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breaks param, tidyr dep change, freq markdown
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15
DESCRIPTION
15
DESCRIPTION
@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.4.0.9005
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Date: 2018-10-19
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Version: 0.4.0.9006
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Date: 2018-10-22
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -38,10 +38,9 @@ Authors@R: c(
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email = "b.sinha@umcg.nl",
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role = "ths",
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comment = c(ORCID = "0000-0003-1634-0010")))
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Description: Functions to simplify the analysis of Antimicrobial Resistance (AMR)
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of microbial isolates, by using new S3 classes and applying EUCAST expert rules
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on antibiograms according to Leclercq (2013)
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<doi:10.1111/j.1469-0691.2011.03703.x>.
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Description: Functions to simplify the analysis and prediction of Antimicrobial
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Resistance (AMR) and work with microbial and antimicrobial properties by using
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evidence-based methods.
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Depends:
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R (>= 3.1.0)
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Imports:
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@ -54,14 +53,14 @@ Imports:
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knitr (>= 1.0.0),
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rlang (>= 0.2.0),
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rvest (>= 0.3.2),
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tidyr (>= 0.7.0),
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xml2 (>= 1.0.0)
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Suggests:
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covr (>= 3.0.1),
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ggplot2,
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rmarkdown,
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rstudioapi,
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testthat (>= 1.0.2),
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tidyr
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testthat (>= 1.0.2)
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VignetteBuilder: knitr
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URL: https://github.com/msberends/AMR
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BugReports: https://github.com/msberends/AMR/issues
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8
NEWS.md
8
NEWS.md
@ -17,25 +17,29 @@
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* Fix for `portion_*(..., as_percent = TRUE)` when minimal amount of isolates would not be met
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* Added parameter `also_single_tested` for `portion_*` and `count_*` functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see `?portion`
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* Using `portion_*` functions now throws a warning when total available isolate is below parameter `minimum`
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* Functions `as.mo`, `as.rsi` and `as.mic` will not set package name as attribute anymore
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* Functions `as.mo`, `as.rsi`, `as.mic` and `as.atc` will not set package name as attribute anymore
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* Data set `septic_patients` is now a `data.frame`, not a tibble anymore
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* Check for `hms::is.hms` in frequency tables (`freq()`)
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* New parameter `header` for frequency tables to turn them off (default when `markdown = TRUE`)
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* Freq now prints in markdown at default in non-interactive sessions
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* Removed diacritics from all authors (columns `microorganisms$ref` and `microorganisms.old$ref`) to comply with CRAN policy to only allow ASCII characters
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* Fix for `mo_property` not working properly
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* Fix for `EUCAST_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
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* Support for class `difftime` in frequency tables
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* Support for named vectors of class `mo`, useful for `top_freq()`
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* `ggplot_rsi` and `scale_y_percent` have `breaks` parameter
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* AI improvements for `as.mo`:
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* `"CRS"` -> *Stenotrophomonas maltophilia*
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* `"CRSM"` -> *Stenotrophomonas maltophilia*
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* `"MSSA"` -> *Staphylococcus aureus*
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* `"MSSE"` -> *Staphylococcus epidermidis*
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* Fix for `join` functions
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* In `g.test`, when `sum(x)` is below 1000, suggest Fisher's Exact Test
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* In `g.test`, when `sum(x)` is below 1000 or any of the expected values is below 5, Fisher's Exact Test will be suggested
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* `ab_name` will try to fall back on `as.atc` when no results are found
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#### Other
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* New dependency on package `crayon`, to support formatted text in the console
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* Dependency `tidyr` is now mandatory (went to `Import` field) since `portion_df` and `count_df` rely on it
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* Updated vignettes to comply with README
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23
R/abname.R
23
R/abname.R
@ -133,18 +133,19 @@ abname <- function(abcode,
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abcode[i] <- abx[which(abx[,from] == abcode[i]),] %>% pull(to) %>% .[1]
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}
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# when nothing found, try first chars of official name
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# if (is.na(abcode[i])) {
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# abcode[i] <- antibiotics %>%
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# filter(official %like% paste0('^', abcode.bak[i])) %>%
