unit tests

.github/prehooks/pre-commit

@@ -37,7 +37,7 @@ if command -v Rscript > /dev/null; then
     Rscript -e "source('data-raw/_pre_commit_hook.R')"
     currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
     echo "- Adding changed files in ./data-raw and ./man to this commit"
-    git add data-raw/* --quiet
+    git add data-raw/* --ignore-missing
     git add man/*
     git add R/sysdata.rda
     git add NAMESPACE

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9135
+Version: 1.8.2.9136
 Date: 2023-02-18
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9135
+# AMR 1.8.2.9136
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/aa_helper_functions.R

@@ -388,7 +388,7 @@ stop_ifnot_installed <- function(package) {
   }
 }
 
-pkg_is_available <- function(pkg, also_load = TRUE, min_version = NULL) {
+pkg_is_available <- function(pkg, also_load = FALSE, min_version = NULL) {
   if (also_load == TRUE) {
     out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE))
   } else {
@@ -1318,14 +1318,14 @@ create_pillar_column <- function(x, ...) {
 }
 
 as_original_data_class <- function(df, old_class = NULL, extra_class = NULL) {
-  if ("tbl_df" %in% old_class && pkg_is_available("tibble", also_load = FALSE)) {
+  if ("tbl_df" %in% old_class && pkg_is_available("tibble")) {
     # this will then also remove groups
     fn <- import_fn("as_tibble", "tibble")
-  } else if ("tbl_ts" %in% old_class && pkg_is_available("tsibble", also_load = FALSE)) {
+  } else if ("tbl_ts" %in% old_class && pkg_is_available("tsibble")) {
     fn <- import_fn("as_tsibble", "tsibble")
-  } else if ("data.table" %in% old_class && pkg_is_available("data.table", also_load = FALSE)) {
+  } else if ("data.table" %in% old_class && pkg_is_available("data.table")) {
     fn <- import_fn("as.data.table", "data.table")
-  } else if ("tabyl" %in% old_class && pkg_is_available("janitor", also_load = FALSE)) {
+  } else if ("tabyl" %in% old_class && pkg_is_available("janitor")) {
     fn <- import_fn("as_tabyl", "janitor")
   } else {
     fn <- function(x) base::as.data.frame(df, stringsAsFactors = FALSE)

R/antibiogram.R

@@ -563,6 +563,7 @@ print.antibiogram <- function(x, as_kable = !interactive(), italicise = TRUE, ..
   meet_criteria(italicise, allow_class = "logical", has_length = 1)
 
   if (isTRUE(as_kable) &&
+      pkg_is_available("knitr") &&
       # be sure not to run kable in pkgdown for our website generation
       !(missing(as_kable) && identical(Sys.getenv("IN_PKGDOWN"), "true"))) {
     out <- knitr::kable(x, ...)

R/eucast_rules.R

@@ -1219,7 +1219,7 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 12.0)
   rownames(out) <- NULL
   out$ab <- ab
   out$name <- ab_name(ab, language = NULL)
-  if (pkg_is_available("tibble", also_load = FALSE)) {
+  if (pkg_is_available("tibble")) {
     import_fn("as_tibble", "tibble")(out)
   } else {
     out

R/join_microorganisms.R

@@ -130,7 +130,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
   add_MO_lookup_to_AMR_env()
 
   if (!is.data.frame(x)) {
-    if (pkg_is_available("tibble", also_load = FALSE)) {
+    if (pkg_is_available("tibble")) {
       x <- import_fn("tibble", "tibble")(mo = x)
     } else {
       x <- data.frame(mo = x, stringsAsFactors = FALSE)

R/sir.R

@@ -1080,7 +1080,7 @@ sir_interpretation_history <- function(clean = FALSE) {
   # sort descending on time
   out <- out[order(out$datetime, decreasing = TRUE), , drop = FALSE]
 
-  if (pkg_is_available("tibble", also_load = FALSE)) {
+  if (pkg_is_available("tibble")) {
     import_fn("as_tibble", "tibble")(out)
   } else {
     out

