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111 lines
4.2 KiB
111 lines
4.2 KiB
# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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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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# LICENCE # |
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# (c) 2018-2021 Berends MS, Luz CF et al. # |
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# Developed at the University of Groningen, the Netherlands, in # |
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# collaboration with non-profit organisations Certe Medical # |
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# Diagnostics & Advice, and University Medical Center Groningen. # |
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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 function still exist in the 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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"anti_join" = "dplyr", |
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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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"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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# functions that are called directly |
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call_functions <- c( |
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# cleaner |
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"freq.default" = "cleaner", |
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# skimr |
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"inline_hist" = "skimr", |
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"sfl" = "skimr", |
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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_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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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" = "tibble", |
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"vec_cast" = "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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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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