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# pull(to) %>%
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# .[1]
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# next
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# }
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if (is.na(abcode[i]) | length(abcode[i] == 0)) {
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abcode[i] <- abcode.bak[i]
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warning('Code "', abcode.bak[i], '" not found in antibiotics list.', call. = FALSE)
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# try as.atc
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try(suppressWarnings(
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abcode[i] <- as.atc(abcode[i])
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), silent = TRUE)
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if (is.na(abcode[i])) {
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# still not found
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abcode[i] <- abcode.bak[i]
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warning('Code "', abcode.bak[i], '" not found in antibiotics list.', call. = FALSE)
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} else {
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# fill in the found ATC code
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abcode[i] <- abname(abcode[i], from = "atc", to = to)
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}
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}
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}
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8
R/atc.R
8
R/atc.R
@ -37,6 +37,7 @@
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#' as.atc("J01FA01")
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#' as.atc("Erythromycin")
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#' as.atc("eryt")
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#' as.atc(" eryt 123")
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#' as.atc("ERYT")
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#' as.atc("ERY")
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#' as.atc("Erythrocin") # Trade name
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@ -50,6 +51,10 @@
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as.atc <- function(x) {
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x.new <- rep(NA_character_, length(x))
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x <- trimws(x, which = "both")
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# keep only a-z when it's not an ATC code
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x[!x %like% "[A-Z][0-9]{2}[A-Z]{2}[0-9]{2}"] <- gsub("[^a-zA-Z]+", "", x[!x %like% "[A-Z][0-9]{2}[A-Z]{2}[0-9]{2}"])
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x.bak <- x
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x <- unique(x[!is.na(x)])
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failures <- character(0)
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@ -64,7 +69,7 @@ as.atc <- function(x) {
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x.new[is.na(x.new) & x.bak == x[i]] <- found[1L]
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}
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# try ATC in code form, even if it does not exist in the antibiotics data set YET
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# try ATC in ATC code form, even if it does not exist in the antibiotics data set YET
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if (length(found) == 0 & x[i] %like% '[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]') {
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warning("ATC code ", x[i], " is not yet in the `antibiotics` data set.")
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fail <- FALSE
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@ -134,7 +139,6 @@ as.atc <- function(x) {
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call. = FALSE)
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}
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class(x.new) <- "atc"
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attr(x.new, 'package') <- 'AMR'
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x.new
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}
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111
R/freq.R
111
R/freq.R
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#' @param ... up to nine different columns of \code{x} when \code{x} is a \code{data.frame} or \code{tibble}, to calculate frequencies from - see Examples
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#' @param sort.count sort on count, i.e. frequencies. This will be \code{TRUE} at default for everything except for factors.
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#' @param nmax number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0}, \code{nmax = Inf}, \code{nmax = NULL} or \code{nmax = NA} to print all rows.
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#' @param na.rm a logical value indicating whether \code{NA} values should be removed from the frequency table. The header_txt will always print the amount of \code{NA}s.
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#' @param na.rm a logical value indicating whether \code{NA} values should be removed from the frequency table. The header will always print the amount of \code{NA}s.
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#' @param row.names a logical value indicating whether row indices should be printed as \code{1:nrow(x)}
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#' @param markdown print table in markdown format (this forces \code{nmax = NA})
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#' @param digits how many significant digits are to be used for numeric values in the header_txt (not for the items themselves, that depends on \code{\link{getOption}("digits")})
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#' @param markdown a logical value indicating whether the frequency table should be printed in markdown format. This will print all rows and is default behaviour in non-interactive R sessions (like when knitting RMarkdown files).
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#' @param digits how many significant digits are to be used for numeric values in the header (not for the items themselves, that depends on \code{\link{getOption}("digits")})
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#' @param quote a logical value indicating whether or not strings should be printed with surrounding quotes
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#' @param header a logical value indicating whether an informative header should be printed
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#' @param sep a character string to separate the terms when selecting multiple columns
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@ -34,7 +34,7 @@
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#' @param n number of top \emph{n} items to return, use -n for the bottom \emph{n} items. It will include more than \code{n} rows if there are ties.
