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icu_exclude in first_isolate(), fixes #110
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Package: AMR
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Version: 2.0.0.9015
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Date: 2023-05-12
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Version: 2.0.0.9018
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Date: 2023-05-17
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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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9
NEWS.md
9
NEWS.md
@ -1,16 +1,17 @@
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# AMR 2.0.0.9015
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# AMR 2.0.0.9018
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## Changed
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* Added oxygen tolerance to over 25,000 bacteria in the `microorganisms` data set
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* Added `mo_oxygen_tolerance()` to retrieve the values
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* Added `mo_is_anaerobic()` to determine which species are obligate anaerobic bacteria
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* Added LPSN and GBIF identifiers, and oxygen tolerance to `mo_info()`
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* formatting fix for `sir_interpretation_history()`
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* Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
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* Added SAS Transport files (file extension `.xpt`) to [our download page](https://msberends.github.io/AMR/articles/datasets.html) to use in SAS software
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* Added microbial codes for Gram-negative/positive anaerobic bacteria
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* `mo_rank()` now returns `NA` for 'unknown' microorganisms (`B_ANAER`, `B_ANAER-NEG`, `B_ANAER-POS`, `B_GRAMN`, `B_GRAMP`, `F_FUNGUS`, `F_YEAST`, and `UNKNOWN`)
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* Fixed formatting for `sir_interpretation_history()`
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* Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
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* Fixed a bug for `as.mo()` that led to coercion of `NA` values when using custom microorganism codes
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* Added SAS Transport files (file extension `.xpt`) to [our download page](https://msberends.github.io/AMR/articles/datasets.html) to use in SAS software
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* Fixed usage of `icu_exclude` in `first_isolates()`
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# AMR 2.0.0
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@ -191,13 +191,13 @@ first_isolate <- function(x = NULL,
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}
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meet_criteria(col_specimen, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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if (is.logical(col_icu)) {
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meet_criteria(col_icu, allow_class = "logical", has_length = c(1, nrow(x)), allow_NULL = TRUE)
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if (length(col_icu) == 1) {
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col_icu <- rep(col_icu, nrow(x))
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}
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} else {
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meet_criteria(col_icu, allow_class = "logical", has_length = c(1, nrow(x)), allow_NA = TRUE)
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x$newvar_is_icu <- col_icu
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} else if (!is.null(col_icu)) {
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meet_criteria(col_icu, allow_class = c("character", "logical"), has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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col_icu <- x[, col_icu, drop = TRUE]
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x$newvar_is_icu <- x[, col_icu, drop = TRUE]
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} else {
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x$newvar_is_icu <- NA_real_
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}
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# method
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method <- coerce_method(method)
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@ -251,14 +251,13 @@ first_isolate <- function(x = NULL,
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"Determining first isolates ",
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ifelse(method %in% c("episode-based", "phenotype-based"),
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ifelse(is.infinite(episode_days),
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"without a specified episode length",
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paste("using an episode length of", episode_days, "days")
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paste(font_bold("without"), " a specified episode length"),
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paste("using an episode length of", font_bold(paste(episode_days, "days")))
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),
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""
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)
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),
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as_note = FALSE,
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add_fn = font_black
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add_fn = font_red
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)
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}
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@ -358,8 +357,7 @@ first_isolate <- function(x = NULL,
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# remove testcodes
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if (!is.null(testcodes_exclude) && isTRUE(info) && message_not_thrown_before("first_isolate", "excludingtestcodes")) {
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message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
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add_fn = font_black,
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as_note = FALSE
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add_fn = font_red
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)
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}
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@ -372,8 +370,7 @@ first_isolate <- function(x = NULL,
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check_columns_existance(col_specimen, x)
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if (isTRUE(info) && message_not_thrown_before("first_isolate", "excludingspecimen")) {
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message_("Excluding other than specimen group '", specimen_group, "'",
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add_fn = font_black,
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as_note = FALSE
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add_fn = font_red
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)
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}
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}
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@ -455,15 +452,13 @@ first_isolate <- function(x = NULL,
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message_("Basing inclusion on key antimicrobials, ",
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ifelse(ignore_I == FALSE, "not ", ""),
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"ignoring I",
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add_fn = font_black,
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as_note = FALSE
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add_fn = font_red
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)
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}
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if (type == "points") {
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message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
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points_threshold,
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add_fn = font_black,
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as_note = FALSE
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add_fn = font_red
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)
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}
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}
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@ -505,34 +500,28 @@ first_isolate <- function(x = NULL,
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x$newvar_genus_species != "" &
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(x$other_pat_or_mo | x$more_than_episode_ago)
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}
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decimal.mark <- getOption("OutDec")
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big.mark <- ifelse(decimal.mark != ",", ",", " ")
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# first one as TRUE
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x[row.start, "newvar_first_isolate"] <- TRUE
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# no tests that should be included, or ICU
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if (!is.null(col_testcode)) {
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x[which(x[, col_testcode] %in% tolower(testcodes_exclude)), "newvar_first_isolate"] <- FALSE
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}
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if (!is.null(col_icu)) {
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if (any(!is.na(x$newvar_is_icu)) && any(x$newvar_is_icu == TRUE, na.rm = TRUE)) {
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if (icu_exclude == TRUE) {
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if (isTRUE(info)) {
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message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = " "), " isolates from ICU.",
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add_fn = font_black,
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as_note = FALSE
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)
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message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.",
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add_fn = font_red)
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}
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x[which(col_icu), "newvar_first_isolate"] <- FALSE
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x[which(x$newvar_is_icu), "newvar_first_isolate"] <- FALSE
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} else if (isTRUE(info)) {
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message_("Including isolates from ICU.",
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add_fn = font_black,
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as_note = FALSE
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)
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message_("Including isolates from ICU.")
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}
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}
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decimal.mark <- getOption("OutDec")
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big.mark <- ifelse(decimal.mark != ",", ",", " ")
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if (isTRUE(info)) {
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# print group name if used in dplyr::group_by()
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cur_group <- import_fn("cur_group", "dplyr", error_on_fail = FALSE)
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@ -560,11 +549,12 @@ first_isolate <- function(x = NULL,
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# handle empty microorganisms
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if (any(x$newvar_mo == "UNKNOWN", na.rm = TRUE) && isTRUE(info)) {
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message_(
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ifelse(include_unknown == TRUE, "Included ", "Excluded "),
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ifelse(include_unknown == TRUE, "Including ", "Excluding "),
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format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
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decimal.mark = decimal.mark, big.mark = big.mark
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),
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" isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')"
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" isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')",
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add_fn = font_red
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)
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}
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x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
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@ -572,10 +562,11 @@ first_isolate <- function(x = NULL,
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# exclude all NAs
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if (anyNA(x$newvar_mo) && isTRUE(info)) {
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message_(
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"Excluded ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
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"Excluding ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
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decimal.mark = decimal.mark, big.mark = big.mark
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),
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" isolates with a microbial ID 'NA' (in column '", font_bold(col_mo), "')"
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" isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')",
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add_fn = font_red
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)
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}
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x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
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