(v1.7.1.9049) unit tests

.github/workflows/check.yaml

@@ -88,6 +88,8 @@ jobs:
       - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
+      
+      - uses: r-lib/actions/setup-pandoc@v1
 
       - name: Install Linux dependencies
         if: runner.os == 'Linux'
@@ -95,7 +97,7 @@ 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 libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
       - name: Restore cached R packages
         # this step will add the step 'Post Restore cached R packages' on a succesful run
         if: runner.os != 'Windows'

.github/workflows/codecovr.yaml

@@ -45,8 +45,10 @@ jobs:
       - uses: r-lib/actions/setup-r@v1
         with:
           r-version: release
-          
-      - uses: r-lib/actions/setup-pandoc@master
+      
+      - uses: r-lib/actions/setup-pandoc@v1
+        # with:
+        #   pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
 
       - name: Query dependencies
         # this will change once a week, so it will cache dependency updates

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9048
-Date: 2021-10-04
+Version: 1.7.1.9049
+Date: 2021-10-05
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.7.1.9048
-## <small>Last updated:  4 October 2021</small>
+# `AMR` 1.7.1.9049
+## <small>Last updated:  5 October 2021</small>
 
 ### Breaking changes
 * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version

R/aa_helper_functions.R

@@ -296,12 +296,15 @@ stop_ifnot_installed <- function(package) {
   return(invisible())
 }
 
-pkg_is_available <- function(pkg, also_load = TRUE) {
+pkg_is_available <- function(pkg, also_load = TRUE, min_version = NULL) {
   if (also_load == TRUE) {
     out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE))
   } else {
     out <- requireNamespace(pkg, quietly = TRUE)
   }
+  if (!is.null(min_version)) {
+    out <- out && packageVersion(pkg) >= min_version
+  }
   isTRUE(out)
 }
 

R/mo.R

@@ -372,7 +372,7 @@ exec_as.mo <- function(x,
   # Laboratory systems: remove (translated) entries like "no growth", etc.
   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"
-
+  
   if (initial_search == TRUE) {
     # keep track of time - give some hints to improve speed if it takes a long time
     start_time <- Sys.time()
@@ -495,9 +495,13 @@ exec_as.mo <- function(x,
     # Fill in fullnames and MO codes directly
     known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
     x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$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
+    known_codes_mo <- toupper(x_backup) %in% MO_lookup$mo
+    x[known_codes_mo] <- MO_lookup[match(toupper(x_backup)[known_codes_mo], MO_lookup$mo), property, drop = TRUE]
+    known_codes_lis <- toupper(x_backup) %in% microorganisms.codes$code
+    x[known_codes_lis] <- MO_lookup[match(microorganisms.codes[match(toupper(x_backup)[known_codes_lis],
+                                                                     microorganisms.codes$code), "mo", drop = TRUE],
+                                          MO_lookup$mo), property, drop = TRUE]
+    already_known <- known_names | known_codes_mo | known_codes_lis
 
     # now only continue where the right taxonomic output is not already known
     if (any(!already_known)) {

codecov.yml

@@ -25,7 +25,7 @@
 
 codecov:
   require_ci_to_pass: no # allow fail
-  branch: master
+  branch: main
 
 comment: no
 

docs/articles/datasets.html

@@ -44,7 +44,7 @@
       </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">1.7.1.9048</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9049</span>
       </span>
     </div>
 
@@ -190,7 +190,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">04 October 2021</h4>
+            <h4 data-toc-skip class="date">05 October 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>

docs/news/index.html

@@ -92,7 +92,7 @@
       </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">1.7.1.9048</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9049</span>
       </span>
     </div>
 
@@ -240,12 +240,12 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1719048" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9048">
-<a href="#amr-1719048" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9048</h1>
-<div id="last-updated-4-october-2021" class="section level2">
+    <div id="amr-1719049" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.1.9049">
+<a href="#amr-1719049" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9049</h1>
+<div id="last-updated-5-october-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-4-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 4 October 2021</small>
+<a href="#last-updated-5-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 5 October 2021</small>
 </h2>
 <div id="breaking-changes" class="section level3">
 <h3 class="hasAnchor">

inst/tinytest/test-_misc.R

@@ -42,12 +42,12 @@ expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
 expect_warning(AMR:::get_column_abx(example_isolates, hard_dependencies = "FUS"))
 expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS"))
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
   expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
 }
 