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#' @details Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the `freq` function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. This package also has a vignette available to explain the use of this function further, run \code{browseVignettes("AMR")} to read it.
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#'
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#' For numeric values of any class, these additional values will all be calculated with \code{na.rm = TRUE} and shown into the header_txt:
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#' For numeric values of any class, these additional values will all be calculated with \code{na.rm = TRUE} and shown into the header:
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#' \itemize{
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#' \item{Mean, using \code{\link[base]{mean}}}
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#' \item{Standard Deviation, using \code{\link[stats]{sd}}}
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@ -46,7 +46,7 @@
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#' \item{Outliers (total count and unique count), using \code{\link[grDevices]{boxplot.stats}}}
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#' }
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#'
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#' For dates and times of any class, these additional values will be calculated with \code{na.rm = TRUE} and shown into the header_txt:
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#' For dates and times of any class, these additional values will be calculated with \code{na.rm = TRUE} and shown into the header:
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#' \itemize{
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#' \item{Oldest, using \code{\link{min}}}
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#' \item{Newest, using \code{\link{max}}, with difference between newest and oldest}
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@ -140,21 +140,13 @@
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#' # check differences between frequency tables
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#' diff(freq(septic_patients$trim),
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#' freq(septic_patients$trsu))
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#'
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#' \dontrun{
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#' # send frequency table to clipboard (e.g. for pasting in Excel)
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#' septic_patients %>%
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#' freq(age) %>%
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#' format() %>% # this will format the percentages
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#' clipboard_export()
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#' }
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frequency_tbl <- function(x,
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...,
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sort.count = TRUE,
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nmax = getOption("max.print.freq"),
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na.rm = TRUE,
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row.names = TRUE,
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markdown = FALSE,
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markdown = !interactive(),
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digits = 2,
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quote = FALSE,
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header = !markdown,
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@ -201,17 +193,14 @@ frequency_tbl <- function(x,
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cols <- NULL
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}
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} else if (any(class(x) == 'table')) {
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if (!"tidyr" %in% rownames(installed.packages())) {
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stop('transformation from `table` to frequency table requires the tidyr package.', call. = FALSE)
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}
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x <- x %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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# paste first two columns
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tidyr::unite(col = "Pasted", 1:2, sep = sep, remove = TRUE)
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x <- rep(x %>% pull(Pasted), x %>% pull(Freq))
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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# now this DF contains 3 columns: the 2 vars and a Freq column
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# paste the first 2 cols and repeat them Freq times:
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x <- rep(x = do.call(paste, c(x[colnames(x)[1:2]], sep = sep)),
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times = x$Freq)
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x.name <- "a `table` object"
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cols <- NULL
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mult.columns <- 2
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#mult.columns <- 2
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} else {
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x.name <- NULL
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cols <- NULL
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@ -221,74 +210,8 @@ frequency_tbl <- function(x,
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if (ncol(x) == 1 & any(class(x) == 'data.frame')) {
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x <- x %>% pull(1)
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} else if (ncol(x) < 10) {
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mult.columns <- ncol(x)
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colnames(x) <- LETTERS[1:ncol(x)]
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if (ncol(x) == 2) {
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x$total <- paste(x$A %>% as.character(),
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x$B %>% as.character(),
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sep = sep)
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} else if (ncol(x) == 3) {
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x$total <- paste(x$A %>% as.character(),
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x$B %>% as.character(),
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x$C %>% as.character(),
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sep = sep)
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} else if (ncol(x) == 4) {
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x$total <- paste(x$A %>% as.character(),
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x$B %>% as.character(),
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x$C %>% as.character(),
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x$D %>% as.character(),
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sep = sep)
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} else if (ncol(x) == 5) {
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x$total <- paste(x$A %>% as.character(),
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x$B %>% as.character(),
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x$C %>% as.character(),
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x$D %>% as.character(),
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x$E %>% as.character(),
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sep = sep)
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} else if (ncol(x) == 6) {
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x$total <- paste(x$A %>% as.character(),
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x$B %>% as.character(),
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x$C %>% as.character(),
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x$D %>% as.character(),
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x$E %>% as.character(),
