(v1.5.0.9022) mo properties speed improvement

.github/workflows/check.yaml

@@ -53,9 +53,11 @@ jobs:
           - {os: macOS-latest,   r: 'devel',   allowfail: false}
           - {os: macOS-latest,   r: 'release', allowfail: false}
           - {os: macOS-latest,   r: 'oldrel',  allowfail: false}
+          
           - {os: windows-latest, r: 'devel',   allowfail: false}
           - {os: windows-latest, r: 'release', allowfail: false}
           - {os: windows-latest, r: 'oldrel',  allowfail: false}
+          
           - {os: ubuntu-20.04,   r: 'devel',   allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04,   r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04,   r: 'oldrel',  allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@@ -66,7 +68,8 @@ jobs:
           - {os: ubuntu-20.04,   r: '3.3',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           # - {os: ubuntu-20.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           # - {os: ubuntu-20.04,   r: '3.1',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.0',     allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          
           - {os: ubuntu-16.04,   r: 'devel',   allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: 'oldrel',  allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
@@ -77,7 +80,7 @@ jobs:
           - {os: ubuntu-16.04,   r: '3.3',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           # - {os: ubuntu-16.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           # - {os: ubuntu-16.04,   r: '3.1',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.0',     allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.5.0.9021
+Version: 1.5.0.9022
 Date: 2021-02-21
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.5.0.9021
+# AMR 1.5.0.9022
 ## <small>Last updated: 21 February 2021</small>
 
 ### New
@@ -58,7 +58,8 @@
 * Functions `print()` and `summary()` on a Principal Components Analysis object (`pca()`) now print additional group info if the original data was grouped using `dplyr::group_by()`
 * Improved speed and reliability of `guess_ab_col()`. As this also internally improves the reliability of `first_isolate()` and `mdro()`, this might have a slight impact on the results of those functions.
 * Fix for `mo_name()` when used in other languages than English
-* The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package
+* The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package (e.g., `as.mo()` is now up to 4 times faster)
+* *Staphylococcus cornubiensis* is now correctly categorised as coagulase-positive
 
 ### Other
 * Big documentation updates

R/aa_helper_functions.R

@@ -112,7 +112,7 @@ check_dataset_integrity <- function() {
     require("AMR")
   })
   stop_if(!valid_microorganisms | !valid_antibiotics,
-          "the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object names was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
+          "the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object name(s) was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
   invisible(TRUE)
 }
 
@@ -538,7 +538,7 @@ meet_criteria <- function(object,
   if (!is.null(pkg_env$meet_criteria_error_txt)) {
     error_txt <- pkg_env$meet_criteria_error_txt
     pkg_env$meet_criteria_error_txt <- NULL
-    stop(error_txt, call. = FALSE)
+    stop(error_txt, call. = FALSE) # don't use stop_() here, pkg may not be loaded yet
   }
   pkg_env$meet_criteria_error_txt <- NULL
 
@@ -867,7 +867,13 @@ font_grey <- function(..., collapse = " ") {
   try_colour(..., before = "\033[38;5;249m", after = "\033[39m", collapse = collapse)
 }
 font_grey_bg <- function(..., collapse = " ") {
+  if (tryCatch(rstudioapi::getThemeInfo()$dark == TRUE, error = function(e) FALSE)) {
+    # similar to HTML #444444
+    try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse)  
+  } else {
+    # similar to HTML #eeeeee
     try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
+  }
 }
 font_green_bg <- function(..., collapse = " ") {
   try_colour(..., before = "\033[42m", after = "\033[49m", collapse = collapse)

R/mo.R

@@ -178,13 +178,6 @@ as.mo <- function(x,
     return(set_clean_class(x, new_class = c("mo", "character")))
   }
 
-  if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
-               & isFALSE(Becker)
-               & isFALSE(Lancefield), error = function(e) FALSE)) {
-    # to improve speed, special case for taxonomically correct full names (case-insensitive)
-    return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
-  }
-
   # start off with replaced language-specific non-ASCII characters with ASCII characters
   x <- parse_and_convert(x)
   # replace mo codes used in older package versions
@@ -199,6 +192,13 @@ as.mo <- function(x,
   x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
   uncertainty_level <- translate_allow_uncertain(allow_uncertain)
   
+  if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
+               & isFALSE(Becker)
+               & isFALSE(Lancefield), error = function(e) FALSE)) {
+    # to improve speed, special case for taxonomically correct full names (case-insensitive)
+    return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
+  }
+
   if (!is.null(reference_df)
       && check_validity_mo_source(reference_df)
       && isFALSE(Becker)
@@ -481,7 +481,7 @@ exec_as.mo <- function(x,
     
     # Fill in fullnames and MO codes at once
     known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
-    x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname), property, drop = TRUE]
+    x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
     known_codes <- toupper(x_backup) %in% MO_lookup$mo
     x[known_codes] <- MO_lookup[match(toupper(x_backup)[known_codes], MO_lookup$mo), property, drop = TRUE]
     already_known <- known_names | known_codes
@@ -984,7 +984,6 @@ exec_as.mo <- function(x,
                               g.x_backup_without_spp %pm>% substr(1, x_length / 2),
                               ".* ",
                               g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
-            print(x_split)
             found <- lookup(fullname_lower %like_case% x_split,
                             haystack = data_to_check)
             if (!is.na(found)) {
@@ -1977,13 +1976,13 @@ parse_and_convert <- function(x) {
       if (NCOL(x) > 2) {
         stop("a maximum of two columns is allowed", call. = FALSE)
       } else if (NCOL(x) == 2) {
-        # support Tidyverse selection like: df %pm>% select(colA, colB)
+        # support Tidyverse selection like: df %>% select(colA, colB)
         # paste these columns together
         x <- as.data.frame(x, stringsAsFactors = FALSE)
         colnames(x) <- c("A", "B")
         x <- paste(x$A, x$B)
       } else {
-        # support Tidyverse selection like: df %pm>% select(colA)
+        # support Tidyverse selection like: df %>% select(colA)
         x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
       }
     }
@@ -1991,6 +1990,8 @@ parse_and_convert <- function(x) {
     parsed <- iconv(x, to = "UTF-8")
     parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
     parsed <- gsub('"', "", parsed, fixed = TRUE)
+    parsed <- gsub(" +", " ", parsed, perl = TRUE)
+    parsed <- trimws(parsed)
   }, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
   parsed
 }

