diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index b2842431..0dd2e0eb 100644 --- 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' diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 51c0205f..7622b76e 100644 --- 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 diff --git a/DESCRIPTION b/DESCRIPTION index 38aea241..8a50098f 100644 --- a/DESCRIPTION +++ b/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 diff --git a/NEWS.md b/NEWS.md index 1166ed5b..ba9bf692 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.7.1.9048 -## Last updated: 4 October 2021 +# `AMR` 1.7.1.9049 +## Last updated: 5 October 2021 ### Breaking changes * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 97efc167..24835eee 100755 --- 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) } diff --git a/R/mo.R b/R/mo.R index d25cbf2c..c6e55cb8 100755 --- 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)) { diff --git a/codecov.yml b/codecov.yml index bd222069..7b57efbe 100644 --- a/codecov.yml +++ b/codecov.yml @@ -25,7 +25,7 @@ codecov: require_ci_to_pass: no # allow fail - branch: master + branch: main comment: no diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 847e34bc..e8b15c52 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 19a1c762..a0913a93 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9048 + 1.7.1.9049 @@ -190,7 +190,7 @@

Data sets for download / own use

-

04 October 2021

+

05 October 2021

Source: vignettes/datasets.Rmd diff --git a/docs/news/index.html b/docs/news/index.html index 72ef8220..103202a9 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9048 + 1.7.1.9049
@@ -240,12 +240,12 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9048

-
+
+

+ Unreleased AMR 1.7.1.9049

+

-Last updated: 4 October 2021 +Last updated: 5 October 2021

diff --git a/inst/tinytest/test-_misc.R b/inst/tinytest/test-_misc.R index 3d0bd421..fecae64f 100755 --- 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))) } diff --git a/inst/tinytest/test-ab_class_selectors.R b/inst/tinytest/test-ab_class_selectors.R index e00b07dc..3dfbd713 100644 --- 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))) +} diff --git a/inst/tinytest/test-ab_property.R b/inst/tinytest/test-ab_property.R index 006c4c53..428aa788 100644 --- 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)) } diff --git a/inst/tinytest/test-bug_drug_combinations.R b/inst/tinytest/test-bug_drug_combinations.R index 769961a4..aa269f5b 100644 --- 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) %>% diff --git a/inst/tinytest/test-count.R b/inst/tinytest/test-count.R index b39f3d7f..0cfeb5ed 100644 --- 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) diff --git a/inst/tinytest/test-disk.R b/inst/tinytest/test-disk.R index 837266ea..b303ab8b 100755 --- 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)))) } diff --git a/inst/tinytest/test-episode.R b/inst/tinytest/test-episode.R index fd6bd680..89932ffd 100644 --- 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)) diff --git a/inst/tinytest/test-eucast_rules.R b/inst/tinytest/test-eucast_rules.R index 087f51e2..26a6fafa 100755 --- 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))) } diff --git a/inst/tinytest/test-first_isolate.R b/inst/tinytest/test-first_isolate.R index f6e48fcd..a599d4b9 100755 --- 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)) %>% diff --git a/inst/tinytest/test-ggplot_rsi.R b/inst/tinytest/test-ggplot_rsi.R index eec8c2a0..d7afc1f3 100644 --- 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 diff --git a/inst/tinytest/test-mdro.R b/inst/tinytest/test-mdro.R index ebdc8356..22c717b2 100755 --- 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)) } diff --git a/inst/tinytest/test-mic.R b/inst/tinytest/test-mic.R index face904d..1d73a8b8 100755 --- 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)))) } diff --git a/inst/tinytest/test-mo.R b/inst/tinytest/test-mo.R index 5623b0d6..7aefe37b 100644 --- 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")))) } diff --git a/inst/tinytest/test-mo_property.R b/inst/tinytest/test-mo_property.R index 35abe717..83a83689 100644 --- 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(), diff --git a/inst/tinytest/test-pca.R b/inst/tinytest/test-pca.R index 24d085c6..e9ab0c70 100644 --- 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)) %>% diff --git a/inst/tinytest/test-proportion.R b/inst/tinytest/test-proportion.R index d27691e5..c0e4e1ed 100755 --- 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) diff --git a/inst/tinytest/test-resistance_predict.R b/inst/tinytest/test-resistance_predict.R index d06e3d02..81a02868 100644 --- 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", diff --git a/inst/tinytest/test-rsi.R b/inst/tinytest/test-rsi.R index 004b177d..d2192806 100644 --- 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) %>%