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x$F %>% as.character(),
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sep = sep)
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} else if (ncol(x) == 7) {
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x$total <- paste(x$A %>% as.character(),
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x$B %>% as.character(),
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x$C %>% as.character(),
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x$D %>% as.character(),
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x$E %>% as.character(),
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x$F %>% as.character(),
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x$G %>% as.character(),
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sep = sep)
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} else if (ncol(x) == 8) {
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x$total <- paste(x$A %>% as.character(),
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x$B %>% as.character(),
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x$C %>% as.character(),
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x$D %>% as.character(),
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x$E %>% as.character(),
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x$F %>% as.character(),
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x$G %>% as.character(),
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x$H %>% as.character(),
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sep = sep)
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} else if (ncol(x) == 9) {
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x$total <- paste(x$A %>% as.character(),
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x$B %>% as.character(),
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x$C %>% as.character(),
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x$D %>% as.character(),
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x$E %>% as.character(),
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x$F %>% as.character(),
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x$G %>% as.character(),
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x$H %>% as.character(),
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x$I %>% as.character(),
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sep = sep)
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}
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x <- x$total
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x <- do.call(paste, c(x[colnames(x)], sep = sep))
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} else {
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stop('A maximum of 9 columns can be analysed at the same time.', call. = FALSE)
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}
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@ -585,7 +508,7 @@ diff.frequency_tbl <- function(x, y, ...) {
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#' @exportMethod print.frequency_tbl
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#' @importFrom knitr kable
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#' @importFrom dplyr n_distinct
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#' @importFrom crayon bold
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#' @importFrom crayon bold silver
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#' @export
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print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default = 15), ...) {
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@ -629,6 +552,9 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
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if (!is.null(opt$header_txt)) {
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cat(opt$header_txt)
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}
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} else if (opt$tbl_format == "markdown") {
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# do print title as caption in markdown
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cat("\n", title, sep = "")
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}
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if (NROW(x) == 0) {
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@ -671,6 +597,9 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
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' (',
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(x.unprinted / (x.unprinted + x.printed)) %>% percent(force_zero = TRUE),
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') ]\n', sep = '')
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if (opt$tbl_format == "pandoc") {
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footer <- silver(footer) # only silver in regular printing
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}
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} else {
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footer <- NULL
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}
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@ -23,6 +23,7 @@
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#' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}
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#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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#' @param breaks numeric vector of positions
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#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
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#' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.
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#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
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@ -136,6 +137,7 @@ ggplot_rsi <- function(data,
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fill = "Interpretation",
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# params = list(),
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facet = NULL,
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breaks = seq(0, 1, 0.1),
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translate_ab = "official",
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fun = count_df,
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nrow = NULL,
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@ -189,7 +191,7 @@ ggplot_rsi <- function(data,
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if (fun_name == "portion_df"
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| (fun_name == "count_df" & position == "fill")) {
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# portions, so use y scale with percentage
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p <- p + scale_y_percent()
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p <- p + scale_y_percent(breaks = breaks)
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}
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if (fun_name == "count_df" & datalabels == TRUE) {
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@ -281,9 +283,9 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
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#' @rdname ggplot_rsi
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#' @export
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scale_y_percent <- function() {
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ggplot2::scale_y_continuous(breaks = seq(0, 1, 0.1),
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labels = percent(seq(0, 1, 0.1)))
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scale_y_percent <- function(breaks = seq(0, 1, 0.1)) {
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ggplot2::scale_y_continuous(breaks = breaks,
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labels = percent(breaks))
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}
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#' @rdname ggplot_rsi
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14
README.md
14
README.md
@ -3,15 +3,17 @@
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This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the Medical Microbiology & Infection Prevention (MMBI) department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl).
