(v1.7.1.9049) unit tests

2 years ago · 2bcf28281d
parent d1b16ce641
commit 2bcf28281d
28 changed files with 64 additions and 44 deletions
--- a/.github/workflows/check.yaml
+++ b/.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'
--- a/.github/workflows/codecovr.yaml
+++ b/.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
--- a/4
+++ b/4
@ -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
--- a/NEWS.md
+++ b/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
--- a/R/aa_helper_functions.R
+++ b/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)
 }

--- a/R/mo.R
+++ b/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)) {
--- a/codecov.yml
+++ b/codecov.yml
@ -25,7 +25,7 @@

 codecov:
  require_ci_to_pass: no # allow fail
-  branch: master
+  branch: main

 comment: no

--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/docs/articles/datasets.html
+++ b/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>
--- a/docs/news/index.html
+++ b/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">
--- a/inst/tinytest/test-_misc.R
+++ b/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)))
 }
--- a/inst/tinytest/test-ab_class_selectors.R
+++ b/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)))
+}
--- a/inst/tinytest/test-ab_property.R
+++ b/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))
 }
--- a/inst/tinytest/test-bug_drug_combinations.R
+++ b/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) %>% 
--- a/inst/tinytest/test-count.R
+++ b/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)
--- a/inst/tinytest/test-disk.R
+++ b/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))))
 }
--- a/inst/tinytest/test-episode.R
+++ b/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))
  
--- a/inst/tinytest/test-eucast_rules.R
+++ b/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)))
 }

--- a/inst/tinytest/test-first_isolate.R
+++ b/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)) %>%
--- a/inst/tinytest/test-ggplot_rsi.R
+++ b/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
  
--- a/inst/tinytest/test-mdro.R
+++ b/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))
 }
--- a/inst/tinytest/test-mic.R
+++ b/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))))
 }

--- a/inst/tinytest/test-mo.R
+++ b/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"))))
 }
--- a/inst/tinytest/test-mo_property.R
+++ b/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(),
--- a/inst/tinytest/test-pca.R
+++ b/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)) %>%
--- a/inst/tinytest/test-proportion.R
+++ b/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)
--- a/inst/tinytest/test-resistance_predict.R
+++ b/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",
--- a/inst/tinytest/test-rsi.R
+++ b/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) %>%