R/zzz.R

@@ -112,7 +112,7 @@ if (utf8_supported && !is_latex) {
   s3_register("cleaner::freq", "mo")
   s3_register("cleaner::freq", "sir")
   # Support for skim() from the skimr package
-  if (pkg_is_available("skimr", also_load = FALSE, min_version = "2.0.0")) {
+  if (pkg_is_available("skimr", min_version = "2.0.0")) {
     s3_register("skimr::get_skimmers", "mo")
     s3_register("skimr::get_skimmers", "sir")
     s3_register("skimr::get_skimmers", "mic")
@@ -178,7 +178,7 @@ if (utf8_supported && !is_latex) {
     try(invisible(get_mo_source()), silent = TRUE)
   }
   # be sure to print tibbles as tibbles
-  if (pkg_is_available("tibble", also_load = FALSE)) {
+  if (pkg_is_available("tibble")) {
     try(loadNamespace("tibble"), silent = TRUE)
   }
 

inst/tinytest/test-_deprecated.R

@@ -54,7 +54,7 @@ expect_identical(suppressWarnings(rsi_df(example_isolates)),
 expect_identical(suppressWarnings(is.rsi.eligible(example_isolates)),
                  suppressWarnings(is_sir_eligible(example_isolates)))
 
-if (AMR:::pkg_is_available("ggplot2", also_load = FALSE)) {
+if (AMR:::pkg_is_available("ggplot2")) {
   expect_equal(suppressWarnings(ggplot_rsi(example_isolates[, c("CIP", "GEN", "TOB")])),
                suppressWarnings(ggplot_sir(example_isolates[, c("CIP", "GEN", "TOB")])))
   

inst/tinytest/test-_misc.R

@@ -50,12 +50,12 @@ expect_equal(AMR:::trimws2(" test ", "r"), " test")
 # 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", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   # 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 run a test that checks for this:
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
 }

inst/tinytest/test-ab_property.R

@@ -82,7 +82,7 @@ expect_identical(
   c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
 )
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_identical(
     example_isolates %>% set_ab_names(),
     example_isolates %>% rename_with(set_ab_names)

inst/tinytest/test-ab_selectors.R

@@ -95,7 +95,7 @@ expect_identical(
   c("gen", "tobra")
 )
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   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)

inst/tinytest/test-antibiogram.R

@@ -120,12 +120,12 @@ expect_silent(plot(ab7))
 expect_silent(plot(ab8))
 
 if (AMR:::pkg_is_available("ggplot2")) {
-  expect_inherits(autoplot(ab1), "gg")
+  expect_inherits(ggplot2::autoplot(ab1), "gg")
-  expect_inherits(autoplot(ab2), "gg")
+  expect_inherits(ggplot2::autoplot(ab2), "gg")
-  expect_inherits(autoplot(ab3), "gg")
+  expect_inherits(ggplot2::autoplot(ab3), "gg")
-  expect_inherits(autoplot(ab4), "gg")
+  expect_inherits(ggplot2::autoplot(ab4), "gg")
-  expect_inherits(autoplot(ab5), "gg")
+  expect_inherits(ggplot2::autoplot(ab5), "gg")
-  expect_inherits(autoplot(ab6), "gg")
+  expect_inherits(ggplot2::autoplot(ab6), "gg")
-  expect_inherits(autoplot(ab7), "gg")
+  expect_inherits(ggplot2::autoplot(ab7), "gg")
-  expect_inherits(autoplot(ab8), "gg")
+  expect_inherits(ggplot2::autoplot(ab8), "gg")
 }

inst/tinytest/test-atc_online.R

@@ -27,9 +27,9 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-if (AMR:::pkg_is_available("curl", also_load = FALSE) &&
+if (AMR:::pkg_is_available("curl") &&
-  AMR:::pkg_is_available("rvest", also_load = FALSE) &&
+  AMR:::pkg_is_available("rvest") &&
-  AMR:::pkg_is_available("xml2", also_load = FALSE) &&
+  AMR:::pkg_is_available("xml2") &&
   tryCatch(curl::has_internet(), error = function(e) FALSE)) {
   expect_true(length(atc_online_groups(ab_atc("AMX"))) >= 1)
   expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "O"), 1.5)

inst/tinytest/test-bug_drug_combinations.R

@@ -32,7 +32,7 @@ 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, add_ab_group = FALSE)))
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_true(example_isolates %>%
     group_by(ward) %>%
     bug_drug_combinations(FUN = mo_gramstain) %>%

inst/tinytest/test-count.R

@@ -58,7 +58,7 @@ expect_error(count_susceptible("test", as_percent = "test"))
 expect_error(count_df(c("A", "B", "C")))
 expect_error(count_df(example_isolates[, "date", drop = TRUE]))
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   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-data.R

