(v1.4.0.9002) bugfix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.4.0.9001
+Version: 1.4.0.9002
 Date: 2020-10-19
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.4.0.9001
+# AMR 1.4.0.9002
 ## <small>Last updated: 19 October 2020</small>
 
 ### New

R/ab.R

@@ -82,7 +82,7 @@
 #' ab_name("J01FA01")    # "Erythromycin"
 #' ab_name("eryt")       # "Erythromycin"
 as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
-  meet_criteria(x, allow_class = c("character", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_class = c("character", "numeric", "integer", "factor"), allow_NA = TRUE)
   meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
   meet_criteria(info, allow_class = "logical", has_length = 1)
   

R/mo.R

@@ -158,7 +158,7 @@ as.mo <- function(x,
                   ignore_pattern = getOption("AMR_ignore_pattern"),
                   language = get_locale(),
                   ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
   meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
   meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
@@ -275,7 +275,7 @@ exec_as.mo <- function(x,
                        actual_uncertainty = 1,
                        actual_input = NULL,
                        language = get_locale()) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
   meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
   meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)

R/mo_property.R

@@ -146,7 +146,7 @@
 #' mo_info("E. coli")
 #' }
 mo_name <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE)
@@ -159,7 +159,7 @@ mo_fullname <- mo_name
 #' @rdname mo_property
 #' @export
 mo_shortname <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   x.mo <- as.mo(x, language = language, ...)
@@ -192,7 +192,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_subspecies <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
@@ -201,7 +201,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_species <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
@@ -210,7 +210,7 @@ mo_species <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_genus <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
@@ -219,7 +219,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_family <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
@@ -228,7 +228,7 @@ mo_family <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_order <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
@@ -237,7 +237,7 @@ mo_order <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_class <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
@@ -246,7 +246,7 @@ mo_class <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_phylum <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
@@ -255,7 +255,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_kingdom <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
@@ -268,7 +268,7 @@ mo_domain <- mo_kingdom
 #' @rdname mo_property
 #' @export
 mo_type <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = FALSE)
@@ -277,7 +277,7 @@ mo_type <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_gramstain <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   x.mo <- as.mo(x, language = language, ...)
@@ -311,7 +311,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 is_gram_negative <- function(x, ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   grams <- mo_gramstain(x, language = NULL, ...)
   "Gram-negative" == grams & !is.na(grams)
 }
@@ -319,7 +319,7 @@ is_gram_negative <- function(x, ...) {
 #' @rdname mo_property
 #' @export
 is_gram_positive <- function(x, ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   grams <- mo_gramstain(x, language = NULL, ...)
   "Gram-positive" == grams & !is.na(grams)
 }
@@ -327,7 +327,7 @@ is_gram_positive <- function(x, ...) {
 #' @rdname mo_property
 #' @export
 mo_snomed <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   mo_validate(x = x, property = "snomed", language = language, ...)
@@ -336,7 +336,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_ref <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   mo_validate(x = x, property = "ref", language = language, ...)
@@ -345,7 +345,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_authors <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   x <- mo_validate(x = x, property = "ref", language = language, ...)
@@ -357,7 +357,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_year <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   x <- mo_validate(x = x, property = "ref", language = language, ...)
@@ -369,7 +369,7 @@ mo_year <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_rank <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   mo_validate(x = x, property = "rank", language = language, ...)
@@ -378,20 +378,20 @@ mo_rank <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_taxonomy <- function(x, language = get_locale(),  ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   x <- as.mo(x, language = language, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
   
   result <- list(kingdom = mo_kingdom(x, language = language),
-                       phylum = mo_phylum(x, language = language),
+                 phylum = mo_phylum(x, language = language),
-                       class = mo_class(x, language = language),
+                 class = mo_class(x, language = language),
-                       order = mo_order(x, language = language),
+                 order = mo_order(x, language = language),
-                       family = mo_family(x, language = language),
+                 family = mo_family(x, language = language),
-                       genus = mo_genus(x, language = language),
+                 genus = mo_genus(x, language = language),
-                       species = mo_species(x, language = language),
+                 species = mo_species(x, language = language),
-                       subspecies = mo_subspecies(x, language = language))
+                 subspecies = mo_subspecies(x, language = language))
   
   load_mo_failures_uncertainties_renamed(metadata)
   result
@@ -400,7 +400,7 @@ mo_taxonomy <- function(x, language = get_locale(),  ...) {
 #' @rdname mo_property
 #' @export
 mo_synonyms <- function(x, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   x <- as.mo(x, language = language, ...)
@@ -429,7 +429,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_info <- function(x, language = get_locale(),  ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
   x <- as.mo(x, language = language, ...)
@@ -455,7 +455,7 @@ mo_info <- function(x, language = get_locale(),  ...) {
 #' @rdname mo_property
 #' @export
 mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(open, allow_class = "logical", has_length = 1)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
@@ -464,7 +464,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
   metadata <- get_mo_failures_uncertainties_renamed()
   
   df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
-   pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
+    pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
   df$url <- ifelse(df$source == "CoL",
                    paste0(catalogue_of_life$url_CoL, "details/species/id/", df$species_id, "/"),
                    ifelse(df$source == "DSMZ",
@@ -488,10 +488,10 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
-  meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
-
+  
   translate_AMR(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = 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">1.4.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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-1409001" class="section level1">
+    <div id="amr-1409002" class="section level1">
-<h1 class="page-header" data-toc-text="1.4.0.9001">
+<h1 class="page-header" data-toc-text="1.4.0.9002">
-<a href="#amr-1409001" class="anchor"></a>AMR 1.4.0.9001<small> Unreleased </small>
+<a href="#amr-1409002" class="anchor"></a>AMR 1.4.0.9002<small> Unreleased </small>
 </h1>
 <div id="last-updated-19-october-2020" class="section level2">
 <h2 class="hasAnchor">

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: 2020-10-19T15:08Z
+last_built: 2020-10-19T18:44Z
 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">1.4.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span>
       </span>
     </div>