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fix documentation

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dr. M.S. (Matthijs) Berends 2022-10-06 11:33:30 +02:00
parent 0d8b098220
commit b9342d103e
8 changed files with 64 additions and 67 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.2.9004 Version: 1.8.2.9006
Date: 2022-10-05 Date: 2022-10-06
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9004 # AMR 1.8.2.9006
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!

7
R/aa_helper_functions.R
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@ -1174,6 +1174,7 @@ font_stripstyle <- function(x) {
progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) { progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
if (print == FALSE || n < n_min) { if (print == FALSE || n < n_min) {
# create fake/empty object
pb <- list() pb <- list()
pb$tick <- function() { pb$tick <- function() {
invisible() invisible()
@ -1183,16 +1184,17 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
} }
set_clean_class(pb, new_class = "txtProgressBar") set_clean_class(pb, new_class = "txtProgressBar")
} else if (n >= n_min) { } else if (n >= n_min) {
# rely on the progress package if it is available - it has a more verbose output # use `progress`, which also has a timer
progress_bar <- import_fn("progress_bar", "progress", error_on_fail = FALSE) progress_bar <- import_fn("progress_bar", "progress", error_on_fail = FALSE)
if (!is.null(progress_bar)) { if (!is.null(progress_bar)) {
# so we use progress::progress_bar # so we use progress::progress_bar
# a close() method was also added, see below this function # a close() method was also added, see below this function
pb <- progress_bar$new( pb <- progress_bar$new(
format = "[:bar] :percent (:current/:total)", format = "(:spin) [:bar] :percent (:current/:total,:eta)",
total = n total = n
) )
} else { } else {
# use base R
pb <- utils::txtProgressBar(max = n, style = 3) pb <- utils::txtProgressBar(max = n, style = 3)
pb$tick <- function() { pb$tick <- function() {
pb$up(pb$getVal() + 1) pb$up(pb$getVal() + 1)
@ -1206,6 +1208,7 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
#' @export #' @export
#' @noRd #' @noRd
close.progress_bar <- function(con, ...) { close.progress_bar <- function(con, ...) {
# for progress::progress_bar$new()
con$terminate() con$terminate()
} }

11
R/mo.R
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@ -113,9 +113,8 @@
#' "staaur", #' "staaur",
#' "S. aureus", #' "S. aureus",
#' "S aureus", #' "S aureus",
#' "Staphylococcus aureus", #' "Sthafilokkockus aureus", # handles incorrect spelling
#' "Staphylococcus aureus (MRSA,", #' "Staphylococcus aureus (MRSA)",
#' "Zthafilokkoockus oureuz", # handles incorrect spelling
#' "MRSA", # Methicillin Resistant S. aureus #' "MRSA", # Methicillin Resistant S. aureus
#' "VISA", # Vancomycin Intermediate S. aureus #' "VISA", # Vancomycin Intermediate S. aureus
#' "VRSA", # Vancomycin Resistant S. aureus #' "VRSA", # Vancomycin Resistant S. aureus
@ -822,6 +821,7 @@ print.mo_uncertainties <- function(x, ...) {
txt <- paste(txt, txt <- paste(txt,
paste0( paste0(
paste0( paste0(
"", strrep(font_grey("-"), times = options()$width), "\n",
'"', x[i, ]$original_input, '"', '"', x[i, ]$original_input, '"',
" -> ", " -> ",
paste0( paste0(
@ -844,7 +844,10 @@ print.mo_uncertainties <- function(x, ...) {
candidates, candidates,
sep = "\n" sep = "\n"
) )
txt <- paste0(gsub("\n\n", "\n", txt), "\n\n") txt <- gsub("[\n]+", "\n", txt)
# remove first and last break
txt <- gsub("(^[\n]|[\n]$)", "", txt)
txt <- paste0("\n", txt, "\n")
} }
cat(txt) cat(txt)
} }