@@ -55,7 +55,7 @@ expect_false(any(is.na(as.disk(clinical_breakpoints[which(clinical_breakpoints$m
 # antibiotic names must always be coercible to their original AB code
 expect_identical(as.ab(antibiotics$name), antibiotics$ab)
 
-if (AMR:::pkg_is_available("tibble", also_load = FALSE)) {
+if (AMR:::pkg_is_available("tibble")) {
   # there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
   datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
   for (i in seq_len(length(datasets))) {

inst/tinytest/test-disk.R

@@ -48,12 +48,12 @@ expect_silent(plot(as.disk(c(10, 20, 40))))
 expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
 expect_silent(plot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"))
 if (AMR:::pkg_is_available("ggplot2")) {
-  expect_inherits(autoplot(as.disk(c(10, 20, 40))), "gg")
+  expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40))), "gg")
-  expect_inherits(autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
+  expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
-  expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
+  expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
 }
 expect_stdout(print(as.disk(12)))
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("tibble")) {
-  expect_stdout(print(tibble(d = as.disk(12))))
+  expect_stdout(print(tibble::tibble(d = as.disk(12))))
 }

inst/tinytest/test-episode.R

@@ -51,7 +51,7 @@ expect_equal(
   c(1, 2, 2, 2, 3)
 )
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   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

@@ -98,7 +98,7 @@ b <- data.frame(
 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", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_equal(
     suppressWarnings(
       example_isolates %>%
@@ -150,7 +150,7 @@ expect_equal(
 )
 
 # also test norf
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_stdout(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
 }
 

inst/tinytest/test-first_isolate.R

@@ -139,7 +139,7 @@ expect_error(first_isolate(example_isolates,
   col_mo = "mo"
 ))
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   # if mo is not an mo class, result should be the same
   expect_identical(
     example_isolates %>%

inst/tinytest/test-ggplot_rsi.R

@@ -27,7 +27,8 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0") & AMR:::pkg_is_available("ggplot2")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE) &&
+    AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
   pdf(NULL) # prevent Rplots.pdf being created
 
   # data should be equal

inst/tinytest/test-mdro.R

@@ -278,7 +278,7 @@ expect_error(custom_mdro_guideline("test" ~ A))
 # ))
 
 # print groups
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_stdout(x <- mdro(example_isolates %>% group_by(ward), info = TRUE, pct_required_classes = 0))
   expect_stdout(x <- mdro(example_isolates %>% group_by(ward), guideline = custom, info = TRUE))
 }

inst/tinytest/test-mic.R

@@ -63,16 +63,16 @@ expect_silent(plot(as.mic(c(1, 2, 4, 8))))
 expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
 expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "Escherichia coli", ab = "cipr"))
 if (AMR:::pkg_is_available("ggplot2")) {
-  expect_inherits(autoplot(as.mic(c(1, 2, 4, 8))), "gg")
+  expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8))), "gg")
-  expect_inherits(autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
+  expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
-  expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "Escherichia coli", ab = "cipr"), "gg")
+  expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "Escherichia coli", ab = "cipr"), "gg")
 }
 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", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("tibble")) {
-  expect_stdout(print(tibble(m = as.mic(2:4))))
+  expect_stdout(print(tibble::tibble(m = as.mic(2:4))))
 }
 
 # all mathematical operations

inst/tinytest/test-mo.R

@@ -160,7 +160,7 @@ expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRP
 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", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   # select with one column
   expect_identical(
     example_isolates %>%
@@ -302,9 +302,9 @@ expect_equal(
   c("F_YEAST", "F_FUNGUS")
 )
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("tibble")) {
   # print tibble
-  expect_stdout(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
+  expect_stdout(print(tibble::tibble(mo = as.mo("B_ESCHR_COLI"))))
 }
 
