mirror of https://github.com/msberends/AMR.git
addins and small improvements to microorganisms dataset
This commit is contained in:
parent
10fce8382c
commit
34ee0247ac
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.2.0.9007
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Date: 2018-07-01
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Version: 0.2.0.9008
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Date: 2018-07-04
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -41,7 +41,8 @@ Imports:
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Suggests:
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testthat (>= 1.0.2),
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covr (>= 3.0.1),
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rmarkdown
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rmarkdown,
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rstudioapi
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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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@ -44,6 +44,7 @@ export(is.mic)
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export(is.rsi)
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export(key_antibiotics)
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export(left_join_microorganisms)
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export(like)
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export(mo_property)
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export(n_rsi)
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export(p.symbol)
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@ -121,6 +122,7 @@ importFrom(stats,mad)
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importFrom(stats,pchisq)
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importFrom(stats,sd)
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importFrom(tibble,tibble)
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importFrom(utils,View)
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importFrom(utils,browseVignettes)
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importFrom(utils,object.size)
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importFrom(utils,packageDescription)
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3
NEWS.md
3
NEWS.md
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@ -1,5 +1,6 @@
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# 0.2.0.90xx (development version)
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#### New
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* Support for Addins menu in RStudio to quickly insert `%in%` or `%like%` (and give them keyboard shortcuts), or to view the datasets that come with this package
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* Function `top_freq` function to get the top/below *n* items of frequency tables
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* Vignette about frequency tables
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* Header of frequency tables now also show MAD and IQR
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@ -14,9 +15,11 @@ ratio(c(772, 1611, 737), ratio = "1:2:1")
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* Function `p.symbol` to transform p value to their related symbol: `0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1`
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#### Changed
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* `%like%` now supports multiple patterns
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* Frequency tables (function `freq`) now supports quasiquotation: `freq(mydata, mycolumn)`, or `mydata %>% freq(mycolumn)`
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* Frequency tables are now actual `data.frame`s with altered console printing to make it look like a frequency table. Because of this, the parameter `toConsole` is not longer needed.
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* Small translational improvements to the `septic_patients` dataset
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* Small improvements to the `microorganisms` dataset, especially for *Salmonella*
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* Combined MIC/RSI values will now be coerced by the `rsi` and `mic` functions:
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* `as.rsi("<=0.002; S")` will return `S`
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* `as.mic("<=0.002; S")` will return `<=0.002`
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@ -17,6 +17,7 @@
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# ==================================================================== #
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globalVariables(c('abname',
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'antibiotics',
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'atc',
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'bactid',
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'cnt',
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@ -36,6 +37,7 @@ globalVariables(c('abname',
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'key_ab_other',
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'median',
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'mic',
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'microorganisms',
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'mocode',
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'molis',
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'n',
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@ -43,7 +45,9 @@ globalVariables(c('abname',
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'patient_id',
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'quantile',
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'real_first_isolate',
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'septic_patients',
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'species',
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'umcg',
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'View',
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'y',
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'.'))
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@ -96,6 +96,10 @@ guess_bactid <- function(x) {
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# avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
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x[i] <- 'Pseudomonas aeruginosa'
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}
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if (tolower(x[i]) %like% 'coagulase') {
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# coerce S. coagulase negative
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x[i] <- 'Coagulase Negative Staphylococcus (CNS)'
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}
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# translate known trivial names to genus+species
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if (!is.na(x.bak[i])) {
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@ -0,0 +1,80 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Pattern Matching
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#'
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#' Convenient wrapper around \code{\link[base]{grepl}} to match a pattern: \code{a \%like\% b}. It always returns a \code{logical} vector and is always case-insensitive. Also, \code{pattern} (\code{b}) can be as long as \code{x} (\code{a}) to compare items of each index in both vectors.
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#' @inheritParams base::grepl
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#' @return A \code{logical} vector
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#' @name like
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#' @rdname like
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#' @export
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#' @details Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like Ctrl+Shift+L or Cmd+Shift+L (see Tools > Modify Keyboard Shortcuts...).
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#' @source Idea from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default and let it support multiple patterns.
