
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"VISA", # Vancomycin Intermediate S. aureus
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"VRSA", # Vancomycin Resistant S. aureus
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mo_authors("Klebsiella pneumoniae")
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mo_year("Klebsiella pneumoniae")
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mo_lpsn("Klebsiella pneumoniae")
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mo_gbif("Klebsiella pneumoniae")
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# abbreviations known in the field -----------------------------------------
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mo_genus("MRSA")
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@ -394,20 +395,15 @@ mo_genus("EHEC")
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mo_species("EHEC")
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# known subspecies ---------------------------------------------------------
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mo_name("doylei")
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mo_genus("doylei")
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mo_species("doylei")
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mo_subspecies("doylei")
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mo_fullname("K. pneu rh")
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mo_shortname("K. pneu rh")
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\donttest{
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# Becker classification, see ?as.mo ----------------------------------------
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mo_fullname("S. epi")
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mo_fullname("S. epi", Becker = TRUE)
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mo_shortname("S. epi")
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mo_shortname("S. epi", Becker = TRUE)
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mo_fullname("Staph. epi")
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mo_fullname("Staph. epi", Becker = TRUE)
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mo_shortname("Staph. epi")
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mo_shortname("Staph. epi", Becker = TRUE)
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# Lancefield classification, see ?as.mo ------------------------------------
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mo_fullname("S. pyo")
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@ -417,23 +413,19 @@ mo_shortname("S. pyo", Lancefield = TRUE)
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# language support --------------------------------------------------------
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mo_gramstain("Klebsiella pneumoniae", language = "de")
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mo_gramstain("Klebsiella pneumoniae", language = "nl")
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mo_gramstain("Klebsiella pneumoniae", language = "es")
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mo_gramstain("Klebsiella pneumoniae", language = "de") # German
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mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
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mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
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mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
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mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
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# mo_type is equal to mo_kingdom, but mo_kingdom will remain official
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mo_kingdom("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae", language = "nl")
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mo_fullname("S. pyogenes",
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Lancefield = TRUE,
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language = "de"
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)
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mo_fullname("S. pyogenes",
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Lancefield = TRUE,
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language = "nl"
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)
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mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
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mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk")
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# other --------------------------------------------------------------------
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@ -443,10 +435,13 @@ mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
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# gram stains and intrinsic resistance can be used as a filter in dplyr verbs
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if (require("dplyr")) {
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example_isolates \%>\%
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filter(mo_is_gram_positive())
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filter(mo_is_gram_positive()) \%>\%
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count(mo_genus(), count = TRUE)
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}
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if (require("dplyr")) {
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example_isolates \%>\%
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filter(mo_is_intrinsic_resistant(ab = "vanco"))
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filter(mo_is_intrinsic_resistant(ab = "vanco")) \%>\%
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count(mo_genus(), count = TRUE)
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}
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