mirror of
https://github.com/msberends/AMR.git
synced 2024-12-24 19:26:12 +01:00
limits for scale_y_percent - Licence update
This commit is contained in:
parent
1ed0cc9bfd
commit
b937662a97
@ -7,3 +7,4 @@ appveyor.yml
|
||||
.zenodo.json
|
||||
_noinclude
|
||||
^cran-comments\.md$
|
||||
git.sh
|
||||
|
1
.gitignore
vendored
1
.gitignore
vendored
@ -15,3 +15,4 @@ vignettes/*.R
|
||||
.DS_Store
|
||||
^cran-comments\.md$
|
||||
^CRAN-RELEASE$
|
||||
git.sh
|
||||
|
5
NEWS.md
5
NEWS.md
@ -4,7 +4,7 @@
|
||||
* Function `mo_failures` to review values that could not be coerced to a valid MO code, using `as.mo`. This latter function will now only show a maximum of 25 uncoerced values.
|
||||
* Function `mo_renamed` to get a list of all returned values from `as.mo` that have had taxonomic renaming
|
||||
* Function `age` to calculate the (patients) age in years
|
||||
* Function `age_groups` to split ages into custom or predefined groups (like children or elderly). This allows for easier antimicrobial resistance per age group.
|
||||
* Function `age_groups` to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis (per age group).
|
||||
|
||||
#### Changed
|
||||
* Improvements for `as.mo`:
|
||||
@ -29,7 +29,10 @@
|
||||
* Now honours the `decimal.mark` setting, which just like `format` defaults to `getOption("OutDec")`
|
||||
* The new `big.mark` parameter will at default be `","` when `decimal.mark = "."` and `"."` otherwise
|
||||
* Fix for header text where all observations are `NA`
|
||||
* Function `scale_y_percent` now has the `limits` parameter
|
||||
|
||||
#### Other
|
||||
* Updated licence text to emphasise GPL 2.0 and that this is an R package.
|
||||
|
||||
# 0.5.0 (latest stable release)
|
||||
**Published on CRAN: 2018-11-30**
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Property of an antibiotic
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Name of an antibiotic
|
||||
|
58
R/age.R
58
R/age.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Age in years of individuals
|
||||
@ -49,7 +49,7 @@ age <- function(x, y = Sys.Date()) {
|
||||
ages
|
||||
}
|
||||
|
||||
#' Split ages in age groups
|
||||
#' Split ages into age groups
|
||||
#'
|
||||
#' Splits ages into groups defined by the \code{split} parameter.
|
||||
#' @param x age, e.g. calculated with \code{\link{age}}
|
||||
@ -61,33 +61,36 @@ age <- function(x, y = Sys.Date()) {
|
||||
#' \item{A character:}
|
||||
#' \itemize{
|
||||
#' \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+.}
|
||||
#' \item{\code{"elderly"} or \code{"seniors"}, equivalent: of \code{c(65, 75, 85, 95)}. This will split on 0-64, 65-74, 75-84, 85-94 and 95+.}
|
||||
#' \item{\code{"fives"}, equivalent: of \code{1:20 * 5}. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.}
|
||||
#' \item{\code{"tens"}, equivalent: of \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29 and so forth.}
|
||||
#' \item{\code{"elderly"} or \code{"seniors"}, equivalent of: \code{c(65, 75, 85, 95)}. This will split on 0-64, 65-74, 75-84, 85-94 and 95+.}
|
||||
#' \item{\code{"fives"}, equivalent of: \code{1:20 * 5}. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.}
|
||||
#' \item{\code{"tens"}, equivalent of: \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29 and so forth.}
|
||||
#' }
|
||||
#' }
|
||||
#' @keywords age_group age
|
||||
#' @return Ordered \code{\link{factor}}
|
||||
#' @seealso age
|
||||
#' @export
|
||||
#' @examples
|
||||
#' ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
|
||||
#'
|
||||
#' # split on 0-49 and 50+
|
||||
#' # split into 0-49 and 50+
|
||||
#' age_groups(ages, 50)
|
||||
#'
|
||||
#' # split on 0-20, 21-49 and 50+
|
||||
#' age_groups(ages, c(21, 50))