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#' @seealso \code{\link[base]{grep}}
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#' @examples
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#' # simple test
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#' a <- "This is a test"
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#' b <- "TEST"
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#' a %like% b
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#' #> TRUE
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#' b %like% a
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#' #> FALSE
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#'
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#' # also supports multiple patterns, length must be equal to x
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#' a <- c("Test case", "Something different", "Yet another thing")
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#' b <- c("case", "diff", "yet")
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#' a %like% b
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#' #> TRUE TRUE TRUE
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#'
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#' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
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#' library(dplyr)
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#' septic_patients %>%
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#' left_join_microorganisms() %>%
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#' filter(genus %like% '^ent') %>%
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#' freq(genus, species)
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like <- function(x, pattern) {
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if (length(pattern) > 1) {
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if (length(x) != length(pattern)) {
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pattern <- pattern[1]
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warning('only the first element of argument `pattern` used for `%like%`', call. = FALSE)
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} else {
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# x and pattern are of same length, so items with each other
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res <- vector(length = length(pattern))
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for (i in 1:length(res)) {
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if (is.factor(x[i])) {
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res[i] <- as.integer(x[i]) %in% base::grep(pattern[i], levels(x[i]), ignore.case = TRUE)
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} else {
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res[i] <- base::grepl(pattern[i], x[i], ignore.case = TRUE)
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}
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}
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return(res)
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}
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}
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# the regular way how grepl works; just one pattern against one or more x
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if (is.factor(x)) {
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as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE)
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} else {
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base::grepl(pattern, x, ignore.case = TRUE)
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}
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}
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#' @rdname like
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#' @export
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"%like%" <- like
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53
R/misc.R
53
R/misc.R
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@ -16,33 +16,32 @@
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Pattern Matching
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#'
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#' Convenience function to compare a vector with a pattern, like \code{\link[base]{grep}}. It always returns a \code{logical} vector and is always case-insensitive.
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#' @inheritParams base::grep
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#' @return A \code{logical} vector
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#' @name like
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#' @rdname like
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#' @export
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#' @source Inherited from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default.
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#' @examples
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#' library(dplyr)
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#' # get unique occurences of bacteria whose name start with 'Ent'
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#' septic_patients %>%
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#' left_join_microorganisms() %>%
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#' filter(fullname %like% '^Ent') %>%
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#' pull(fullname) %>%
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#' unique()
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"%like%" <- function(x, pattern) {
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if (length(pattern) > 1) {
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pattern <- pattern[1]
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warning('only the first element of argument `pattern` used for `%like%`', call. = FALSE)
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}
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if (is.factor(x)) {
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as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE)
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} else {
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base::grepl(pattern, x, ignore.case = TRUE)
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}
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# No export, no Rd
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addin_insert_in <- function() {
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rstudioapi::insertText(" %in% ")
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}
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# No export, no Rd
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addin_insert_like <- function() {
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rstudioapi::insertText(" %like% ")
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}
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# No export, no Rd
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#' @importFrom utils View
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addin_open_antibiotics <- function() {
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View(antibiotics)
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}
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# No export, no Rd
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#' @importFrom utils View
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addin_open_microorganisms <- function() {
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View(microorganisms)
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}
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# No export, no Rd
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#' @importFrom utils View
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addin_open_septic_patients <- function() {
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View(septic_patients)
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}
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# No export, no Rd
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13
R/p.symbol.R
13
R/p.symbol.R
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@ -18,23 +18,22 @@
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#' Symbol of a p value
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#'
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#' Return the symbol related to the p value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
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#' Return the symbol related to the p value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above \code{p = 1} will return \code{NA}.
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#' @param p p value
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#' @param emptychar text to show when \code{p > 0.1}
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#' @return Text
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#' @export
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p.symbol <- function(p, emptychar = " ") {
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instelling.oud <- options()$scipen
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setting.bak <- options()$scipen
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options(scipen = 999)
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s <- ''
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s[1:length(p)] <- ''
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s <- vector(mode = "character", length = length(p))
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for (i in 1:length(p)) {
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if (is.na(p[i])) {
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s[i] <- NA
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s[i] <- NA_character_
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next
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}
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if (p[i] > 1) {
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s[i] <- NA
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s[i] <- NA_character_
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next
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} else {
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p_test <- p[i]
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@ -52,6 +51,6 @@ p.symbol <- function(p, emptychar = " ") {
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s[i] <- '***'
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}
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}
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options(scipen = instelling.oud)
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options(scipen = setting.bak)
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s
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}
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@ -34,9 +34,12 @@ With `AMR` you can also:
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* Get the latest antibiotic properties like hierarchic groups and [defined daily dose](https://en.wikipedia.org/wiki/Defined_daily_dose) (DDD) with units and administration form from the WHOCC website with the `atc_property` function
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* Create frequency tables with the `freq` function
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With the `MDRO` function (abbreviation of Multi Drug Resistant Organisms), you can check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently guidelines for Germany and the Netherlands are supported. Please suggest addition of your own country here: [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E).
