mirror of
https://github.com/msberends/AMR.git
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158 lines
5.6 KiB
R
158 lines
5.6 KiB
R
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# 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 #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# Check if these functions still exist in their package (all are in Suggests field)
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# 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()
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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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"cli_abort" = "cli",
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"cur_column" = "dplyr",
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"full_join" = "dplyr",
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"has_internet" = "curl",
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"html_attr" = "rvest",
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"html_children" = "rvest",
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"html_node" = "rvest",
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"html_nodes" = "rvest",
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"html_table" = "rvest",
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"html_text" = "rvest",
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"inner_join" = "dplyr",
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"insertText" = "rstudioapi",
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"left_join" = "dplyr",
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"new_pillar_shaft_simple" = "pillar",
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"progress_bar" = "progress",
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"read_html" = "xml2",
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"right_join" = "dplyr",
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"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(
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# cleaner
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"freq.default" = "cleaner",
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# cli
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"symbol" = "cli",
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"ansi_has_hyperlink_support" = "cli",
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# rstudioapi (RStudio)
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"isAvailable" = "rstudioapi",
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"versionInfo" = "rstudioapi",
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# readxl
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"read_excel" = "readxl",
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# ggplot2
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"aes" = "ggplot2",
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"aes_string" = "ggplot2",
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"arrow" = "ggplot2",
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"autoplot" = "ggplot2",
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"element_blank" = "ggplot2",
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"element_line" = "ggplot2",
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"element_text" = "ggplot2",
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"expand_limits" = "ggplot2",
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"facet_wrap" = "ggplot2",
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"geom_errorbar" = "ggplot2",
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"geom_path" = "ggplot2",
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"geom_point" = "ggplot2",
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"geom_ribbon" = "ggplot2",
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"geom_segment" = "ggplot2",
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"geom_text" = "ggplot2",
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"ggplot" = "ggplot2",
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"labs" = "ggplot2",
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"layer" = "ggplot2",
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"position_dodge2" = "ggplot2",
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"position_fill" = "ggplot2",
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"scale_colour_discrete" = "ggplot2",
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"scale_fill_discrete" = "ggplot2",
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"scale_fill_manual" = "ggplot2",
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"scale_x_discrete" = "ggplot2",
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"scale_y_continuous" = "ggplot2",
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"scale_y_discrete" = "ggplot2",
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"theme" = "ggplot2",
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"theme_minimal" = "ggplot2",
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"unit" = "ggplot2",
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"xlab" = "ggplot2",
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"ylab" = "ggplot2",
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"vec_arith" = "vctrs"
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)
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if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
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call_functions <- c(call_functions,
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# skimr
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"inline_hist" = "skimr",
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"sfl" = "skimr"
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)
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}
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extended_functions <- c(
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"freq" = "cleaner",
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"autoplot" = "ggplot2",
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"pillar_shaft" = "pillar",
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"get_skimmers" = "skimr",
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"type_sum" = "pillar",
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"vec_cast" = "vctrs",
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"vec_math" = "vctrs",
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"vec_ptype2" = "vctrs"
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)
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import_functions <- c(import_functions, call_functions, extended_functions)
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for (i in seq_len(length(import_functions))) {
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fn <- names(import_functions)[i]
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pkg <- unname(import_functions[i])
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# function should exist in foreign pkg namespace
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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)),
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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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}
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}
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if (AMR:::pkg_is_available("cli")) {
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expect_true(!is.null(cli::symbol$info))
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}
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if (AMR:::pkg_is_available("cli")) {
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}
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if (AMR:::pkg_is_available("cli")) {
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expect_true(!is.null(cli::symbol$ellipsis))
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}
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if (AMR:::pkg_is_available("ggplot2")) {
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# the scale_*_mic() functions rely on these
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expect_true(is.function(ggplot2::scale_x_discrete()$transform))
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expect_true(is.function(ggplot2::scale_y_discrete()$transform))
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expect_true(is.function(ggplot2::scale_colour_discrete()$transform))
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expect_true(is.function(ggplot2::scale_fill_discrete()$transform))
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}
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