AMR/inst/tinytest/test-zzz.R

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# ==================================================================== #
# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
# SOURCE CODE: #
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# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
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# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
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# Check if these functions still exist in their package (all are in Suggests field)
# Since GitHub Actions runs every night, we will get emailed when a dependency fails based on this unit test
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# functions used by import_fn()
import_functions <- c(
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"%chin%" = "data.table",
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"anti_join" = "dplyr",
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"chmatch" = "data.table",
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"cur_column" = "dplyr",
"full_join" = "dplyr",
"has_internet" = "curl",
"html_attr" = "rvest",
"html_children" = "rvest",
"html_node" = "rvest",
"html_nodes" = "rvest",
"html_table" = "rvest",
"html_text" = "rvest",
"inner_join" = "dplyr",
"insertText" = "rstudioapi",
"left_join" = "dplyr",
"new_pillar_shaft_simple" = "pillar",
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"progress_bar" = "progress",
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"read_html" = "xml2",
"right_join" = "dplyr",
"semi_join" = "dplyr",
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"showQuestion" = "rstudioapi"
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)
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# functions that are called directly with ::
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call_functions <- c(
# cleaner
"freq.default" = "cleaner",
# cli
"symbol" = "cli",
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"ansi_has_hyperlink_support" = "cli",
# rstudioapi (RStudio)
"isAvailable" = "rstudioapi",
"versionInfo" = "rstudioapi",
# readxl
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"read_excel" = "readxl",
# ggplot2
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"aes" = "ggplot2",
"aes_string" = "ggplot2",
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"arrow" = "ggplot2",
"autoplot" = "ggplot2",
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"element_blank" = "ggplot2",
"element_line" = "ggplot2",
"element_text" = "ggplot2",
"expand_limits" = "ggplot2",
"facet_wrap" = "ggplot2",
"geom_errorbar" = "ggplot2",
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"geom_path" = "ggplot2",
"geom_point" = "ggplot2",
"geom_ribbon" = "ggplot2",
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"geom_segment" = "ggplot2",
"geom_text" = "ggplot2",
"ggplot" = "ggplot2",
"labs" = "ggplot2",
"layer" = "ggplot2",
"position_dodge2" = "ggplot2",
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"position_fill" = "ggplot2",
"scale_colour_discrete" = "ggplot2",
"scale_fill_discrete" = "ggplot2",
"scale_fill_manual" = "ggplot2",
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"scale_x_discrete" = "ggplot2",
"scale_y_continuous" = "ggplot2",
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"scale_y_discrete" = "ggplot2",
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"theme" = "ggplot2",
"theme_minimal" = "ggplot2",
"unit" = "ggplot2",
"xlab" = "ggplot2",
"ylab" = "ggplot2",
"vec_arith" = "vctrs"
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)
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if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
call_functions <- c(call_functions,
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# skimr
"inline_hist" = "skimr",
"sfl" = "skimr"
)
}
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extended_functions <- c(
"freq" = "cleaner",
"autoplot" = "ggplot2",
"pillar_shaft" = "pillar",
"get_skimmers" = "skimr",
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"type_sum" = "pillar",
"vec_cast" = "vctrs",
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"vec_math" = "vctrs",
"vec_ptype2" = "vctrs"
)
import_functions <- c(import_functions, call_functions, extended_functions)
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for (i in seq_len(length(import_functions))) {
fn <- names(import_functions)[i]
pkg <- unname(import_functions[i])
# function should exist in foreign pkg namespace
if (AMR:::pkg_is_available(pkg,
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also_load = FALSE,
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min_version = if (pkg == "dplyr") "1.0.0" else NULL
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)) {
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expect_true(!is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
info = paste0("does not exist (anymore): function `", pkg, "::", fn, "()`")
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)
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} else if (pkg != "rstudioapi") {
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warning("Package '", pkg, "' does not exist anymore")
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}
}
if (AMR:::pkg_is_available("cli")) {
expect_true(!is.null(cli::symbol$info))
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}
if (AMR:::pkg_is_available("cli")) {
}
if (AMR:::pkg_is_available("cli")) {
expect_true(!is.null(cli::symbol$ellipsis))
}
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if (AMR:::pkg_is_available("ggplot2")) {
# the scale_*_mic() functions rely on these
expect_true(is.function(ggplot2::scale_x_discrete()$transform))
expect_true(is.function(ggplot2::scale_y_discrete()$transform))
expect_true(is.function(ggplot2::scale_colour_discrete()$transform))
expect_true(is.function(ggplot2::scale_fill_discrete()$transform))
}