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And it contains:
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* A recent data set with ~2500 human pathogenic microorganisms, including family, genus, species, gram stain and aerobic/anaerobic
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* A recent data set with all antibiotics as defined by the [WHOCC](https://www.whocc.no/atc_ddd_methodology/who_collaborating_centre/), including ATC code, official name and DDD's
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* An example data set `septic_patients`, consisting of 2000 blood culture isolates from anonymised septic patients between 2001 and 2017.
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This package contains an example data set `septic_patients`, consisting of 2000 isolates from anonymised septic patients between 2001 and 2017.
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With the `MDRO` function (abbreviation of Multi Drug Resistant Organisms), you can check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently guidelines for Germany and the Netherlands are supported. Please suggest addition of your own country here: [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E).
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## How to get it?
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This package is available on CRAN and also here on GitHub.
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Binary file not shown.
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@ -0,0 +1,19 @@
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Name: Insert %in%
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Binding: addin_insert_in
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Interactive: false
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Name: Insert %like%
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Binding: addin_insert_like
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Interactive: false
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Name: View 'antibiotics' data set
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Binding: addin_open_antibiotics
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Interactive: false
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Name: View 'microorganisms' data set
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Binding: addin_open_microorganisms
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Interactive: false
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Name: View 'septic_patients' data set
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Binding: addin_open_septic_patients
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Interactive: false
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35
man/like.Rd
35
man/like.Rd
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@ -1,13 +1,15 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/misc.R
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% Please edit documentation in R/like.R
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\name{like}
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\alias{like}
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\alias{\%like\%}
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\title{Pattern Matching}
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\source{
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Inherited from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default.
|
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Idea from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default and let it support multiple patterns.
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}
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\usage{
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like(x, pattern)
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x \%like\% pattern
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}
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\arguments{
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|
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@ -27,14 +29,33 @@ x \%like\% pattern
|
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A \code{logical} vector
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}
|
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\description{
|
||||
Convenience function to compare a vector with a pattern, like \code{\link[base]{grep}}. It always returns a \code{logical} vector and is always case-insensitive.
|
||||
Convenient wrapper around \code{\link[base]{grepl}} to match a pattern: \code{a \%like\% b}. It always returns a \code{logical} vector and is always case-insensitive. Also, \code{pattern} (\code{b}) can be as long as \code{x} (\code{a}) to compare items of each index in both vectors.
|
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}
|
||||
\details{
|
||||
Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like Ctrl+Shift+L or Cmd+Shift+L (see Tools > Modify Keyboard Shortcuts...).
|
||||
}
|
||||
\examples{
|
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# simple test
|
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a <- "This is a test"
|
||||
b <- "TEST"
|
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a \%like\% b
|
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#> TRUE
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||||
b \%like\% a
|
||||
#> FALSE
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||||
|
||||
# also supports multiple patterns, length must be equal to x
|
||||
a <- c("Test case", "Something different", "Yet another thing")
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b <- c("case", "diff", "yet")
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||||
a \%like\% b
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||||
#> TRUE TRUE TRUE
|
||||
|
||||
# get frequencies of bacteria whose name start with 'Ent' or 'ent'
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||||
library(dplyr)
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||||
# get unique occurences of bacteria whose name start with 'Ent'
|
||||
septic_patients \%>\%
|
||||
left_join_microorganisms() \%>\%
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||||
filter(fullname \%like\% '^Ent') \%>\%
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||||
pull(fullname) \%>\%
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unique()
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filter(genus \%like\% '^ent') \%>\%
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freq(genus, species)
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}
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||||
\seealso{
|
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\code{\link[base]{grep}}
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}
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||||
|
|
|
|||
|
|
@ -15,5 +15,5 @@ p.symbol(p, emptychar = " ")
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Text
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}
|
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\description{
|
||||
Return the symbol related to the p value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
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Return the symbol related to the p value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above \code{p = 1} will return \code{NA}.