R/mo_property.R

@@ -694,21 +694,21 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
 
 mo_validate <- function(x, property, language, ...) {
   check_dataset_integrity()
-  
-  if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & length(list(...)) == 0, error = function(e) FALSE)) {
-    # special case for mo_* functions where class is already <mo>
-    return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
-  }
-  
   dots <- list(...)
   Becker <- dots$Becker
-  if (is.null(Becker)) {
+  if (is.null(Becker) | property %in% c("kingdom", "phylum", "class", "order", "family", "genus")) {
     Becker <- FALSE
   }
   Lancefield <- dots$Lancefield
-  if (is.null(Lancefield)) {
+  if (is.null(Lancefield) | property %in% c("kingdom", "phylum", "class", "order", "family", "genus")) {
     Lancefield <- FALSE
   }
+  has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") | Lancefield %in% c(TRUE, "all")
+  
+  if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
+    # special case for mo_* functions where class is already <mo>
+    return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
+  }
 
   # try to catch an error when inputting an invalid argument
   # so the 'call.' can be set to FALSE
@@ -722,8 +722,13 @@ mo_validate <- function(x, property, language, ...) {
     # because it's already a valid MO
     x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...)
   } else if (!all(x %in% MO_lookup[, property, drop = TRUE])
-             | Becker %in% c(TRUE, "all")
+             | has_Becker_or_Lancefield) {
-             | Lancefield %in% c(TRUE, "all")) {
+    accepted_args <- names(as.list(args("as.mo")))
+    accepted_args <- accepted_args[!accepted_args %in% c("", "...", "x", "property")]
+    stop_if(!all(names(dots) %in% names(as.list(args("as.mo")))),
+            "invalid argument(s): ", vector_and(names(dots)[!names(dots) %in% names(as.list(args("as.mo")))], quotes = "'"),
+            ".\nAccepted arguments are ", vector_and(accepted_args, quotes = "'"), ".",
+            call = FALSE)
     x <- exec_as.mo(x, property = property, language = language, ...)
   }
   

data-raw/_internals.R

@@ -51,18 +51,19 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
                                            "lentus", "lugdunensis", "massiliensis", "microti",
                                            "muscae", "nepalensis", "pasteuri", "petrasii",
                                            "pettenkoferi", "piscifermentans", "pseudoxylosus",
-                                           "rostri", "saccharolyticus", "saprophyticus",
+                                           "pulvereri", "rostri", "saccharolyticus", "saprophyticus",
                                            "sciuri", "simulans", "stepanovicii", "succinus",
-                                           "vitulinus", "warneri", "xylosus")
+                                           "vitulinus", "vitulus", "warneri", "xylosus")
                    | (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
              "mo", drop = TRUE]
   } else if (type == "CoPS") {
     MO_staph[which(MO_staph$species %in% c("coagulase-positive",
-                                           "simiae", "agnetis",
+                                           "agnetis", "argenteus",
+                                           "cornubiensis",
                                            "delphini", "lutrae",
                                            "hyicus", "intermedius",
                                            "pseudintermedius", "pseudointermedius",
-                                           "schweitzeri", "argenteus")
+                                           "schweitzeri", "simiae")
                    | (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
              "mo", drop = TRUE]
   }

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
       </span>
     </div>
 
@@ -236,9 +236,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1509021" class="section level1">
+    <div id="amr-1509022" class="section level1">
-<h1 class="page-header" data-toc-text="1.5.0.9021">
+<h1 class="page-header" data-toc-text="1.5.0.9022">
-<a href="#amr-1509021" class="anchor"></a>AMR 1.5.0.9021<small> Unreleased </small>
+<a href="#amr-1509022" class="anchor"></a>AMR 1.5.0.9022<small> Unreleased </small>
 </h1>
 <div id="last-updated-21-february-2021" class="section level2">
 <h2 class="hasAnchor">
@@ -326,7 +326,9 @@
 </li>
 <li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
 <li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
-<li>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package</li>
+<li>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package (e.g., <code><a href="../reference/as.mo.html">as.mo()</a></code> is now up to 4 times faster)</li>
+<li>
+<em>Staphylococcus cornubiensis</em> is now correctly categorised as coagulase-positive</li>
 </ul>
 </div>
 <div id="other" class="section level3">

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-02-21T19:14Z
+last_built: 2021-02-21T21:55Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
       </span>
     </div>
 

tests/testthat/test-data.R

@@ -86,3 +86,13 @@ test_that("CoL version info works", {
   
   expect_output(print(catalogue_of_life_version()))
 })
+
+test_that("CoNS/CoPS are up to date", {
+  uncategorised <- subset(microorganisms,
+                          genus == "Staphylococcus" &
+                            !species %in% c("", "aureus") &
+                            !mo %in% c(MO_CONS, MO_COPS))
+  expect(NROW(uncategorised) == 0,
+         failure_message = paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
+                                  uncategorised$species, " (", uncategorised$mo, ")"))
+})