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fix for binding rows
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.8.2.9118
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Date: 2023-02-11
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Version: 1.8.2.9119
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Date: 2023-02-12
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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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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 1.8.2.9118
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# AMR 1.8.2.9119
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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@ -163,26 +163,23 @@ quick_case_when <- function(...) {
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out
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}
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# copied and slightly rewritten from {poorman} under permissive license (2023-02-11)
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# https://github.com/nathaneastwood/poorman, MIT licensed, Nathan Eastwood, 2020
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pm_bind_rows <- function (..., stringsAsFactors = FALSE) {
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lsts <- Filter(Negate(is.null), list(...))
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nms <- unique(unlist(lapply(lsts, names)))
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lsts <- lapply(lsts, function(x) {
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if (!is.data.frame(x)) {
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x <- data.frame(as.list(x), stringsAsFactors = stringsAsFactors)
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}
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for (i in nms[!nms %in% names(x)]) {
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rbind2 <- function (...) {
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# this is just rbind(), but then with the functionality of dplyr::bind_rows(),
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# to allow differences in available columns
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l <- list(...)
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l_names <- unique(unlist(lapply(l, names)))
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l_new <- lapply(l, function(df) {
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rownames(df) <- NULL
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for (col in l_names[!l_names %in% colnames(df)]) {
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# create the new column, could also be length 0
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x[[i]] <- rep(NA, NROW(x))
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df[, col] <- rep(NA, NROW(df))
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}
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x
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df
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})
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names(lsts) <- NULL
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do.call(rbind, lsts)
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fun <- function(...) rbind(..., stringsAsFactors = FALSE)
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do.call(fun, l_new)
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}
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# No export, no Rd
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addin_insert_in <- function() {
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import_fn("insertText", "rstudioapi")(" %in% ")
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6
R/ab.R
6
R/ab.R
@ -495,15 +495,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# save to package env to save time for next time
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if (isTRUE(initial_search)) {
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AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
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AMR_env$ab_previously_coerced <- unique(pm_bind_rows(AMR_env$ab_previously_coerced,
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AMR_env$ab_previously_coerced <- unique(rbind2(AMR_env$ab_previously_coerced,
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data.frame(
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x = x,
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ab = x_new,
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x_bak = x_bak[match(x, x_bak_clean)],
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stringsAsFactors = FALSE
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),
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stringsAsFactors = FALSE
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))
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)))
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}
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# take failed ATC codes apart from rest
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@ -404,7 +404,7 @@ antibiogram <- function(x,
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if (i == 1) {
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new_df <- long_to_wide(out[which(out$syndromic_group == grp), , drop = FALSE], digs = digits)
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} else {
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new_df <- pm_bind_rows(new_df,
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new_df <- rbind2(new_df,
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long_to_wide(out[which(out$syndromic_group == grp), , drop = FALSE], digs = digits))
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}
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}
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6
R/av.R
6
R/av.R
@ -461,15 +461,13 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# save to package env to save time for next time
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if (isTRUE(initial_search)) {
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AMR_env$av_previously_coerced <- AMR_env$av_previously_coerced[which(!AMR_env$av_previously_coerced$x %in% x), , drop = FALSE]
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AMR_env$av_previously_coerced <- unique(pm_bind_rows(AMR_env$av_previously_coerced,
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AMR_env$av_previously_coerced <- unique(rbind2(AMR_env$av_previously_coerced,
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data.frame(
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x = x,
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av = x_new,
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x_bak = x_bak[match(x, x_bak_clean)],
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stringsAsFactors = FALSE
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),
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stringsAsFactors = FALSE
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))
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)))
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}
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# take failed ATC codes apart from rest
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@ -124,7 +124,7 @@ bug_drug_combinations <- function(x,
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m <- as.matrix(table(x))
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data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
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})
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merged <- do.call(pm_bind_rows, pivot)
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merged <- do.call(rbind2, pivot)
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out_group <- data.frame(
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mo = rep(unique_mo[i], NROW(merged)),
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ab = rownames(merged),
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@ -144,14 +144,14 @@ bug_drug_combinations <- function(x,
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}
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out_group <- cbind(group_values, out_group)
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}
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out <- pm_bind_rows(out, out_group)
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out <- rbind2(out, out_group)
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}
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out
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}
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# based on pm_apply_grouped_function
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apply_group <- function(.data, fn, groups, drop = FALSE, ...) {
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grouped <- pm_split_into_groups(.data, groups, drop)
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res <- do.call(pm_bind_rows, unname(lapply(grouped, fn, ...)))
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res <- do.call(rbind2, unname(lapply(grouped, fn, ...)))
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if (any(groups %in% colnames(res))) {
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class(res) <- c("grouped_data", class(res))
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res <- pm_set_groups(res, groups[groups %in% colnames(res)])
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@ -153,7 +153,7 @@ add_custom_antimicrobials <- function(x) {
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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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AMR_env$AB_lookup <- unique(pm_bind_rows(AMR_env$AB_lookup, new_df))
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AMR_env$AB_lookup <- unique(rbind2(AMR_env$AB_lookup, new_df))
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AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% x$ab), , drop = FALSE]
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class(AMR_env$AB_lookup$ab) <- c("ab", "character")
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@ -279,7 +279,7 @@ add_custom_microorganisms <- function(x) {
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# clear previous coercions
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suppressMessages(mo_reset_session())
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AMR_env$MO_lookup <- unique(pm_bind_rows(AMR_env$MO_lookup, new_df))
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AMR_env$MO_lookup <- unique(rbind2(AMR_env$MO_lookup, new_df))
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class(AMR_env$MO_lookup$mo) <- c("mo", "character")
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if (nrow(x) <= 3) {
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message_("Added ", vector_and(italicise(x$fullname), quotes = FALSE), " to the internal `microorganisms` data set.")