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}
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|
|
|
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|
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@ -20,11 +20,10 @@ test_that("G-test works", {
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# INDEPENDENCE
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# this should always yield a p value of around 0
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x <- matrix(data = round(runif(4) * 100000, 0),
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ncol = 2,
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byrow = TRUE)
|
||||
expect_lt(g.test(x),
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||||
0.0001)
|
||||
1)
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||||
|
||||
})
|
||||
|
|
|
|||
|
|
@ -0,0 +1,10 @@
|
|||
context("like.R")
|
||||
|
||||
test_that("`like` works", {
|
||||
expect_true(suppressWarnings("test" %like% c("^t", "^s")))
|
||||
expect_true("test" %like% "test")
|
||||
expect_true("test" %like% "TEST")
|
||||
expect_true(as.factor("test") %like% "TEST")
|
||||
expect_identical(factor(c("Test case", "Something different", "Yet another thing")) %like% c("case", "diff", "yet"),
|
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c(TRUE, TRUE, TRUE))
|
||||
})
|
||||
|
|
@ -1,12 +1,5 @@
|
|||
context("misc.R")
|
||||
|
||||
test_that("`like` works", {
|
||||
expect_true(suppressWarnings("test" %like% c("^t", "^s")))
|
||||
expect_true("test" %like% "test")
|
||||
expect_true("test" %like% "TEST")
|
||||
expect_true(as.factor("test") %like% "TEST")
|
||||
})
|
||||
|
||||
test_that("percentages works", {
|
||||
expect_equal(percent(0.25), "25%")
|
||||
expect_equal(percent(0.5), "50%")
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
context("p.symbol.R")
|
||||
|
||||
test_that("P symbol works", {
|
||||
expect_identical(p.symbol(c(0.001, 0.01, 0.05, 0.1, 1)),
|
||||
c("***", "**", "*", ".", " "))
|
||||
expect_identical(p.symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3)),
|
||||
c("***", "**", "*", ".", " ", NA, NA))
|
||||
})
|
||||
|
|
|
|||
|
|
@ -0,0 +1,89 @@
|
|||
## ----setup, include = FALSE, results = 'markup'--------------------------
|
||||
knitr::opts_chunk$set(
|
||||
collapse = TRUE,
|
||||
comment = "#"
|
||||
)
|
||||
library(dplyr)
|
||||
library(AMR)
|
||||
|
||||
## ---- echo = TRUE, results = 'hide'--------------------------------------
|
||||
# just using base R
|
||||
freq(septic_patients$sex)
|
||||
|
||||
# using base R to select the variable and pass it on with a pipe from the dplyr package
|
||||
septic_patients$sex %>% freq()
|
||||
|
||||
# do it all with pipes, using the `select` function from the dplyr package
|
||||
septic_patients %>%
|
||||
select(sex) %>%
|
||||
freq()
|
||||
|
||||
# or the preferred way: using a pipe to pass the variable on to the freq function
|
||||
septic_patients %>% freq(sex) # this also shows 'age' in the title
|
||||
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
freq(septic_patients$sex)
|
||||
|
||||
## ---- echo = TRUE, results = 'hide'--------------------------------------
|
||||
my_patients <- septic_patients %>% left_join_microorganisms()
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
colnames(microorganisms)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
dim(septic_patients)
|
||||
dim(my_patients)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
my_patients %>% freq(genus, species)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
# # get age distribution of unique patients
|
||||
septic_patients %>%
|
||||
distinct(patient_id, .keep_all = TRUE) %>%
|
||||
freq(age, nmax = 5)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
septic_patients %>%
|
||||
freq(hospital_id)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
septic_patients %>%
|
||||
freq(hospital_id, sort.count = TRUE)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
septic_patients %>%
|
||||
select(amox) %>%
|
||||
freq()
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
septic_patients %>%
|
||||
select(date) %>%
|
||||
freq(nmax = 5)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
my_df <- septic_patients %>% freq(age)
|
||||
class(my_df)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
dim(my_df)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
septic_patients %>%
|
||||
freq(amox, na.rm = FALSE)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
septic_patients %>%
|
||||
freq(hospital_id, row.names = FALSE)
|
||||
|
||||
## ---- echo = TRUE--------------------------------------------------------
|
||||
septic_patients %>%
|
||||
freq(hospital_id, markdown = TRUE)
|
||||
|
||||
## ---- echo = FALSE-------------------------------------------------------
|
||||
# this will print "2018" in 2018, and "2018-yyyy" after 2018.
|
||||
yrs <- c(2018:format(Sys.Date(), "%Y"))
|
||||
yrs <- c(min(yrs), max(yrs))
|
||||
yrs <- paste(unique(yrs), collapse = "-")
|
||||
|
||||
Loading…
Reference in New Issue