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freq/age fix
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.6.1.9002
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Date: 2019-04-09
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Date: 2019-04-11
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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1
NEWS.md
1
NEWS.md
@ -8,6 +8,7 @@
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* Removed all hardcoded EUCAST rules and replaced them with a new reference file: `./inst/eucast/eucast.tsv`.
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* Added ceftazidim intrinsic resistance to *Streptococci*
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* Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+.
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* Fix for `freq()` for when all values are `NA`.
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#### Other
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* Prevented [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html) in R 3.6.0 and later by adding `StagedInstall: false` to the DESCRIPTION file
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4
R/age.R
4
R/age.R
@ -64,11 +64,11 @@ age <- function(x, reference = Sys.Date()) {
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#'
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#' Split ages into age groups defined by the \code{split} parameter. This allows for easier demographic (antimicrobial resistance) analysis.
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#' @param x age, e.g. calculated with \code{\link{age}}
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#' @param split_at values to split \code{x} at, defaults to age groups 0-11, 12-24, 26-54, 55-74 and 75+. See Details.
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#' @param split_at values to split \code{x} at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See Details.
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#' @details To split ages, the input can be:
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#' \itemize{
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#' \item{A numeric vector. A vector of e.g. \code{c(10, 20)} will split on 0-9, 10-19 and 20+. A value of only \code{50} will split on 0-49 and 50+.
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#' The default is to split on young children (0-11), youth (12-24), young adults (26-54), middle-aged adults (55-74) and elderly (75+).}
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#' The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).}
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#' \item{A character:}
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#' \itemize{
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#' \item{\code{"children"}, equivalent of: \code{c(0, 1, 2, 4, 6, 13, 18)}. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.}
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10
R/freq.R
10
R/freq.R
@ -666,7 +666,7 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
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# format all numeric values
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header <- lapply(header, function(x) {
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if (is.numeric(x)) {
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if (any(x < 1000)) {
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if (any(x < 1000, na.rm = TRUE)) {
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format(round2(x, digits = digits), decimal.mark = decimal.mark, big.mark = big.mark)
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} else {
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format(x, digits = digits, decimal.mark = decimal.mark, big.mark = big.mark)
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@ -885,8 +885,12 @@ print.frequency_tbl <- function(x,
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cat(title, "\n\n")
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if (NROW(x) == 0) {
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cat("No observations.\n")
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if (NROW(x) == 0 | isTRUE(all(is.na(x$item)))) {
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cat("No observations")
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if (isTRUE(all(is.na(x$item)))) {
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cat(" - all values are missing (<NA>)")
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}
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cat(".\n")
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if (opt$tbl_format == "markdown") {
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cat("\n")
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}
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