|
||||
#' # split into 0-19, 20-49 and 50+
|
||||
#' age_groups(ages, c(20, 50))
|
||||
#'
|
||||
#' # split on every ten years
|
||||
#' # split into groups of ten years
|
||||
#' age_groups(ages, 1:10 * 10)
|
||||
#' age_groups(ages, "tens")
|
||||
#' age_groups(ages, split_at = "tens")
|
||||
#'
|
||||
#' # split on every five years
|
||||
#' # split into groups of five years
|
||||
#' age_groups(ages, 1:20 * 5)
|
||||
#' age_groups(ages, "fives")
|
||||
#' age_groups(ages, split_at = "fives")
|
||||
#'
|
||||
#' # split on children
|
||||
#' # split specifically for children
|
||||
#' age_groups(ages, "children")
|
||||
#' # same:
|
||||
#' age_groups(ages, c(1, 2, 4, 6, 13, 17))
|
||||
#'
|
||||
#' # resistance of ciprofloxacine per age group
|
||||
#' library(dplyr)
|
||||
@ -101,20 +104,18 @@ age <- function(x, y = Sys.Date()) {
|
||||
#' ggplot_rsi(x = "age_group")
|
||||
age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
|
||||
if (is.character(split_at)) {
|
||||
split_at <- split_at[1]
|
||||
split_at <- split_at[1L]
|
||||
if (split_at %like% "^child") {
|
||||
split_at <- c(0, 1, 2, 4, 6, 13, 18)
|
||||
}
|
||||
if (split_at %like% "^elder" | split_at %like% "^senior") {
|
||||
} else if (split_at %like% "^(elder|senior)") {
|
||||
split_at <- c(65, 75, 85, 95)
|
||||
}
|
||||
if (split_at %like% "fives") {
|
||||
} else if (split_at %like% "^five") {
|
||||
split_at <- 1:20 * 5
|
||||
}
|
||||
if (split_at %like% "^tens") {
|
||||
} else if (split_at %like% "^ten") {
|
||||
split_at <- 1:10 * 10
|
||||
}
|
||||
}
|
||||
split_at <- as.integer(split_at)
|
||||
if (!is.numeric(x) | !is.numeric(split_at)) {
|
||||
stop("`x` and `split_at` must both be numeric.")
|
||||
}
|
||||
@ -129,19 +130,14 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
|
||||
|
||||
# turn input values to 'split_at' indices
|
||||
y <- x
|
||||
labs <- split_at
|
||||
for (i in 1:length(split_at)) {
|
||||
y[x >= split_at[i]] <- i
|
||||
# create labels
|
||||
# when age group consists of only one age
|
||||
labs[i - 1] <- paste0(unique(c(split_at[i - 1], split_at[i] - 1)), collapse = "-")
|
||||
}
|
||||
|
||||
# create labels
|
||||
labs <- split_at
|
||||
for (i in 2:length(labs)) {
|
||||
if (split_at[i - 1] == split_at[i] - 1) {
|
||||
labs[i - 1] <- split_at[i - 1]
|
||||
} else {
|
||||
labs[i - 1] <- paste0(split_at[i - 1], "-", split_at[i] - 1)
|
||||
}
|
||||
}
|
||||
# last category
|
||||
labs[length(labs)] <- paste0(split_at[length(split_at)], "+")
|
||||
|
||||
|
6
R/atc.R
6
R/atc.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Count isolates
|
||||
|
6
R/data.R
6
R/data.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Data set with 423 antibiotics
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Deprecated functions
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' EUCAST rules
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Determine first (weighted) isolates
|
||||
|
6
R/freq.R
6
R/freq.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Frequency table
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' \emph{G}-test for Count Data
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Get language for AMR
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' AMR bar plots with \code{ggplot}
|
||||
@ -24,6 +24,7 @@
|
||||
#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
|
||||
#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
|
||||
#' @param breaks numeric vector of positions
|
||||
#' @param limits numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum
|
||||
#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
|
||||
#' @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.