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|
||||
:arrow_forward: Get it with `install.packages("AMR")` or see below for other possibilities. Read all changes and new functions in **[NEWS.md](https://github.com/msberends/AMR/blob/master/NEWS.md)**.
|
||||
:arrow_forward: Get it with `install.packages("AMR")` or see below for other possibilities.
|
||||
|
||||
:arrow_forward: Read the [changelog here](https://github.com/msberends/AMR/blob/master/NEWS.md).
|
||||
|
||||
## Authors
|
||||
<a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Matthijs S. Berends<sup>1,2,a</sup>,
|
||||
<a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Christian F. Luz<sup>1,a</sup>,
|
||||
Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>,
|
||||
Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,a</sup>,
|
||||
Erwin E.A. Hassing<sup>2</sup>,
|
||||
<a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Corinna Glasner<sup>1,b</sup>,
|
||||
<a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Alex W. Friedrich<sup>1,b</sup>,
|
||||
<a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Bhanu Sinha<sup>1,b</sup>
|
||||
Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
|
||||
Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
|
||||
Bhanu Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
|
||||
|
||||
<sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl) [umcg.nl](http://www.umcg.nl)<br>
|
||||
<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>
|
||||
|
||||
@ -33,6 +33,7 @@ In the ATC classification system, the active substances are classified in a hier
|
||||
as.atc("J01FA01")
|
||||
as.atc("Erythromycin")
|
||||
as.atc("eryt")
|
||||
as.atc(" eryt 123")
|
||||
as.atc("ERYT")
|
||||
as.atc("ERY")
|
||||
as.atc("Erythrocin") # Trade name
|
||||
|
||||
26
man/freq.Rd
26
man/freq.Rd
@ -9,12 +9,12 @@
|
||||
\usage{
|
||||
frequency_tbl(x, ..., sort.count = TRUE,
|
||||
nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
|
||||
markdown = FALSE, digits = 2, quote = FALSE, header = !markdown,
|
||||
sep = " ")
|
||||
markdown = !interactive(), digits = 2, quote = FALSE,
|
||||
header = !markdown, sep = " ")
|
||||
|
||||
freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
|
||||
na.rm = TRUE, row.names = TRUE, markdown = FALSE, digits = 2,
|
||||
quote = FALSE, header = !markdown, sep = " ")
|
||||
na.rm = TRUE, row.names = TRUE, markdown = !interactive(),
|
||||
digits = 2, quote = FALSE, header = !markdown, sep = " ")
|
||||
|
||||
top_freq(f, n)
|
||||
|
||||
@ -30,13 +30,13 @@ top_freq(f, n)
|
||||
|
||||
\item{nmax}{number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0}, \code{nmax = Inf}, \code{nmax = NULL} or \code{nmax = NA} to print all rows.}
|
||||
|
||||
\item{na.rm}{a logical value indicating whether \code{NA} values should be removed from the frequency table. The header_txt will always print the amount of \code{NA}s.}
|
||||
\item{na.rm}{a logical value indicating whether \code{NA} values should be removed from the frequency table. The header will always print the amount of \code{NA}s.}
|
||||
|
||||
\item{row.names}{a logical value indicating whether row indices should be printed as \code{1:nrow(x)}}
|
||||
|
||||
\item{markdown}{print table in markdown format (this forces \code{nmax = NA})}
|
||||
\item{markdown}{a logical value indicating whether the frequency table should be printed in markdown format. This will print all rows and is default behaviour in non-interactive R sessions (like when knitting RMarkdown files).}
|
||||
|
||||
\item{digits}{how many significant digits are to be used for numeric values in the header_txt (not for the items themselves, that depends on \code{\link{getOption}("digits")})}
|
||||
\item{digits}{how many significant digits are to be used for numeric values in the header (not for the items themselves, that depends on \code{\link{getOption}("digits")})}
|
||||
|
||||
\item{quote}{a logical value indicating whether or not strings should be printed with surrounding quotes}
|
||||
|
||||
@ -57,7 +57,7 @@ Create a frequency table of a vector with items or a data frame. Supports quasiq
|
||||
\details{
|
||||
Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the `freq` function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. This package also has a vignette available to explain the use of this function further, run \code{browseVignettes("AMR")} to read it.
