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(v1.1.0.9004) lose dependencies
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@ -52,7 +52,7 @@ unique_ip <- unique(data$ipaddress)
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ip_tbl <- GET_df(unique_ip[1])
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p <- AMR:::progress_estimated(n = length(unique_ip) - 1, min_time = 0)
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for (i in 2:length(unique_ip)) {
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p$tick()$print()
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p$tick()
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ip_tbl <- ip_tbl %>%
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bind_rows(GET_df(unique_ip[i]))
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}
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@ -128,24 +128,24 @@ genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints
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genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints
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genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints
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genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints
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order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Enterobacter aerogenes aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Escherichia hermanni aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Enterobacter aerogenes aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Escherichia hermanni aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
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genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordatella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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Can't render this file because it contains an unexpected character in line 6 and column 96.
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@ -70,15 +70,14 @@ rm(translations_file)
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rm(microorganisms.translation)
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# Save to raw data to repository ----
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library(dplyr, warn.conflicts = FALSE, quietly = TRUE)
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usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
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devtools::load_all(quiet = TRUE)
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# give official names to ABs and MOs
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write.table(rsi_translation %>% mutate(ab = ab_name(ab), mo = mo_name(mo)),
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write.table(dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo)),
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"data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
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write.table(microorganisms %>% mutate_if(~!is.numeric(.), as.character),
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write.table(dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character),
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"data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE)
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write.table(antibiotics %>% mutate_if(~!is.numeric(.), as.character),
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write.table(dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character),
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"data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE)
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write.table(antivirals %>% mutate_all(as.character),
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write.table(dplyr::mutate_all(antivirals, as.character),
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"data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE)
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40
data-raw/poorman_prepend.R
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40
data-raw/poorman_prepend.R
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@ -0,0 +1,40 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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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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# #
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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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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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# ------------------------------------------------
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# THIS FILE WAS CREATED AUTOMATICALLY!
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# Source file: data-raw/reproduction_of_poorman.R
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# ------------------------------------------------
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# Poorman: a package to replace all dplyr functions with base R so we can lose dependency on dplyr.
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# These functions were downloaded from https://github.com/nathaneastwood/poorman,
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# from this commit: https://github.com/nathaneastwood/poorman/tree/{commit}
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#
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# All code below was released under MIT license, that permits 'free of charge, to any person obtaining a
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# copy of the software and associated documentation files (the "Software"), to deal in the Software
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# without restriction, including without limitation the rights to use, copy, modify, merge, publish,
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# distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software
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# is furnished to do so', given that a copyright notice is given in the software.
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#
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# Copyright notice as found on https://github.com/nathaneastwood/poorman/blob/master/LICENSE on 2 May 2020:
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# YEAR: 2020
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# COPYRIGHT HOLDER: Nathan Eastwood
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38
data-raw/reproduction_of_poorman.R
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38
data-raw/reproduction_of_poorman.R
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@ -0,0 +1,38 @@
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# get complete filenames of all R files in the GitHub repository of nathaneastwood/poorman
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commit <- "7d76d77f8f7bc663bf30fb5a161abb49801afa17"
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files <- xml2::read_html(paste0("https://github.com/nathaneastwood/poorman/tree/", commit, "/R")) %>%
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rvest::html_nodes("table") %>%
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rvest::html_table()
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files <- files[[1]][,"Name"]
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# remove files with only pkg specific code
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files <- files[!files %in% c("zzz.R", "init.R")]
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files <- paste0("https://raw.githubusercontent.com/nathaneastwood/poorman/", commit, "/R/",
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files[grepl("[.]R$", files)])
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# add our prepend file, containing info about the source of the data
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files <- c("data-raw/poorman_prepend.R", files)
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# read all contents to a character vector
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contents <- character(0)
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sapply(files, function(file) {
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contents <<- c(contents, readLines(file))
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invisible()
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})
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# remove lines starting with "#'" and NULL and write to file
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contents <- contents[!grepl("^(#'|NULL|\"_PACKAGE)", contents)]
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# now make it independent on UseMethod, since we will not export these functions
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contents <- gsub('UseMethod[(]"(.*?)"[)]',
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'if ("grouped_data" %in% class(.data)) {||| \\1.grouped_data(.data, ...)||| } else {||| \\1.default(.data, ...)||| }',
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paste(contents, collapse = "|||"),
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perl = TRUE) %>%
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# add commit to intro part
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gsub("{commit}", commit, ., fixed = TRUE) %>%
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strsplit(split = "|||", fixed = TRUE) %>%
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unlist()
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writeLines(contents, "R/aa_helper_functions_dplyr.R")
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