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(v1.2.0.9034) code cleaning
This commit is contained in:
parent
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.2.0.9033
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Date: 2020-07-12
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Version: 1.2.0.9034
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Date: 2020-07-13
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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4
NEWS.md
4
NEWS.md
@ -1,5 +1,5 @@
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# AMR 1.2.0.9033
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## <small>Last updated: 12-Jul-2020</small>
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# AMR 1.2.0.9034
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## <small>Last updated: 13-Jul-2020</small>
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### New
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* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
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2
R/ab.R
2
R/ab.R
@ -188,7 +188,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
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# exact LOINC code
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loinc_found <- unlist(lapply(antibiotics$loinc,
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function(s) x[i] %in% s))
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function(s) x[i] %in% s))
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found <- antibiotics$ab[loinc_found == TRUE]
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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@ -136,8 +136,8 @@ ab_from_text <- function(text,
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text_split[text_split %like_case% to_regex(names_atc)],
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text_split[text_split %like_case% to_regex(synonyms_part1)],
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text_split[text_split %like_case% to_regex(synonyms_part2)])
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),
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...)
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),
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...)
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)
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})
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}
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4
R/age.R
4
R/age.R
@ -51,8 +51,8 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) {
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# from https://stackoverflow.com/a/25450756/4575331
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years_gap <- reference$year - x$year
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ages <- ifelse(reference$mon < x$mon | (reference$mon == x$mon & reference$mday < x$mday),
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as.integer(years_gap - 1),
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as.integer(years_gap))
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as.integer(years_gap - 1),
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as.integer(years_gap))
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# add decimals
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if (exact == TRUE) {
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@ -172,8 +172,8 @@ format.bug_drug_combinations <- function(x,
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y <- y %>%
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create_var(txt = paste0(percentage(y$isolates / y$total, decimal.mark = decimal.mark, big.mark = big.mark),
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" (", trimws(format(y$isolates, big.mark = big.mark)), "/",
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trimws(format(y$total, big.mark = big.mark)), ")")) %>%
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" (", trimws(format(y$isolates, big.mark = big.mark)), "/",
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trimws(format(y$total, big.mark = big.mark)), ")")) %>%
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select(ab, ab_txt, mo, txt) %>%
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arrange(mo)
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@ -117,7 +117,7 @@ print.catalogue_of_life_version <- function(x, ...) {
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" Available at: ", lst$catalogue_of_life$url, "\n",
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" Number of included species: ", format(lst$catalogue_of_life$n, big.mark = ","), "\n",
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font_underline(paste0(lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$version, " (",
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lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$yearmonth, ")")), "\n",
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lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$yearmonth, ")")), "\n",
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" Available at: ", lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$url, "\n",
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" Number of included species: ", format(lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$n, big.mark = ","), "\n\n",
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"=> Total number of species included: ", format(lst$total_included$n_total_species, big.mark = ","), "\n",
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@ -702,8 +702,8 @@ eucast_rules <- function(x,
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if (info == TRUE & !rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
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cat(paste0("\n", font_grey(strrep("-", options()$width - 1)),
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"\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
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"\n", font_blue("http://eucast.org/"), "\n"))
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"\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
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"\n", font_blue("http://eucast.org/"), "\n"))
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eucast_notification_shown <- TRUE
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}
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@ -843,9 +843,9 @@ eucast_rules <- function(x,
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cat(paste0("\n", font_grey(strrep("-", options()$width - 1)), "\n"))
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cat(font_bold(paste("The rules", paste0(wouldve, "affected"),
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formatnr(n_distinct(verbose_info$row)),
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"out of", formatnr(nrow(x_original)),
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"rows, making a total of", formatnr(nrow(verbose_info)), "edits\n")))
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formatnr(n_distinct(verbose_info$row)),
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"out of", formatnr(nrow(x_original)),
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"rows, making a total of", formatnr(nrow(verbose_info)), "edits\n")))
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n_added <- verbose_info %>% filter(is.na(old)) %>% nrow()
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n_changed <- verbose_info %>% filter(!is.na(old)) %>% nrow()
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@ -858,8 +858,8 @@ eucast_rules <- function(x,
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}
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cat(colour(paste0("=> ", wouldve, "added ",
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font_bold(formatnr(verbose_info %>%
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filter(is.na(old)) %>%
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nrow()), "test results"),