|
||||
#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
|
||||
@ -150,6 +151,7 @@ ggplot_rsi <- function(data,
|
||||
# params = list(),
|
||||
facet = NULL,
|
||||
breaks = seq(0, 1, 0.1),
|
||||
limits = NULL,
|
||||
translate_ab = "official",
|
||||
fun = count_df,
|
||||
nrow = NULL,
|
||||
@ -203,7 +205,7 @@ ggplot_rsi <- function(data,
|
||||
if (fun_name == "portion_df"
|
||||
| (fun_name == "count_df" & position == "fill")) {
|
||||
# portions, so use y scale with percentage
|
||||
p <- p + scale_y_percent(breaks = breaks)
|
||||
p <- p + scale_y_percent(breaks = breaks, limits = limits)
|
||||
}
|
||||
|
||||
if (fun_name == "count_df" & datalabels == TRUE) {
|
||||
@ -295,9 +297,10 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
|
||||
|
||||
#' @rdname ggplot_rsi
|
||||
#' @export
|
||||
scale_y_percent <- function(breaks = seq(0, 1, 0.1)) {
|
||||
scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
|
||||
ggplot2::scale_y_continuous(breaks = breaks,
|
||||
labels = percent(breaks))
|
||||
labels = percent(breaks),
|
||||
limits = limits)
|
||||
}
|
||||
|
||||
#' @rdname ggplot_rsi
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
globalVariables(c(".",
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Join a table with \code{microorganisms}
|
||||
#'
|
||||
#' Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Key antibiotics for first \emph{weighted} isolates
|
||||
|
18
R/kurtosis.R
18
R/kurtosis.R
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Kurtosis of the sample
|
||||
#'
|
||||
#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.
|
||||
|
6
R/like.R
6
R/like.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Pattern Matching
|
||||
|
6
R/mdro.R
6
R/mdro.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Determine multidrug-resistant organisms (MDRO)
|
||||
|
6
R/mic.R
6
R/mic.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Class 'mic'
|
||||
|
6
R/misc.R
6
R/misc.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
# No export, no Rd
|
||||
|
6
R/mo.R
6
R/mo.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Transform to microorganism ID
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Property of a microorganism
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Symbol of a p value
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Calculate resistance of isolates
|
||||
|
22
R/read.4d.R
22
R/read.4d.R
@ -6,19 +6,19 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Read data from 4D database
|
||||
#'
|
||||
#' This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
|
||||
#' This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
|
||||
#' @inheritParams utils::read.table
|
||||
#' @param info a logical to indicate whether info about the import should be printed, defaults to \code{TRUE} in interactive sessions
|
||||
#' @details Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.
|
||||
@ -59,7 +59,7 @@ read.4D <- function(file,
|
||||
fileEncoding = fileEncoding,
|
||||
encoding = encoding)
|
||||
|
||||
# helper functions
|
||||
# helper function for dates
|
||||
to_date_4D <- function(x) {
|
||||
date_regular <- as.Date(x, format = "%d-%m-%y")
|
||||
posixlt <- as.POSIXlt(date_regular)
|
||||
@ -68,16 +68,6 @@ read.4D <- function(file,
|
||||
posixlt[date_regular > Sys.Date() & !is.na(posixlt)]$year <- posixlt[date_regular > Sys.Date() & !is.na(posixlt)]$year - 100
|
||||
as.Date(posixlt)
|
||||
}
|
||||
to_age_4D <- function(from, to) {
|
||||
from_lt = as.POSIXlt(from)
|
||||
to_lt = as.POSIXlt(to)
|
||||
|
||||
age = to_lt$year - from_lt$year
|
||||
|
||||
ifelse(to_lt$mon < from_lt$mon |
|
||||
(to_lt$mon == from_lt$mon & to_lt$mday < from_lt$mday),
|
||||
age - 1, age)
|
||||
}
|
||||
|
||||
if (info == TRUE) {
|
||||
message("OK\nTransforming column names... ", appendLF = FALSE)
|
||||
@ -136,7 +126,7 @@ read.4D <- function(file,
|
||||
data_4D$date_received <- to_date_4D(data_4D$date_received)
|
||||
}
|
||||
if ("age" %in% colnames(data_4D)) {
|
||||
data_4D$age <- to_age_4D(data_4D$date_birth, data_4D$date_received)
|
||||
data_4D$age <- age(data_4D$date_birth, data_4D$date_received)
|
||||
}
|
||||
if ("gender" %in% colnames(data_4D)) {
|
||||
data_4D$gender[data_4D$gender == "V"] <- "F"
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Predict antimicrobial resistance
|
||||
|
6
R/rsi.R
6
R/rsi.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Class 'rsi'
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all
|
||||
|
18
R/skewness.R
18
R/skewness.R
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Skewness of the sample
|
||||
#'
|
||||
#' @description Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
|
||||
|
8
R/zzz.R
8
R/zzz.R
@ -6,21 +6,21 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' The \code{AMR} Package
|
||||
#'
|
||||
#' Welcome to the \code{AMR} package. This page gives some additional contact information about the authors.
