diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index ec4a771a..e410f250 100644 --- a/.github/workflows/check.yaml +++ b/.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 diff --git a/DESCRIPTION b/DESCRIPTION index 6d116959..06cfaf99 100644 --- a/DESCRIPTION +++ b/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( diff --git a/NEWS.md b/NEWS.md index d72e9568..3bff0fa0 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9011 +# `AMR` 1.7.1.9012 ## Last updated: 4 July 2021 ### Changed diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index a6954a03..710b3b95 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 1cf6a7e5..50a019da 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 9fa02834..bbf8de67 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 50329e3a..72227cc8 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012 diff --git a/docs/articles/index.html b/docs/articles/index.html index 70aea4d0..e8518cde 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012 diff --git a/docs/authors.html b/docs/authors.html index 8e5921d3..19a5c235 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012 diff --git a/docs/index.html b/docs/index.html index 5ba3ed2b..d91fdb02 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012 diff --git a/docs/news/index.html b/docs/news/index.html index f8fb0430..a6fbacb2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9011

+
+

+ Unreleased AMR 1.7.1.9012

Last updated: 4 July 2021 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9f0933e2..7b6d3b14 100644 --- 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: 2021-07-04T13:26Z +last_built: 2021-07-04T18:25Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 4c55f404..e6155322 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012

diff --git a/docs/survey.html b/docs/survey.html index b9d9e164..d44082ce 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9011 + 1.7.1.9012
diff --git a/inst/tinytest/test-mo_property.R b/inst/tinytest/test-mo_property.R index c6fd2644..ea6f94e2 100644 --- a/inst/tinytest/test-mo_property.R +++ b/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(),