(v1.5.0.9022) mo properties speed improvement

2 years ago · 062c49fca1
parent 5ef8cb41a7
commit 062c49fca1
19 changed files with 76 additions and 47 deletions
--- a/.github/workflows/check.yaml
+++ b/.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
--- a/2
+++ b/2
@ -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(
--- a/NEWS.md
+++ b/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
--- a/R/aa_helper_functions.R
+++ b/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 = " ") {
-  try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = 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)
--- a/R/mo.R
+++ b/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
@ -198,6 +191,13 @@ as.mo <- function(x,
  x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
  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)
@ -481,11 +481,11 @@ 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$mo), property, drop = TRUE]
    already_known <- known_names | known_codes
-    
+
    # now only continue where the right taxonomic output is not already known
    if (any(!already_known)) {
      x_known <- x[already_known]
@ -984,7 +984,6 @@ exec_as.mo <- function(x,
                              g.x_backup_without_spp %pm>% substr(1, x_length / 2),
                              ".* ",
                              g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
-            print(x_split)
            found <- lookup(fullname_lower %like_case% x_split,
                            haystack = data_to_check)
            if (!is.na(found)) {
@ -1977,13 +1976,13 @@ parse_and_convert <- function(x) {
      if (NCOL(x) > 2) {
        stop("a maximum of two columns is allowed", call. = FALSE)
      } else if (NCOL(x) == 2) {
-        # support Tidyverse selection like: df %pm>% select(colA, colB)
+        # support Tidyverse selection like: df %>% select(colA, colB)
        # paste these columns together
        x <- as.data.frame(x, stringsAsFactors = FALSE)
        colnames(x) <- c("A", "B")
        x <- paste(x$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
 }
--- a/R/mo_property.R
+++ b/R/mo_property.R
@ -694,22 +694,22 @@ 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
  tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
@ -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")
-             | Lancefield %in% c(TRUE, "all")) {
+             | has_Becker_or_Lancefield) {
+    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, ...)
  }
  
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/data-raw/_internals.R
+++ b/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]
  }
--- a/docs/404.html
+++ b/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>

--- a/docs/LICENSE-text.html
+++ b/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>

--- a/docs/articles/index.html
+++ b/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>

--- a/docs/authors.html
+++ b/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>

--- a/docs/index.html
+++ b/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>

--- a/docs/news/index.html
+++ b/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">
-<h1 class="page-header" data-toc-text="1.5.0.9021">
-<a href="#amr-1509021" class="anchor"></a>AMR 1.5.0.9021<small> Unreleased </small>
+    <div id="amr-1509022" class="section level1">
+<h1 class="page-header" data-toc-text="1.5.0.9022">
+<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">
--- a/docs/pkgdown.yml
+++ b/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
--- a/docs/reference/index.html
+++ b/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>

--- a/docs/survey.html
+++ b/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>

--- a/tests/testthat/test-data.R
+++ b/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, ")"))
+})