 # assigning and subsetting

inst/tinytest/test-mo_property.R

@@ -198,7 +198,7 @@ expect_equal(
   mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
   "Escherichia coli"
 )
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
     730,
     tolerance = 0.5

inst/tinytest/test-pca.R

@@ -57,7 +57,7 @@ if (AMR:::pkg_is_available("ggplot2")) {
   ggplot_pca(pca_model, arrows_textangled = FALSE)
 }
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   resistance_data <- example_isolates %>%
     group_by(
       order = mo_order(mo),

inst/tinytest/test-proportion.R

@@ -47,7 +47,7 @@ expect_equal(
   proportion_SI(example_isolates$AMX)
 )
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_equal(example_isolates %>% proportion_SI(AMC),
     0.7626397,
     tolerance = 0.0001

inst/tinytest/test-resistance_predict.R

@@ -27,7 +27,7 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_stdout(AMX_R <- example_isolates %>%
     filter(mo == "B_ESCHR_COLI") %>%
     sir_predict(
@@ -52,7 +52,7 @@ pdf(NULL) # prevent Rplots.pdf being created
 expect_silent(plot(x))
 if (AMR:::pkg_is_available("ggplot2")) {
   expect_silent(ggplot_sir_predict(x))
-  expect_silent(autoplot(x))
+  expect_silent(ggplot2::autoplot(x))
   expect_error(ggplot_sir_predict(example_isolates))
 }
 expect_stdout(sir_predict(

inst/tinytest/test-rsi.R

@@ -45,7 +45,7 @@ pdf(NULL) # prevent Rplots.pdf being created
 expect_silent(barplot(as.sir(c("S", "I", "R"))))
 expect_silent(plot(as.sir(c("S", "I", "R"))))
 if (AMR:::pkg_is_available("ggplot2")) {
-  expect_inherits(autoplot(as.sir(c("S", "I", "R"))), "gg")
+  expect_inherits(ggplot2::autoplot(as.sir(c("S", "I", "R"))), "gg")
 }
 expect_stdout(print(as.sir(c("S", "I", "R"))))
 expect_equal(as.character(as.sir(c(1:3))), c("S", "I", "R"))
@@ -68,7 +68,7 @@ expect_identical(
 expect_error(as.sir.mic(as.mic(16)))
 expect_error(as.sir.disk(as.disk(16)))
 expect_error(get_guideline("this one does not exist"))
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   # 40 sir columns
   expect_equal(
     example_isolates %>%
@@ -88,12 +88,12 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
                 pull(MEM) %>% 
                 is.sir())
 }
-if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
+if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
   expect_inherits(
     skim(example_isolates),
     "data.frame"
   )
-  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
     expect_inherits(
       example_isolates %>%
         mutate(
@@ -146,7 +146,7 @@ expect_equal(
   suppressMessages(as.sir(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
   as.sir("R")
 )
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_true(suppressWarnings(example_isolates %>%
     mutate(amox_mic = as.mic(2)) %>%
     select(mo, amox_mic) %>%
@@ -188,7 +188,7 @@ expect_equal(
   ),
   "R"
 )
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
   expect_true(example_isolates %>%
     mutate(amox_disk = as.disk(15)) %>%
     select(mo, amox_disk) %>%

inst/tinytest/test-vctrs.R

@@ -28,12 +28,12 @@
 # ==================================================================== #
 
 # extra tests for {vctrs} pkg support
-if (AMR:::pkg_is_available("dplyr", also_load = FALSE)) {
+if (AMR:::pkg_is_available("tibble")) {
-  test <- dplyr::tibble(ab = as.ab("CIP"),
+  test <- tibble::tibble(ab = as.ab("CIP"),
-                        mo = as.mo("Escherichia coli"),
+                         mo = as.mo("Escherichia coli"),
-                        mic = as.mic(2),
+                         mic = as.mic(2),
-                        disk = as.disk(20),
+                         disk = as.disk(20),
-                        sir = as.sir("S"))
+                         sir = as.sir("S"))
   check1 <- lapply(test, class)
   test[1, "ab"] <- "GEN"
   test[1, "mo"] <- "B_KLBSL_PNMN"
@@ -46,8 +46,8 @@ if (AMR:::pkg_is_available("dplyr", also_load = FALSE)) {
   check2 <- lapply(test, class)
   expect_identical(check1, check2)
   
-  test <- dplyr::tibble(cipro = as.sir("S"),
+  test <- tibble::tibble(cipro = as.sir("S"),
-                        variable = "test")
+                         variable = "test")
   expect_equal(nrow(test[quinolones() == "S", ]), 1)
   expect_equal(nrow(test[quinolones() == "R", ]), 0)
 }

inst/tinytest/test-zzz.R

@@ -90,7 +90,7 @@ call_functions <- c(
   "xlab" = "ggplot2",
   "ylab" = "ggplot2"
 )
-if (AMR:::pkg_is_available("skimr", also_load = FALSE, min_version = "2.0.0")) {
+if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
   call_functions <- c(call_functions,
     # skimr
     "inline_hist" = "skimr",