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unit tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends 2023-02-18 14:56:06 +01:00
parent 8dcf101a9c
commit 8d902410f9
33 changed files with 73 additions and 71 deletions
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2
.github/prehooks/pre-commit vendored
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@ -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

2
DESCRIPTION
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@ -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)

2
NEWS.md
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@ -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!)*

10
R/aa_helper_functions.R
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@ -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)

1
R/antibiogram.R
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@ -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, ...)

2
R/eucast_rules.R
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@ -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

2
R/join_microorganisms.R
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@ -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)

2
R/sir.R
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@ -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

4
R/zzz.R
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@ -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)
}

2
inst/tinytest/test-_deprecated.R
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@ -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")])))

4
inst/tinytest/test-_misc.R
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@ -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)))
}

2
inst/tinytest/test-ab_property.R
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@ -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)

2
inst/tinytest/test-ab_selectors.R
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@ -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)

16
inst/tinytest/test-antibiogram.R
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@ -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(autoplot(ab2), "gg")
expect_inherits(autoplot(ab3), "gg")
expect_inherits(autoplot(ab4), "gg")
expect_inherits(autoplot(ab5), "gg")
expect_inherits(autoplot(ab6), "gg")
expect_inherits(autoplot(ab7), "gg")
expect_inherits(autoplot(ab8), "gg")
expect_inherits(ggplot2::autoplot(ab1), "gg")
expect_inherits(ggplot2::autoplot(ab2), "gg")
expect_inherits(ggplot2::autoplot(ab3), "gg")
expect_inherits(ggplot2::autoplot(ab4), "gg")
expect_inherits(ggplot2::autoplot(ab5), "gg")
expect_inherits(ggplot2::autoplot(ab6), "gg")
expect_inherits(ggplot2::autoplot(ab7), "gg")
expect_inherits(ggplot2::autoplot(ab8), "gg")
}

6
inst/tinytest/test-atc_online.R
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@ -27,9 +27,9 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (AMR:::pkg_is_available("curl", also_load = FALSE) &&
AMR:::pkg_is_available("rvest", also_load = FALSE) &&
AMR:::pkg_is_available("xml2", also_load = FALSE) &&
if (AMR:::pkg_is_available("curl") &&
AMR:::pkg_is_available("rvest") &&
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)

2
inst/tinytest/test-bug_drug_combinations.R
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@ -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) %>%

2
inst/tinytest/test-count.R
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@ -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)

2
inst/tinytest/test-data.R
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@ -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))) {

10
inst/tinytest/test-disk.R
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@ -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(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))), "gg")
expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "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")) {
expect_stdout(print(tibble(d = as.disk(12))))
if (AMR:::pkg_is_available("tibble")) {
expect_stdout(print(tibble::tibble(d = as.disk(12))))
}

2
inst/tinytest/test-episode.R
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@ -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)

4
inst/tinytest/test-eucast_rules.R
View File

@ -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)))
}

2
inst/tinytest/test-first_isolate.R
View File

@ -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 %>%

3
inst/tinytest/test-ggplot_rsi.R
View File

@ -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

2
inst/tinytest/test-mdro.R
View File

@ -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))
}

10
inst/tinytest/test-mic.R
View File

@ -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(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))), "gg")
expect_inherits(ggplot2::autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "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")) {
expect_stdout(print(tibble(m = as.mic(2:4))))
if (AMR:::pkg_is_available("tibble")) {
expect_stdout(print(tibble::tibble(m = as.mic(2:4))))
}
# all mathematical operations

6
inst/tinytest/test-mo.R
View File

@ -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

2
inst/tinytest/test-mo_property.R
View File

@ -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

2
inst/tinytest/test-pca.R
View File

@ -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),

2
inst/tinytest/test-proportion.R
View File

@ -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

4
inst/tinytest/test-resistance_predict.R
View File

@ -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(

12
inst/tinytest/test-rsi.R
View File

@ -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) %>%

16
inst/tinytest/test-vctrs.R
View File

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

2
inst/tinytest/test-zzz.R
View File

@ -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",