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fix add manual ab
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4
.github/workflows/check-devel.yaml
vendored
4
.github/workflows/check-devel.yaml
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@ -33,6 +33,10 @@ on:
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branches: '**'
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branches: '**'
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push:
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push:
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branches: '**'
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branches: '**'
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schedule:
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# run a schedule everyday at 1 AM.
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# this is to check that all dependencies are still available (see R/zzz.R)
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cron: '0 1 * * *'
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name: check-devel
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name: check-devel
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2
.github/workflows/check-release.yaml
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2
.github/workflows/check-release.yaml
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@ -34,7 +34,7 @@ on:
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schedule:
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schedule:
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# run a schedule everyday at 1 AM.
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# run a schedule everyday at 1 AM.
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# this is to check that all dependencies are still available (see R/zzz.R)
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# this is to check that all dependencies are still available (see R/zzz.R)
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- cron: '0 1 * * *'
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cron: '0 1 * * *'
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name: check-release
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name: check-release
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@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 1.8.2.9018
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Version: 1.8.2.9019
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Date: 2022-10-15
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Date: 2022-10-18
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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data analysis and to work with microbial and antimicrobial properties by
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9018
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# AMR 1.8.2.9019
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -112,13 +112,19 @@ add_custom_antimicrobials <- function(x) {
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AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
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AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
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class(AMR_env$AB_lookup$ab) <- "character"
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class(AMR_env$AB_lookup$ab) <- "character"
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bind_rows <- import_fn("bind_rowtts", "dplyr", error_on_fail = FALSE)
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bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
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if (is.null(bind_rows)) {
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if (is.null(bind_rows)) {
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# do the binding in base R
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# do the binding in base R
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new_df <- AMR_env$AB_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
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new_df <- AMR_env$AB_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
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rownames(new_df) <- NULL
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rownames(new_df) <- NULL
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list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
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for (l in which(list_cols)) {
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# prevent binding NULLs in lists, replace with NA
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new_df[, l] <- as.list(NA_character_)
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}
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for (col in colnames(x)) {
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for (col in colnames(x)) {
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new_df[, col] <- x[, col, drop = TRUE]
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# assign new values
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new_df[, col] <- x[, col, drop = TRUE]
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}
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}
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AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df))
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AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df))
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} else {
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} else {
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@ -34,6 +34,7 @@
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import_functions <- c(
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import_functions <- c(
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"%chin%" = "data.table",
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"%chin%" = "data.table",
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"anti_join" = "dplyr",
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"anti_join" = "dplyr",
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"bind_rows" = "dplyr",
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"chmatch" = "data.table",
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"chmatch" = "data.table",
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"cur_column" = "dplyr",
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"cur_column" = "dplyr",
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"full_join" = "dplyr",
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"full_join" = "dplyr",
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@ -54,8 +55,8 @@ import_functions <- c(
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"semi_join" = "dplyr",
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"semi_join" = "dplyr",
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"showQuestion" = "rstudioapi"
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"showQuestion" = "rstudioapi"
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)
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)
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# functions that are called directly
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# functions that are called directly with ::
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call_functions <- c(
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call_functions <- c(
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# cleaner
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# cleaner
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"freq.default" = "cleaner",
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"freq.default" = "cleaner",
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@ -104,6 +105,7 @@ extended_functions <- c(
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"get_skimmers" = "skimr",
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"get_skimmers" = "skimr",
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"type_sum" = "tibble",
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"type_sum" = "tibble",
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"vec_cast" = "vctrs",
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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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"vec_ptype2" = "vctrs"
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)
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)
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