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@ -475,7 +475,7 @@ eucast_rules <- function(x,
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amox$base_ab <- "AMX"
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amox$base_name <- ab_name("AMX", language = NULL)
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# merge and sort
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ab_enzyme <- pm_bind_rows(ab_enzyme, ampi, amox)
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ab_enzyme <- rbind2(ab_enzyme, ampi, amox)
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ab_enzyme <- ab_enzyme[order(ab_enzyme$enzyme_name), , drop = FALSE]
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for (i in seq_len(nrow(ab_enzyme))) {
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@ -1161,7 +1161,7 @@ edit_sir <- function(x,
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)
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verbose_new <- verbose_new %pm>% pm_filter(old != new | is.na(old) | is.na(new) & !is.na(old))
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# save changes to data set 'verbose_info'
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track_changes$verbose_info <- pm_bind_rows(track_changes$verbose_info,
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track_changes$verbose_info <- rbind2(track_changes$verbose_info,
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verbose_new)
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# count adds and changes
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track_changes$added <- track_changes$added + verbose_new %pm>%
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@ -1213,7 +1213,7 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 12.0)
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)
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)
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}
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out <- do.call("pm_bind_rows", lapply(lst, as.data.frame, stringsAsFactors = FALSE))
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out <- do.call(rbind2, lapply(lst, as.data.frame, stringsAsFactors = FALSE))
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rownames(out) <- NULL
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out$ab <- ab
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out$name <- ab_name(ab, language = NULL)
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12
R/mo.R
12
R/mo.R
@ -325,7 +325,7 @@ as.mo <- function(x,
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result_mo <- NA_character_
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} else {
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result_mo <- AMR_env$MO_lookup$mo[match(top_hits[1], AMR_env$MO_lookup$fullname)]
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AMR_env$mo_uncertainties <- pm_bind_rows(AMR_env$mo_uncertainties,
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AMR_env$mo_uncertainties <- rbind2(AMR_env$mo_uncertainties,
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data.frame(
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original_input = x_search,
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input = x_search_cleaned,
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@ -335,18 +335,14 @@ as.mo <- function(x,
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minimum_matching_score = ifelse(is.null(minimum_matching_score), "NULL", minimum_matching_score),
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keep_synonyms = keep_synonyms,
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stringsAsFactors = FALSE
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),
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stringsAsFactors = FALSE
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)
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))
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# save to package env to save time for next time
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AMR_env$mo_previously_coerced <- unique(pm_bind_rows(AMR_env$mo_previously_coerced,
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AMR_env$mo_previously_coerced <- unique(rbind2(AMR_env$mo_previously_coerced,
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data.frame(
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x = paste(x_search, minimum_matching_score),
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mo = result_mo,
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stringsAsFactors = FALSE
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),
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stringsAsFactors = FALSE
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))
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)))
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}
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# the actual result:
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as.character(result_mo)
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12
R/plot.R
12
R/plot.R
@ -585,19 +585,13 @@ plot.sir <- function(x,
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data$s <- round((data$n / sum(data$n)) * 100, 1)
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if (!"S" %in% data$x) {
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data <- pm_bind_rows(data, data.frame(x = "S", n = 0, s = 0, stringsAsFactors = FALSE),
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stringsAsFactors = FALSE
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)
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data <- rbind2(data, data.frame(x = "S", n = 0, s = 0, stringsAsFactors = FALSE))
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}
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if (!"I" %in% data$x) {
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data <- pm_bind_rows(data, data.frame(x = "I", n = 0, s = 0, stringsAsFactors = FALSE),
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stringsAsFactors = FALSE
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)
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data <- rbind2(data, data.frame(x = "I", n = 0, s = 0, stringsAsFactors = FALSE))
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}
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if (!"R" %in% data$x) {
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data <- pm_bind_rows(data, data.frame(x = "R", n = 0, s = 0, stringsAsFactors = FALSE),
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stringsAsFactors = FALSE
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)
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data <- rbind2(data, data.frame(x = "R", n = 0, s = 0, stringsAsFactors = FALSE))
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}
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data$x <- factor(data$x, levels = c("S", "I", "R"), ordered = TRUE)
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2
R/sir.R
2
R/sir.R
@ -998,7 +998,7 @@ as_sir_method <- function(method_short,
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}
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# write to verbose output
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AMR_env$sir_interpretation_history <- pm_bind_rows(
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AMR_env$sir_interpretation_history <- rbind2(
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AMR_env$sir_interpretation_history,
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# recycling 1 to 2 rows does not seem to work, which is why rep() was added
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data.frame(
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@ -322,7 +322,7 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
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}
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out_new <- cbind(group_values, out_new)
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}
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out <- pm_bind_rows(out, out_new)
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out <- rbind2(out, out_new)
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}
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}
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out
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@ -331,7 +331,7 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
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# based on pm_apply_grouped_function
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apply_group <- function(.data, fn, groups, drop = FALSE, ...) {
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grouped <- pm_split_into_groups(.data, groups, drop)
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res <- do.call(pm_bind_rows, unname(lapply(grouped, fn, ...)))
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res <- do.call(rbind2, unname(lapply(grouped, fn, ...)))
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if (any(groups %in% colnames(res))) {
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class(res) <- c("grouped_data", class(res))
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res <- pm_set_groups(res, groups[groups %in% colnames(res)])
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2
index.md
2
index.md
@ -28,7 +28,7 @@ After installing this package, R knows [**~52,000 distinct microbial species**](
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Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
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With the help of contributors from all corners of the world, the `AMR` package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, and <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
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With the help of contributors from all corners of the world, the `AMR` package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_no.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Norwegian, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ro.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Romanian, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, and <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
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### Practical examples
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