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(v1.7.1.9012) update unit tests

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dr. M.S. (Matthijs) Berends 2021-07-04 20:25:30 +02:00
parent 5b5741f681
commit 350dbe6a11
15 changed files with 34 additions and 31 deletions
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2
.github/workflows/check.yaml vendored
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@ -104,7 +104,7 @@ jobs:
# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version # 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 # 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: | 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 - name: Query dependencies
# this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates # this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.7.1.9011 Version: 1.7.1.9012
Date: 2021-07-04 Date: 2021-07-04
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.7.1.9011 # `AMR` 1.7.1.9012
## <small>Last updated: 4 July 2021</small> ## <small>Last updated: 4 July 2021</small>
### Changed ### Changed

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data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </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"> <div id="last-updated-4-july-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-4-july-2021" class="anchor"></a><small>Last updated: 4 July 2021</small> <a href="#last-updated-4-july-2021" class="anchor"></a><small>Last updated: 4 July 2021</small>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-07-04T13:26Z last_built: 2021-07-04T18:25Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

33
inst/tinytest/test-mo_property.R
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@ -28,12 +28,23 @@ expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria") expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria") expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
expect_equal(mo_order("Escherichia coli"), "Enterobacterales") 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_species("Escherichia coli"), "coli")
expect_equal(mo_subspecies("Escherichia 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_type("Escherichia coli", language = "en"), "Bacteria")
expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative") expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
expect_inherits(mo_taxonomy("Escherichia coli"), "list") 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_authors("Escherichia coli"), "Castellani et al.")
expect_equal(mo_year("Escherichia coli"), 1919) 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("Candida albicans") %like% "catalogueoflife.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de") expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity # test integrity
MOs <- microorganisms 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 # check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien") 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")) expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again dutch <- mo_name(microorganisms$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 # manual property function
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname"))) 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"), "vanco"),
c(TRUE, FALSE, FALSE)) c(TRUE, FALSE, FALSE))
# with reference data # 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") "Escherichia coli")
if (AMR:::pkg_is_available("dplyr")) { if (AMR:::pkg_is_available("dplyr")) {
expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(), expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),