43
R/mo_property.R
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@ -98,6 +98,7 @@
#' mo_authors("Klebsiella pneumoniae") #' mo_authors("Klebsiella pneumoniae")
#' mo_year("Klebsiella pneumoniae") #' mo_year("Klebsiella pneumoniae")
#' mo_lpsn("Klebsiella pneumoniae") #' mo_lpsn("Klebsiella pneumoniae")
#' mo_gbif("Klebsiella pneumoniae")
#' #'
#' # abbreviations known in the field ----------------------------------------- #' # abbreviations known in the field -----------------------------------------
#' mo_genus("MRSA") #' mo_genus("MRSA")
@ -109,20 +110,15 @@
#' mo_species("EHEC") #' mo_species("EHEC")
#' #'
#' # known subspecies --------------------------------------------------------- #' # known subspecies ---------------------------------------------------------
#' mo_name("doylei")
#' mo_genus("doylei")
#' mo_species("doylei")
#' mo_subspecies("doylei")
#'
#' mo_fullname("K. pneu rh") #' mo_fullname("K. pneu rh")
#' mo_shortname("K. pneu rh") #' mo_shortname("K. pneu rh")
#' #'
#' \donttest{ #' \donttest{
#' # Becker classification, see ?as.mo ---------------------------------------- #' # Becker classification, see ?as.mo ----------------------------------------
#' mo_fullname("S. epi") #' mo_fullname("Staph. epi")
#' mo_fullname("S. epi", Becker = TRUE) #' mo_fullname("Staph. epi", Becker = TRUE)
#' mo_shortname("S. epi") #' mo_shortname("Staph. epi")
#' mo_shortname("S. epi", Becker = TRUE) #' mo_shortname("Staph. epi", Becker = TRUE)
#' #'
#' # Lancefield classification, see ?as.mo ------------------------------------ #' # Lancefield classification, see ?as.mo ------------------------------------
#' mo_fullname("S. pyo") #' mo_fullname("S. pyo")
@ -132,23 +128,19 @@
#' #'
#' #'
#' # language support -------------------------------------------------------- #' # language support --------------------------------------------------------
#' mo_gramstain("Klebsiella pneumoniae", language = "de") #' mo_gramstain("Klebsiella pneumoniae", language = "de") # German
#' mo_gramstain("Klebsiella pneumoniae", language = "nl") #' mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
#' mo_gramstain("Klebsiella pneumoniae", language = "es") #' mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
#' mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
#' mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#' #'
#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official #' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official
#' mo_kingdom("Klebsiella pneumoniae") #' mo_kingdom("Klebsiella pneumoniae")
#' mo_type("Klebsiella pneumoniae") #' mo_type("Klebsiella pneumoniae")
#' mo_type("Klebsiella pneumoniae") #' mo_type("Klebsiella pneumoniae", language = "nl")
#' #'
#' mo_fullname("S. pyogenes", #' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
#' Lancefield = TRUE, #' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk")
#' language = "de"
#' )
#' mo_fullname("S. pyogenes",
#' Lancefield = TRUE,
#' language = "nl"
#' )
#' #'
#' #'
#' # other -------------------------------------------------------------------- #' # other --------------------------------------------------------------------
@ -158,10 +150,13 @@
#' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs #' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs
#' if (require("dplyr")) { #' if (require("dplyr")) {
#' example_isolates %>% #' example_isolates %>%
#' filter(mo_is_gram_positive()) #' filter(mo_is_gram_positive()) %>%
#' #' count(mo_genus(), count = TRUE)
#' }
#' if (require("dplyr")) {
#' example_isolates %>% #' example_isolates %>%
#' filter(mo_is_intrinsic_resistant(ab = "vanco")) #' filter(mo_is_intrinsic_resistant(ab = "vanco")) %>%
#' count(mo_genus(), count = TRUE)
#' } #' }
#' #'
#' #'

16
inst/tinytest/test-mo.R
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@ -84,18 +84,20 @@ expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAM
expect_identical( expect_identical(
suppressWarnings(as.character( suppressWarnings(as.character(
as.mo(c( as.mo(c(
"stau", "stau", # WHONET code
"STAU", "STAU",
"staaur", "staaur",
"S. aureus", "S. aureus",
"S aureus", "S aureus",
"Sthafilokkockus aureus", "Sthafilokkockus aureus", # handles incorrect spelling
"Staphylococcus aureus", "Staphylococcus aureus (MRSA)",
"MRSA", "MRSA", # Methicillin Resistant S. aureus
"VISA" "VISA", # Vancomycin Intermediate S. aureus
), minimum_matching_score = 0) "VRSA", # Vancomycin Resistant S. aureus
115329001 # SNOMED CT code
))
)), )),
rep("B_STPHY_AURS", 9) rep("B_STPHY_AURS", 11)
) )
expect_identical( expect_identical(
as.character( as.character(