 # we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
 }

inst/tinytest/test-ab_class_selectors.R

@@ -65,6 +65,9 @@ expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tole
 # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
 expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
 expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
+expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
+expect_equal(nrow(example_isolates[any(carbapenems() != "R"), ]), 910, tolerance = 0.5)
+expect_equal(nrow(example_isolates[carbapenems() != "R", ]), 704, tolerance = 0.5)
 
 # filter with multiple antibiotic selectors using c()
 expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
@@ -73,3 +76,9 @@ expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R
 expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
 expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
 
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+  expect_equal(example_isolates %>% select(administrable_per_os() & penicillins()) %>% ncol(), 5, tolerance = 0.5)
+  expect_equal(example_isolates %>% select(administrable_iv() & penicillins()) %>% ncol(), 7, tolerance = 0.5)
+  expect_equal(example_isolates %>% select(administrable_iv() | penicillins()) %>% ncol(), 37, tolerance = 0.5)
+  expect_warning(example_isolates %>% select(GEH = GEN) %>% select(aminoglycosides(only_treatable = TRUE)))
+}

inst/tinytest/test-ab_property.R

@@ -69,7 +69,7 @@ expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl
                  c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine"))
 expect_identical(colnames(set_ab_names(example_isolates[, 20:25], "atc")),
                  c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01"))
-if (AMR:::pkg_is_available("dplyr") && packageVersion("dplyr") >= "1.0.0") {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_identical(example_isolates %>% set_ab_names(),
                    example_isolates %>% rename_with(set_ab_names))
 }

inst/tinytest/test-bug_drug_combinations.R

@@ -28,7 +28,7 @@ expect_inherits(b, "bug_drug_combinations")
 expect_stdout(suppressMessages(print(b)))
 expect_true(is.data.frame(format(b)))
 expect_true(is.data.frame(format(b, combine_IR = TRUE, add_ab_group = FALSE)))
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_true(example_isolates %>% 
                 group_by(hospital_id) %>% 
                 bug_drug_combinations(FUN = mo_gramstain) %>% 

inst/tinytest/test-count.R

@@ -51,7 +51,7 @@ expect_error(count_susceptible("test", as_percent = "test"))
 expect_error(count_df(c("A", "B", "C")))
 expect_error(count_df(example_isolates[, "date"]))
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
   expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
   expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)

inst/tinytest/test-disk.R

@@ -50,6 +50,6 @@ if (AMR:::pkg_is_available("ggplot2")) {
 }
 expect_stdout(print(as.disk(12)))
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_stdout(print(tibble(d = as.disk(12))))
 }

inst/tinytest/test-episode.R

@@ -36,7 +36,7 @@ test_df <- rbind(
 expect_equal(get_episode(test_df$date, 365),
              c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3))
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f),
                    c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE))
   

inst/tinytest/test-eucast_rules.R

@@ -72,7 +72,7 @@ b <- data.frame(mo = c("Staphylococcus aureus",
 expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
 
 # piperacillin must be R in Enterobacteriaceae when tica is R
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_equal(suppressWarnings(
     example_isolates %>%
       filter(mo_family(mo) == "Enterobacteriaceae") %>%
@@ -110,7 +110,7 @@ expect_equal(
   "S")
 