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filter(is.na(old)) %>%
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nrow()), "test results"),
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"\n")))
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if (n_added > 0) {
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added_summary <- verbose_info %>%
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@ -882,8 +882,8 @@ eucast_rules <- function(x,
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}
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cat(colour(paste0("=> ", wouldve, "changed ",
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font_bold(formatnr(verbose_info %>%
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filter(!is.na(old)) %>%
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nrow()), "test results"),
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filter(!is.na(old)) %>%
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nrow()), "test results"),
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"\n")))
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if (n_changed > 0) {
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changed_summary <- verbose_info %>%
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@ -387,9 +387,9 @@ labels_rsi_count <- function(position = NULL,
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lineheight = 0.75,
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data = function(x) {
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transformed <- rsi_df(data = x,
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translate_ab = translate_ab,
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combine_SI = combine_SI,
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combine_IR = combine_IR)
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translate_ab = translate_ab,
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combine_SI = combine_SI,
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combine_IR = combine_IR)
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transformed$gr <- transformed[, x_name, drop = TRUE]
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transformed %>%
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group_by(gr) %>%
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@ -100,7 +100,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
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} else {
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if (verbose == TRUE) {
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message(font_blue(paste0("NOTE: Using column `", font_bold(ab_result), "` as input for `", search_string,
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"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").")))
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"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").")))
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}
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return(ab_result)
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}
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@ -183,12 +183,12 @@ get_column_abx <- function(x,
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for (i in seq_len(length(x))) {
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if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
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message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
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"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")))
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"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")))
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}
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if (names(x[i]) %in% names(duplicates)) {
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warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
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"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
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"), although it was matched for multiple antibiotics or columns.")),
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"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
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"), although it was matched for multiple antibiotics or columns.")),
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call. = FALSE,
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immediate. = verbose)
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}
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@ -210,8 +210,8 @@ get_column_abx <- function(x,
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# missing a soft dependency may lower the reliability
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missing <- soft_dependencies[!soft_dependencies %in% names(x)]
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missing_txt <- paste(paste0(ab_name(missing, tolower = TRUE, language = NULL),
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" (", font_bold(missing, collapse = NULL), ")"),
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collapse = ", ")
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" (", font_bold(missing, collapse = NULL), ")"),
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collapse = ", ")
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message(font_blue("NOTE: Reliability would be improved if these antimicrobial results would be available too:",
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missing_txt))
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}
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@ -195,8 +195,8 @@ key_antibiotics <- function(x,
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universal_4, universal_5, universal_6)
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gram_positive <- c(universal,
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GramPos_1, GramPos_2, GramPos_3,
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GramPos_4, GramPos_5, GramPos_6)
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GramPos_1, GramPos_2, GramPos_3,
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GramPos_4, GramPos_5, GramPos_6)
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gram_positive <- gram_positive[!is.null(gram_positive)]
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gram_positive <- gram_positive[!is.na(gram_positive)]
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if (length(gram_positive) < 12) {
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@ -204,8 +204,8 @@ key_antibiotics <- function(x,
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}
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gram_negative <- c(universal,
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GramNeg_1, GramNeg_2, GramNeg_3,
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GramNeg_4, GramNeg_5, GramNeg_6)
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GramNeg_1, GramNeg_2, GramNeg_3,
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GramNeg_4, GramNeg_5, GramNeg_6)
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gram_negative <- gram_negative[!is.null(gram_negative)]
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gram_negative <- gram_negative[!is.na(gram_negative)]
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if (length(gram_negative) < 12) {
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32
R/mdro.R
32
R/mdro.R
@ -145,7 +145,7 @@ mdro <- function(x,
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}
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if (is.null(col_mo) & guideline$code == "tb") {
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message(font_blue("NOTE: No column found as input for `col_mo`,",
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font_bold("assuming all records contain", font_italic("Mycobacterium tuberculosis."))))