|
||||
|
||||
For numeric values of any class, these additional values will all be calculated with \code{na.rm = TRUE} and shown into the header_txt:
|
||||
For numeric values of any class, these additional values will all be calculated with \code{na.rm = TRUE} and shown into the header:
|
||||
\itemize{
|
||||
\item{Mean, using \code{\link[base]{mean}}}
|
||||
\item{Standard Deviation, using \code{\link[stats]{sd}}}
|
||||
@ -69,7 +69,7 @@ For numeric values of any class, these additional values will all be calculated
|
||||
\item{Outliers (total count and unique count), using \code{\link[grDevices]{boxplot.stats}}}
|
||||
}
|
||||
|
||||
For dates and times of any class, these additional values will be calculated with \code{na.rm = TRUE} and shown into the header_txt:
|
||||
For dates and times of any class, these additional values will be calculated with \code{na.rm = TRUE} and shown into the header:
|
||||
\itemize{
|
||||
\item{Oldest, using \code{\link{min}}}
|
||||
\item{Newest, using \code{\link{max}}, with difference between newest and oldest}
|
||||
@ -153,14 +153,6 @@ table(septic_patients$gender,
|
||||
# check differences between frequency tables
|
||||
diff(freq(septic_patients$trim),
|
||||
freq(septic_patients$trsu))
|
||||
|
||||
\dontrun{
|
||||
# send frequency table to clipboard (e.g. for pasting in Excel)
|
||||
septic_patients \%>\%
|
||||
freq(age) \%>\%
|
||||
format() \%>\% # this will format the percentages
|
||||
clipboard_export()
|
||||
}
|
||||
}
|
||||
\keyword{freq}
|
||||
\keyword{frequency}
|
||||
|
||||
@ -11,9 +11,10 @@
|
||||
\title{AMR bar plots with \code{ggplot}}
|
||||
\usage{
|
||||
ggplot_rsi(data, position = NULL, x = "Antibiotic",
|
||||
fill = "Interpretation", facet = NULL, translate_ab = "official",
|
||||
fun = count_df, nrow = NULL, datalabels = TRUE,
|
||||
datalabels.size = 3, datalabels.colour = "grey15", ...)
|
||||
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
|
||||
translate_ab = "official", fun = count_df, nrow = NULL,
|
||||
datalabels = TRUE, datalabels.size = 3,
|
||||
datalabels.colour = "grey15", ...)
|
||||
|
||||
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
|
||||
fill = "Interpretation", translate_ab = "official", fun = count_df,
|
||||
@ -21,7 +22,7 @@ geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
|
||||
|
||||
facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL)
|
||||
|
||||
scale_y_percent()
|
||||
scale_y_percent(breaks = seq(0, 1, 0.1))
|
||||
|
||||
scale_rsi_colours()
|
||||
|
||||
@ -41,6 +42,8 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
|
||||
|
||||
\item{facet}{variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable}
|
||||
|
||||
\item{breaks}{numeric vector of positions}
|
||||
|
||||
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.}
|
||||
|
||||
\item{fun}{function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}}
|
||||
|
||||
@ -13,7 +13,10 @@ test_that("abname works", {
|
||||
|
||||
expect_error(abname("AMOX", to = c(1:3)))
|
||||
expect_error(abname("AMOX", to = "test"))
|
||||
expect_warning(abname("TEST
|
||||
expect_warning(abname("NOTEXISTING
|
||||
"))
|
||||
expect_warning(abname("AMOX or GENT"))
|
||||
|
||||
# this one is being found with as.atc internally
|
||||
expect_equal(abname("flu_clox123"), "Flucloxacillin")
|
||||
})
|
||||
|
||||
Loading…
Reference in New Issue
Block a user