mirror of https://github.com/msberends/AMR.git
151 lines
5.2 KiB
R
151 lines
5.2 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 #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi: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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"%>%" = "dplyr",
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"%chin%" = "data.table",
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"across" = "dplyr",
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"anti_join" = "dplyr",
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"arrange" = "dplyr",
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"bind_rows" = "dplyr",
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"chmatch" = "data.table",
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"count" = "dplyr",
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"cur_column" = "dplyr",
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"desc" = "dplyr",
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"distinct" = "dplyr",
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"everything" = "dplyr",
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"full_join" = "dplyr",
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"group_by" = "dplyr",
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"group_vars" = "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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"kable" = "knitr",
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"lag" = "dplyr",
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"left_join" = "dplyr",
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"mutate" = "dplyr",
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"n_distinct" = "dplyr",
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"new_pillar_shaft_simple" = "pillar",
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"pivot_longer" = "tidyr",
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"progress_bar" = "progress",
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"pull" = "dplyr",
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"read_html" = "xml2",
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"rename" = "dplyr",
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"right_join" = "dplyr",
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"row_number" = "dplyr",
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"select" = "dplyr",
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"semi_join" = "dplyr",
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"showQuestion" = "rstudioapi",
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"summarise" = "dplyr",
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"ungroup" = "dplyr"
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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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# 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_col" = "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_fill" = "ggplot2",
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"scale_fill_manual" = "ggplot2",
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"scale_y_continuous" = "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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)
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if (AMR:::pkg_is_available("skimr", also_load = FALSE, 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 %in% c("dplyr", "tidyr")) "1.0.0" else NULL
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)) {
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tst <- !is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE))
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expect_true(tst,
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info = ifelse(tst,
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"All external function references exist.",
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paste0("Function ", pkg, "::", fn, "() does not exist anymore")
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)
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)
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}
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}
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