|
||||
#' @details
|
||||
#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
|
||||
#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and ti work with antibiotic properties by using evidence-based methods.
|
||||
#'
|
||||
#' This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
|
||||
#' @section Authors:
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
Name: Insert %in%
|
||||
Binding: addin_insert_in
|
||||
Interactive: false
|
||||
|
@ -7,7 +7,7 @@
|
||||
Welcome to the \code{AMR} package. This page gives some additional contact information about the authors.
|
||||
}
|
||||
\details{
|
||||
This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
|
||||
This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and ti work with antibiotic properties by using evidence-based methods.
|
||||
|
||||
This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
|
||||
}
|
||||
|
@ -2,7 +2,7 @@
|
||||
% Please edit documentation in R/age.R
|
||||
\name{age_groups}
|
||||
\alias{age_groups}
|
||||
\title{Split ages in age groups}
|
||||
\title{Split ages into age groups}
|
||||
\usage{
|
||||
age_groups(x, split_at = c(12, 25, 55, 75))
|
||||
}
|
||||
@ -25,31 +25,33 @@ To split ages, the input can be:
|
||||
\item{A character:}
|
||||
\itemize{
|
||||
\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+.}
|
||||
\item{\code{"elderly"} or \code{"seniors"}, equivalent: of \code{c(65, 75, 85, 95)}. This will split on 0-64, 65-74, 75-84, 85-94 and 95+.}
|
||||
\item{\code{"fives"}, equivalent: of \code{1:20 * 5}. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.}
|
||||
\item{\code{"tens"}, equivalent: of \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29 and so forth.}
|
||||
\item{\code{"elderly"} or \code{"seniors"}, equivalent of: \code{c(65, 75, 85, 95)}. This will split on 0-64, 65-74, 75-84, 85-94 and 95+.}
|
||||
\item{\code{"fives"}, equivalent of: \code{1:20 * 5}. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.}
|
||||
\item{\code{"tens"}, equivalent of: \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29 and so forth.}
|
||||
}
|
||||
}
|
||||
}
|
||||
\examples{
|
||||
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
|
||||
|
||||
# split on 0-49 and 50+
|
||||
# split into 0-49 and 50+
|
||||
age_groups(ages, 50)
|
||||
|
||||
# split on 0-20, 21-49 and 50+
|
||||
age_groups(ages, c(21, 50))
|
||||
# split into 0-19, 20-49 and 50+
|
||||
age_groups(ages, c(20, 50))
|
||||
|
||||
# split on every ten years
|
||||
# split into groups of ten years
|
||||
age_groups(ages, 1:10 * 10)
|
||||
age_groups(ages, "tens")
|
||||
age_groups(ages, split_at = "tens")
|
||||
|
||||
# split on every five years
|
||||
# split into groups of five years
|
||||
age_groups(ages, 1:20 * 5)
|
||||
age_groups(ages, "fives")
|
||||
age_groups(ages, split_at = "fives")
|
||||
|
||||
# split on children
|
||||
# split specifically for children
|
||||
age_groups(ages, "children")
|
||||
# same:
|
||||
age_groups(ages, c(1, 2, 4, 6, 13, 17))
|
||||
|
||||
# resistance of ciprofloxacine per age group
|
||||
library(dplyr)
|
||||
@ -65,3 +67,5 @@ septic_patients \%>\%
|
||||
\seealso{
|
||||
age
|
||||
}
|
||||
\keyword{age}
|
||||
\keyword{age_group}
|
||||
|
@ -12,8 +12,8 @@
|
||||
\usage{
|
||||
ggplot_rsi(data, position = NULL, x = "Antibiotic",
|
||||
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
|
||||
translate_ab = "official", fun = count_df, nrow = NULL,
|
||||
datalabels = TRUE, datalabels.size = 3,
|
||||
limits = NULL, translate_ab = "official", fun = count_df,
|
||||
nrow = NULL, datalabels = TRUE, datalabels.size = 3,
|
||||
datalabels.colour = "grey15", ...)
