fix documentation

DESCRIPTION

@@ -1,6 +1,6 @@
 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
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -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!
 

R/aa_helper_functions.R

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

R/mo.R

@@ -113,9 +113,8 @@
 #'   "staaur",
 #'   "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
 #'   "VISA", # Vancomycin Intermediate S. aureus
 #'   "VRSA", # Vancomycin Resistant S. aureus
@@ -822,6 +821,7 @@ print.mo_uncertainties <- function(x, ...) {
     txt <- paste(txt,
       paste0(
         paste0(
+          "", strrep(font_grey("-"), times = options()$width), "\n",
           '"', x[i, ]$original_input, '"',
           " -> ",
           paste0(
@@ -844,7 +844,10 @@ print.mo_uncertainties <- function(x, ...) {
       candidates,
       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)
 }

R/mo_property.R

@@ -98,6 +98,7 @@
 #' mo_authors("Klebsiella pneumoniae")
 #' mo_year("Klebsiella pneumoniae")
 #' mo_lpsn("Klebsiella pneumoniae")
+#' mo_gbif("Klebsiella pneumoniae")
 #'
 #' # abbreviations known in the field -----------------------------------------
 #' mo_genus("MRSA")
@@ -109,20 +110,15 @@
 #' mo_species("EHEC")
 #'
 #' # known subspecies ---------------------------------------------------------
-#' mo_name("doylei")
-#' mo_genus("doylei")
-#' mo_species("doylei")
-#' mo_subspecies("doylei")
-#'
 #' mo_fullname("K. pneu rh")
 #' mo_shortname("K. pneu rh")
 #'
 #' \donttest{
 #' # 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 ------------------------------------
 #' mo_fullname("S. pyo")
@@ -132,23 +128,19 @@
 #'
 #'
 #' # 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_kingdom("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 --------------------------------------------------------------------
@@ -158,10 +150,13 @@
 #' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs
 #' if (require("dplyr")) {
 #'   example_isolates %>%
-#'     filter(mo_is_gram_positive())
+#'     filter(mo_is_gram_positive()) %>% 
-#'
+#'     count(mo_genus(), count = TRUE)
+#' }
+#' if (require("dplyr")) {
 #'   example_isolates %>%
-#'     filter(mo_is_intrinsic_resistant(ab = "vanco"))
+#'     filter(mo_is_intrinsic_resistant(ab = "vanco")) %>% 
+#'     count(mo_genus(), count = TRUE)
 #' }
 #'
 #'

inst/tinytest/test-mo.R

@@ -84,18 +84,20 @@ expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAM
 expect_identical(
   suppressWarnings(as.character(
     as.mo(c(
-      "stau",
+      "stau", # WHONET code
       "STAU",
       "staaur",
       "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(
   as.character(

man/as.mo.Rd

@@ -170,9 +170,8 @@ as.mo(c(
   "staaur",
   "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
   "VISA", # Vancomycin Intermediate S. aureus
   "VRSA", # Vancomycin Resistant S. aureus

man/mo_property.Rd

@@ -383,6 +383,7 @@ mo_ref("Klebsiella pneumoniae")
 mo_authors("Klebsiella pneumoniae")
 mo_year("Klebsiella pneumoniae")
 mo_lpsn("Klebsiella pneumoniae")
+mo_gbif("Klebsiella pneumoniae")
 
 # abbreviations known in the field -----------------------------------------
 mo_genus("MRSA")
@@ -394,20 +395,15 @@ mo_genus("EHEC")
 mo_species("EHEC")
 
 # known subspecies ---------------------------------------------------------
-mo_name("doylei")
-mo_genus("doylei")
-mo_species("doylei")
-mo_subspecies("doylei")
-
 mo_fullname("K. pneu rh")
 mo_shortname("K. pneu rh")
 
 \donttest{
 # 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 ------------------------------------
 mo_fullname("S. pyo")
@@ -417,23 +413,19 @@ mo_shortname("S. pyo", Lancefield = TRUE)
 
 
 # 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_kingdom("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 --------------------------------------------------------------------
@@ -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
 if (require("dplyr")) {
   example_isolates \%>\%
-    filter(mo_is_gram_positive())
+    filter(mo_is_gram_positive()) \%>\% 
-
+    count(mo_genus(), count = TRUE)
+}
+if (require("dplyr")) {
   example_isolates \%>\%
-    filter(mo_is_intrinsic_resistant(ab = "vanco"))
+    filter(mo_is_intrinsic_resistant(ab = "vanco")) \%>\% 
+    count(mo_genus(), count = TRUE)
 }