5
man/as.mo.Rd
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@ -170,9 +170,8 @@ as.mo(c(
"staaur", "staaur",
"S. aureus", "S. aureus",
"S aureus", "S aureus",
"Staphylococcus aureus", "Sthafilokkockus aureus", # handles incorrect spelling
"Staphylococcus aureus (MRSA,", "Staphylococcus aureus (MRSA)",
"Zthafilokkoockus oureuz", # handles incorrect spelling
"MRSA", # Methicillin Resistant S. aureus "MRSA", # Methicillin Resistant S. aureus
"VISA", # Vancomycin Intermediate S. aureus "VISA", # Vancomycin Intermediate S. aureus
"VRSA", # Vancomycin Resistant S. aureus "VRSA", # Vancomycin Resistant S. aureus

43
man/mo_property.Rd
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@ -383,6 +383,7 @@ mo_ref("Klebsiella pneumoniae")
mo_authors("Klebsiella pneumoniae") mo_authors("Klebsiella pneumoniae")
mo_year("Klebsiella pneumoniae") mo_year("Klebsiella pneumoniae")
mo_lpsn("Klebsiella pneumoniae") mo_lpsn("Klebsiella pneumoniae")
mo_gbif("Klebsiella pneumoniae")
# abbreviations known in the field ----------------------------------------- # abbreviations known in the field -----------------------------------------
mo_genus("MRSA") mo_genus("MRSA")
@ -394,20 +395,15 @@ mo_genus("EHEC")
mo_species("EHEC") mo_species("EHEC")
# known subspecies --------------------------------------------------------- # known subspecies ---------------------------------------------------------
mo_name("doylei")
mo_genus("doylei")
mo_species("doylei")
mo_subspecies("doylei")
mo_fullname("K. pneu rh") mo_fullname("K. pneu rh")
mo_shortname("K. pneu rh") mo_shortname("K. pneu rh")
\donttest{ \donttest{
# Becker classification, see ?as.mo ---------------------------------------- # Becker classification, see ?as.mo ----------------------------------------
mo_fullname("S. epi") mo_fullname("Staph. epi")
mo_fullname("S. epi", Becker = TRUE) mo_fullname("Staph. epi", Becker = TRUE)
mo_shortname("S. epi") mo_shortname("Staph. epi")
mo_shortname("S. epi", Becker = TRUE) mo_shortname("Staph. epi", Becker = TRUE)
# Lancefield classification, see ?as.mo ------------------------------------ # Lancefield classification, see ?as.mo ------------------------------------
mo_fullname("S. pyo") mo_fullname("S. pyo")
@ -417,23 +413,19 @@ mo_shortname("S. pyo", Lancefield = TRUE)
# language support -------------------------------------------------------- # language support --------------------------------------------------------
mo_gramstain("Klebsiella pneumoniae", language = "de") mo_gramstain("Klebsiella pneumoniae", language = "de") # German
mo_gramstain("Klebsiella pneumoniae", language = "nl") mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
mo_gramstain("Klebsiella pneumoniae", language = "es") mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
# mo_type is equal to mo_kingdom, but mo_kingdom will remain official # mo_type is equal to mo_kingdom, but mo_kingdom will remain official
mo_kingdom("Klebsiella pneumoniae") mo_kingdom("Klebsiella pneumoniae")
mo_type("Klebsiella pneumoniae") mo_type("Klebsiella pneumoniae")
mo_type("Klebsiella pneumoniae") mo_type("Klebsiella pneumoniae", language = "nl")
mo_fullname("S. pyogenes", mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
Lancefield = TRUE, mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk")
language = "de"
)
mo_fullname("S. pyogenes",
Lancefield = TRUE,
language = "nl"
)
# other -------------------------------------------------------------------- # other --------------------------------------------------------------------
@ -443,10 +435,13 @@ mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
# gram stains and intrinsic resistance can be used as a filter in dplyr verbs # gram stains and intrinsic resistance can be used as a filter in dplyr verbs
if (require("dplyr")) { if (require("dplyr")) {
example_isolates \%>\% example_isolates \%>\%
filter(mo_is_gram_positive()) filter(mo_is_gram_positive()) \%>\%
count(mo_genus(), count = TRUE)
}
if (require("dplyr")) {
example_isolates \%>\% example_isolates \%>\%
filter(mo_is_intrinsic_resistant(ab = "vanco")) filter(mo_is_intrinsic_resistant(ab = "vanco")) \%>\%
count(mo_genus(), count = TRUE)
} }