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font_bold("assuming all records contain", font_italic("Mycobacterium tuberculosis."))))
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x$mo <- as.mo("Mycobacterium tuberculosis")
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col_mo <- "mo"
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}
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@ -470,7 +470,7 @@ mdro <- function(x,
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}
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x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE])))
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row_filter <- sapply(x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
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row_filter <- x[row_filter, "row_number", drop = TRUE]
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row_filter <- x[which(row_filter), "row_number", drop = TRUE]
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rows <- rows[rows %in% row_filter]
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x[rows, "MDRO"] <<- to
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x[rows, "reason"] <<- paste0(any_all, " of the required antibiotics ", ifelse(any_all == "any", "is", "are"), " R")
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@ -492,23 +492,23 @@ mdro <- function(x,
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if (verbose == TRUE) {
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x[rows, "columns_nonsusceptible"] <<- sapply(rows,
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function(row, group_vct = lst_vector) {
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cols_nonsus <- sapply(x[row, group_vct, drop = FALSE], function(y) y %in% search_result)
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paste(sort(names(cols_nonsus)[cols_nonsus]), collapse = ", ")
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})
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function(row, group_vct = lst_vector) {
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cols_nonsus <- sapply(x[row, group_vct, drop = FALSE], function(y) y %in% search_result)
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paste(sort(names(cols_nonsus)[cols_nonsus]), collapse = ", ")
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})
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}
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x[rows, "classes_affected"] <<- sapply(rows,
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function(row, group_tbl = lst) {
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sum(sapply(group_tbl,
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function(group) {
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any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% search_result, na.rm = TRUE)
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}),
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na.rm = TRUE)
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})
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function(row, group_tbl = lst) {
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sum(sapply(group_tbl,
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function(group) {
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any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% search_result, na.rm = TRUE)
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}),
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na.rm = TRUE)
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})
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# for PDR; all agents are R (or I if combine_SI = FALSE)
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x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE])))
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row_filter <- sapply(x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
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x[row_filter, "classes_affected"] <<- 999
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x[which(row_filter), "classes_affected"] <<- 999
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}
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if (info == TRUE) {
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@ -718,7 +718,7 @@ mdro <- function(x,
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x[which((x$classes_in_guideline - x$classes_affected) <= 2), "MDRO"] <- 3
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if (verbose == TRUE) {
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x[which(x$MDRO == 3), "reason"] <- paste0("less than 3 classes remain susceptible (", x$classes_in_guideline[which((x$classes_in_guideline - x$classes_affected) <= 2)] - x$classes_affected[which(x$MDRO == 3)],
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" out of ", x$classes_in_guideline[which(x$MDRO == 3)], " classes)")
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" out of ", x$classes_in_guideline[which(x$MDRO == 3)], " classes)")
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}
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# PDR (=4): all agents are R
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@ -1002,7 +1002,7 @@ mdro <- function(x,
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# some more info on negative results
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if (verbose == TRUE) {
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if (guideline$code == "cmi2012") {
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x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))], " of ", x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))], " available classes contain R or I (3 required for MDR)")
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x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))], " of ", x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))], " available classes contain R or I (3 required for MDR)")
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} else {
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x[which(x$MDRO == 1), "reason"] <- "too few antibiotics are R"
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}
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@ -304,13 +304,13 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
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metadata <- get_mo_failures_uncertainties_renamed()
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result <- base::list(kingdom = mo_kingdom(x, language = language),
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phylum = mo_phylum(x, language = language),
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class = mo_class(x, language = language),
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order = mo_order(x, language = language),
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family = mo_family(x, language = language),
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genus = mo_genus(x, language = language),
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species = mo_species(x, language = language),
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subspecies = mo_subspecies(x, language = language))
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phylum = mo_phylum(x, language = language),
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class = mo_class(x, language = language),
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order = mo_order(x, language = language),
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family = mo_family(x, language = language),
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genus = mo_genus(x, language = language),
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species = mo_species(x, language = language),
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subspecies = mo_subspecies(x, language = language))
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load_mo_failures_uncertainties_renamed(metadata)
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result
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@ -127,7 +127,7 @@ resistance_predict <- function(x,
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stop_if(any(dim(x) == 0), "`x` must contain rows and columns")
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stop_if(is.null(model), 'choose a regression model with the `model` parameter, e.g. resistance_predict(..., model = "binomial")')
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stop_ifnot(col_ab %in% colnames(x),
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"column `", col_ab, "` not found")
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"column `", col_ab, "` not found")
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dots <- unlist(list(...))