|
||||
|
||||
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
|
||||
@ -22,7 +22,7 @@ geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
|
||||
|
||||
facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL)
|
||||
|
||||
scale_y_percent(breaks = seq(0, 1, 0.1))
|
||||
scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)
|
||||
|
||||
scale_rsi_colours()
|
||||
|
||||
@ -44,6 +44,8 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
|
||||
|
||||
\item{breaks}{numeric vector of positions}
|
||||
|
||||
\item{limits}{numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum}
|
||||
|
||||
\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}}}
|
||||
|
@ -117,7 +117,7 @@ read.4D(file, info = interactive(), header = TRUE, row.names = NULL,
|
||||
}
|
||||
}
|
||||
\description{
|
||||
This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
|
||||
This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
|
||||
}
|
||||
\details{
|
||||
Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
library(testthat)
|
||||
library(AMR)
|
||||
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("ab_property.R")
|
||||
|
||||
test_that("ab_property works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("abname.R")
|
||||
|
||||
test_that("abname works", {
|
||||
|
@ -1,4 +1,22 @@
|
||||
context("g.test.R")
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("age.R")
|
||||
|
||||
test_that("age works", {
|
||||
expect_equal(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
|
||||
@ -22,8 +40,16 @@ test_that("age_groups works", {
|
||||
2)
|
||||
expect_equal(length(unique(age_groups(ages, c(50, 60)))),
|
||||
3)
|
||||
expect_identical(class(age_groups(ages)),
|
||||
expect_identical(class(age_groups(ages, "child")),
|
||||
c("ordered", "factor"))
|
||||
|
||||
expect_identical(class(age_groups(ages, "elderly")),
|
||||
c("ordered", "factor"))
|
||||
|
||||
expect_identical(class(age_groups(ages, "tens")),
|
||||
c("ordered", "factor"))
|
||||
|
||||
expect_identical(class(age_groups(ages, "fives")),
|
||||
c("ordered", "factor"))
|
||||
|
||||
})
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("atc.R")
|
||||
|
||||
# test_that("atc_property works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("count.R")
|
||||
|
||||
test_that("counts work", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("data.R")
|
||||
|
||||
test_that("data sets are valid", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("deprecated.R")
|
||||
|
||||
test_that("deprecated functions work", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("eucast_rules.R")
|
||||
|
||||
test_that("EUCAST rules work", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("first_isolate.R")
|
||||
|
||||
test_that("first isolates work", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("freq.R")
|
||||
|
||||
test_that("frequency table works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("g.test.R")
|
||||
|
||||
test_that("G-test works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("get_locale.R")
|
||||
|
||||
test_that("get_locale works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("ggplot_rsi.R")
|
||||
|
||||
test_that("ggplot_rsi works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("join_microorganisms.R")
|
||||
|
||||
test_that("joins work", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("key_antibiotics.R")
|
||||
|
||||
test_that("keyantibiotics work", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("kurtosis.R")
|
||||
|
||||
test_that("kurtosis works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("like.R")
|
||||
|
||||
test_that("`like` works", {
|
||||
|
@ -1,5 +1,22 @@
|
||||
context("mdro.R")
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("mdro.R")
|
||||
|
||||
test_that("mdro works", {
|
||||
library(dplyr)
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("mic.R")
|
||||
|
||||
test_that("mic works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("misc.R")
|
||||
|
||||
test_that("percentages works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("mo.R")
|
||||
|
||||
test_that("as.mo works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("mo_property.R")
|
||||
|
||||
test_that("mo_property works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("p.symbol.R")
|
||||
|
||||
test_that("P symbol works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("portion.R")
|
||||
|
||||
test_that("portions works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("read.4d.R")
|
||||
|
||||
test_that("read 4D works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("rsi.R")
|
||||
|
||||
test_that("rsi works", {
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("skewness.R")
|
||||
|
||||
test_that("skewness works", {
|
||||
|
Loading…
Reference in New Issue
Block a user