 # also test norf
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_stdout(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
 }
 

inst/tinytest/test-first_isolate.R

@@ -110,7 +110,7 @@ expect_error(first_isolate(example_isolates,
                            col_date = "non-existing col",
                            col_mo = "mo"))
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   # if mo is not an mo class, result should be the same
   expect_identical(example_isolates %>%
                      mutate(mo = as.character(mo)) %>%

inst/tinytest/test-ggplot_rsi.R

@@ -23,7 +23,7 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-if (AMR:::pkg_is_available("dplyr") & AMR:::pkg_is_available("ggplot2")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0") & AMR:::pkg_is_available("ggplot2")) {
   
   pdf(NULL) # prevent Rplots.pdf being created
   

inst/tinytest/test-mdro.R

@@ -232,7 +232,7 @@ expect_warning(mdro(example_isolates,
                     info = FALSE))
 
 # print groups
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_stdout(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
   expect_stdout(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
 }

inst/tinytest/test-mic.R

@@ -58,7 +58,7 @@ expect_stdout(print(as.mic(c(1, 2, 4, 8))))
 
 expect_inherits(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_stdout(print(tibble(m = as.mic(2:4))))
 }
 

inst/tinytest/test-mo.R

@@ -143,7 +143,7 @@ expect_identical(as.character(as.mo("S. sanguinis",   Lancefield = TRUE)),  "B_S
 expect_identical(as.character(as.mo("S. salivarius",  Lancefield = FALSE)), "B_STRPT_SLVR")
 expect_identical(as.character(as.mo("S. salivarius",  Lancefield = TRUE)),  "B_STRPT_GRPK") # group K
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   # select with one column
   expect_identical(
     example_isolates[1:10, ] %>%
@@ -272,7 +272,7 @@ expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
 expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))), 
              c("F_YEAST", "F_FUNGUS"))
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   # print tibble
   expect_stdout(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
 }

inst/tinytest/test-mo_property.R

@@ -119,7 +119,7 @@ expect_equal(mo_is_intrinsic_resistant(c("Escherichia coli", "Staphylococcus aur
 # with reference data
 expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")), 
              "Escherichia coli")
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
                730, tolerance = 0.5)
   expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),

inst/tinytest/test-pca.R

@@ -47,7 +47,7 @@ if (AMR:::pkg_is_available("ggplot2")) {
   ggplot_pca(pca_model, arrows_textangled = FALSE)
 }
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   resistance_data <- example_isolates %>% 
     group_by(order = mo_order(mo),
              genus = mo_genus(mo)) %>%

inst/tinytest/test-proportion.R

@@ -35,7 +35,7 @@ expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$
 expect_equal(proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
              proportion_SI(example_isolates$AMX))
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_equal(example_isolates %>% proportion_SI(AMC),
                0.7626397,
                tolerance = 0.0001)

inst/tinytest/test-resistance_predict.R

@@ -23,7 +23,7 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_stdout(AMX_R <- example_isolates %>%
                   filter(mo == "B_ESCHR_COLI") %>%
                   rsi_predict(col_ab = "AMX",

inst/tinytest/test-rsi.R

@@ -51,7 +51,7 @@ expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
 expect_error(as.rsi.mic(as.mic(16)))
 expect_error(as.rsi.disk(as.disk(16)))
 expect_error(get_guideline("this one does not exist"))
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   # 40 rsi columns
   expect_equal(example_isolates %>%
                  mutate_at(vars(PEN:RIF), as.character) %>%
@@ -66,7 +66,7 @@ if (AMR:::pkg_is_available("dplyr")) {
 if (AMR:::pkg_is_available("skimr")) {
   expect_inherits(skim(example_isolates),
                   "data.frame")
-  if (AMR:::pkg_is_available("dplyr")) {
+  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
     expect_inherits(example_isolates %>%
                       mutate(m = as.mic(2),
                              d = as.disk(20)) %>% 
@@ -96,7 +96,7 @@ expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020
              as.rsi("S"))
 expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
              as.rsi("R"))
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_true(suppressWarnings(example_isolates %>%
                                  mutate(amox_mic = as.mic(2)) %>%
                                  select(mo, amox_mic) %>%
@@ -123,7 +123,7 @@ expect_equal(as.character(
          ab = "ERY",
          guideline = "CLSI")),
   "R")
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_true(example_isolates %>%
                 mutate(amox_disk = as.disk(15)) %>%
                 select(mo, amox_disk) %>%