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if (length(dots) != 0) {
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22
R/rsi.R
22
R/rsi.R
@ -232,8 +232,8 @@ as.rsi.mic <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST",
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}
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message(font_blue(paste0("=> Interpreting MIC values of `", font_bold(ab), "` (",
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ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
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ab_name(ab_coerced, tolower = TRUE), ") using guideline ", font_bold(guideline_coerced), " ... ")),
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ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
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ab_name(ab_coerced, tolower = TRUE), ") using guideline ", font_bold(guideline_coerced), " ... ")),
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appendLF = FALSE)
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result <- exec_as.rsi(method = "mic",
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x = x,
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@ -268,8 +268,8 @@ as.rsi.disk <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST"
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}
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message(font_blue(paste0("=> Interpreting disk zones of `", font_bold(ab), "` (",
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ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
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ab_name(ab_coerced, tolower = TRUE), ") using guideline ", font_bold(guideline_coerced), " ... ")),
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ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
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ab_name(ab_coerced, tolower = TRUE), ") using guideline ", font_bold(guideline_coerced), " ... ")),
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appendLF = FALSE)
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result <- exec_as.rsi(method = "disk",
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x = x,
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@ -319,9 +319,9 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", uti = NULL
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plural <- c("", "s", "a ")
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}
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message(font_blue(paste0("NOTE: Assuming value", plural[1], " ",
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paste(paste0('"', values, '"'), collapse = ", "),
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" in column `", font_bold(col_specimen),
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"` reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1], ".\n Use `as.rsi(uti = FALSE)` to prevent this.")))
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paste(paste0('"', values, '"'), collapse = ", "),
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" in column `", font_bold(col_specimen),
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"` reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1], ".\n Use `as.rsi(uti = FALSE)` to prevent this.")))
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} else {
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# no data about UTI's found
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uti <- FALSE
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@ -339,13 +339,13 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", uti = NULL
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return(FALSE)
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} else if (!check & all_valid_mics(y)) {
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message(font_blue(paste0("NOTE: Assuming column `", ab, "` (",
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ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
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ab_name(ab_coerced, tolower = TRUE), ") contains MIC values.")))
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ") contains MIC values.")))
|
||||
return(TRUE)
|
||||
} else if (!check & all_valid_disks(y)) {
|
||||
message(font_blue(paste0("NOTE: Assuming column `", ab, "` (",
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ") contains disk zones.")))
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ") contains disk zones.")))
|
||||
return(TRUE)
|
||||
} else {
|
||||
return(check)
|
||||
|
||||
@ -21,6 +21,7 @@
|
||||
|
||||
codecov:
|
||||
require_ci_to_pass: no # allow fail
|
||||
branch: master
|
||||
|
||||
comment: no
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -43,7 +43,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -229,13 +229,13 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1209033" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.2.0.9033">
|
||||
<a href="#amr-1209033" class="anchor"></a>AMR 1.2.0.9033<small> Unreleased </small>
|
||||
<div id="amr-1209034" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.2.0.9034">
|
||||
<a href="#amr-1209034" class="anchor"></a>AMR 1.2.0.9034<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-12-jul-2020" class="section level2">
|
||||
<div id="last-updated-13-jul-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-12-jul-2020" class="anchor"></a><small>Last updated: 12-Jul-2020</small>
|
||||
<a href="#last-updated-13-jul-2020" class="anchor"></a><small>Last updated: 13-Jul-2020</small>
|
||||
</h2>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
|
||||
@ -10,7 +10,7 @@ articles:
|
||||
WHONET: WHONET.html
|
||||
benchmarks: benchmarks.html
|
||||
resistance_predict: resistance_predict.html
|
||||
last_built: 2020-07-12T09:42Z
|
||||
last_built: 2020-07-13T07:17Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user