(v1.7.1.9012) update unit tests

.github/workflows/check.yaml

@@ -104,7 +104,7 @@ jobs:
         # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
         # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
         run: |
-          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
+          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev
 
       - name: Query dependencies
         # this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.7.1.9011
+Version: 1.7.1.9012
 Date: 2021-07-04
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.7.1.9011
+# `AMR` 1.7.1.9012
 ## <small>Last updated:  4 July 2021</small>
 
 ### Changed

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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -39,7 +39,7 @@
       </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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</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-1719011" class="section level1">
+    <div id="amr-1719012" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9011">
+<h1 class="page-header" data-toc-text="1.7.1.9012">
-<a href="#amr-1719011" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9011</h1>
+<a href="#amr-1719012" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9012</h1>
 <div id="last-updated-4-july-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-4-july-2021" class="anchor"></a><small>Last updated: 4 July 2021</small>

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: 2021-07-04T13:26Z
+last_built: 2021-07-04T18:25Z
 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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</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">1.7.1.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9012</span>
       </span>
     </div>
 

inst/tinytest/test-mo_property.R

@@ -28,12 +28,23 @@ expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
 expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
 expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
 expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
-expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
+
-expect_equal(mo_genus("Escherichia coli"), "Escherichia")
+# S3 class for taxonomic names
+expect_inherits(mo_family("Escherichia coli"), "taxonomic_name")
+expect_equal(as.character(mo_family("Escherichia coli")), "Enterobacteriaceae")
+expect_equal(as.character(mo_fullname("Escherichia coli")), "Escherichia coli")
+expect_equal(as.character(mo_genus("Escherichia coli")), "Escherichia")
+expect_equal(as.character(mo_name("Escherichia coli")), "Escherichia coli")
+expect_equal(as.character(mo_shortname("Escherichia coli")), "E. coli")
+expect_equal(as.character(mo_shortname("Escherichia")), "Escherichia")
+expect_equal(as.character(mo_shortname("Staphylococcus aureus")), "S. aureus")
+expect_equal(as.character(mo_shortname("Staphylococcus aureus", Becker = TRUE)), "S. aureus")
+expect_equal(as.character(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en")), "CoPS")
+expect_equal(as.character(mo_shortname("Streptococcus agalactiae")), "S. agalactiae")
+expect_equal(as.character(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE)), "GBS")
+
 expect_equal(mo_species("Escherichia coli"), "coli")
 expect_equal(mo_subspecies("Escherichia coli"), "")
-expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
-expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
 expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
 expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
 expect_inherits(mo_taxonomy("Escherichia coli"), "list")
@@ -52,20 +63,12 @@ expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
 expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
 expect_equal(mo_year("Escherichia coli"), 1919)
 
-expect_equal(mo_shortname("Escherichia coli"), "E. coli")
-expect_equal(mo_shortname("Escherichia"), "Escherichia")
-expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
-expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
-expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
-expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
-expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
-
 expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
 expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
 
 # test integrity
 MOs <- microorganisms
-expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
+expect_identical(MOs$fullname, as.character(mo_fullname(MOs$fullname, language = "en")))
 
 # check languages
 expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
@@ -81,7 +84,7 @@ expect_stdout(print(mo_gramstain("Escherichia coli", language = "fr")))
 
 expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
 dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
-expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
+expect_identical(as.character(mo_name(dutch, language = NULL)), microorganisms$fullname) # gigantic test - will run ALL names
 
 # manual property function
 expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
@@ -117,7 +120,7 @@ expect_equal(mo_is_intrinsic_resistant(c("Escherichia coli", "Staphylococcus aur
                                        "vanco"),
              c(TRUE, FALSE, FALSE))
 # with reference data
-expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")), 
+expect_equal(as.character(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI"))), 
              "Escherichia coli")
 if (AMR:::pkg_is_available("dplyr")) {
   expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),