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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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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
View File

@@ -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)
}