P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity

limits for scale_y_percent - Licence update

This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-12-16 22:45:12 +01:00
parent 1ed0cc9bfd
commit b937662a97
67 changed files with 733 additions and 150 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
.Rbuildignore
View File

@ -7,3 +7,4 @@ appveyor.yml
.zenodo.json .zenodo.json
_noinclude _noinclude
^cran-comments\.md$ ^cran-comments\.md$
git.sh

1
.gitignore vendored
View File

@ -15,3 +15,4 @@ vignettes/*.R
.DS_Store .DS_Store
^cran-comments\.md$ ^cran-comments\.md$
^CRAN-RELEASE$ ^CRAN-RELEASE$
git.sh

5
NEWS.md
View File

@ -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_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 `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` 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 #### Changed
* Improvements for `as.mo`: * Improvements for `as.mo`:
@ -29,7 +29,10 @@
* Now honours the `decimal.mark` setting, which just like `format` defaults to `getOption("OutDec")` * 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 * The new `big.mark` parameter will at default be `","` when `decimal.mark = "."` and `"."` otherwise
* Fix for header text where all observations are `NA` * 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) # 0.5.0 (latest stable release)
**Published on CRAN: 2018-11-30** **Published on CRAN: 2018-11-30**

6
R/ab_property.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Property of an antibiotic

6
R/abname.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Name of an antibiotic

58
R/age.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Age in years of individuals
@ -49,7 +49,7 @@ age <- function(x, y = Sys.Date()) {
ages ages
} }
#' Split ages in age groups #' Split ages into age groups
#' #'
#' Splits ages into groups defined by the \code{split} parameter. #' Splits ages into groups defined by the \code{split} parameter.
#' @param x age, e.g. calculated with \code{\link{age}} #' @param x age, e.g. calculated with \code{\link{age}}
@ -61,33 +61,36 @@ age <- function(x, y = Sys.Date()) {
#' \item{A character:} #' \item{A character:}
#' \itemize{ #' \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{"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{"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{"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{"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}} #' @return Ordered \code{\link{factor}}
#' @seealso age #' @seealso age
#' @export #' @export
#' @examples #' @examples
#' ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21) #' 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) #' age_groups(ages, 50)
#' #'
#' # split on 0-20, 21-49 and 50+ #' # split into 0-19, 20-49 and 50+
#' age_groups(ages, c(21, 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, 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, 1:20 * 5)
#' age_groups(ages, "fives") #' age_groups(ages, split_at = "fives")
#' #'
#' # split on children #' # split specifically for children
#' age_groups(ages, "children") #' age_groups(ages, "children")
#' # same:
#' age_groups(ages, c(1, 2, 4, 6, 13, 17))
#' #'
#' # resistance of ciprofloxacine per age group #' # resistance of ciprofloxacine per age group
#' library(dplyr) #' library(dplyr)
@ -101,20 +104,18 @@ age <- function(x, y = Sys.Date()) {
#' ggplot_rsi(x = "age_group") #' ggplot_rsi(x = "age_group")
age_groups <- function(x, split_at = c(12, 25, 55, 75)) { age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
if (is.character(split_at)) { if (is.character(split_at)) {
split_at <- split_at[1] split_at <- split_at[1L]
if (split_at %like% "^child") { if (split_at %like% "^child") {
split_at <- c(0, 1, 2, 4, 6, 13, 18) split_at <- c(0, 1, 2, 4, 6, 13, 18)
} } else if (split_at %like% "^(elder|senior)") {
if (split_at %like% "^elder" | split_at %like% "^senior") {
split_at <- c(65, 75, 85, 95) split_at <- c(65, 75, 85, 95)
} } else if (split_at %like% "^five") {
if (split_at %like% "fives") {
split_at <- 1:20 * 5 split_at <- 1:20 * 5
} } else if (split_at %like% "^ten") {
if (split_at %like% "^tens") {
split_at <- 1:10 * 10 split_at <- 1:10 * 10
} }
} }
split_at <- as.integer(split_at)
if (!is.numeric(x) | !is.numeric(split_at)) { if (!is.numeric(x) | !is.numeric(split_at)) {
stop("`x` and `split_at` must both be numeric.") 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 # turn input values to 'split_at' indices
y <- x y <- x
labs <- split_at
for (i in 1:length(split_at)) { for (i in 1:length(split_at)) {
y[x >= split_at[i]] <- i 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 # last category
labs[length(labs)] <- paste0(split_at[length(split_at)], "+") labs[length(labs)] <- paste0(split_at[length(split_at)], "+")

6
R/atc.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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
R/count.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Count isolates

6
R/data.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Data set with 423 antibiotics

6
R/deprecated.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Deprecated functions

6
R/eucast_rules.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' EUCAST rules

6
R/first_isolate.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Determine first (weighted) isolates

6
R/freq.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Frequency table

6
R/g.test.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' \emph{G}-test for Count Data

6
R/get_locale.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Get language for AMR

15
R/ggplot_rsi.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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} #' 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 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 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 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 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 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}} #' @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(), # params = list(),
facet = NULL, facet = NULL,
breaks = seq(0, 1, 0.1), breaks = seq(0, 1, 0.1),
limits = NULL,
translate_ab = "official", translate_ab = "official",
fun = count_df, fun = count_df,
nrow = NULL, nrow = NULL,
@ -203,7 +205,7 @@ ggplot_rsi <- function(data,
if (fun_name == "portion_df" if (fun_name == "portion_df"
| (fun_name == "count_df" & position == "fill")) { | (fun_name == "count_df" & position == "fill")) {
# portions, so use y scale with percentage # 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) { if (fun_name == "count_df" & datalabels == TRUE) {
@ -295,9 +297,10 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
#' @rdname ggplot_rsi #' @rdname ggplot_rsi
#' @export #' @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, ggplot2::scale_y_continuous(breaks = breaks,
labels = percent(breaks)) labels = percent(breaks),
limits = limits)
} }
#' @rdname ggplot_rsi #' @rdname ggplot_rsi

6
R/globals.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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(".", globalVariables(c(".",

18
R/join_microorganisms.R
View File

@ -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 a table with \code{microorganisms}
#' #'
#' Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector. #' Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.

6
R/key_antibiotics.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Key antibiotics for first \emph{weighted} isolates

18
R/kurtosis.R
View File

@ -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 #' Kurtosis of the sample
#' #'
#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. #' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.

6
R/like.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Pattern Matching

6
R/mdro.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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) #' Determine multidrug-resistant organisms (MDRO)

6
R/mic.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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' #' Class 'mic'

6
R/misc.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 # No export, no Rd

6
R/mo.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Transform to microorganism ID

6
R/mo_property.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Property of a microorganism

6
R/p.symbol.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Symbol of a p value

6
R/portion.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Calculate resistance of isolates

22
R/read.4d.R
View File

@ -6,19 +6,19 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' 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 #' @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 #' @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. #' @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, fileEncoding = fileEncoding,
encoding = encoding) encoding = encoding)
# helper functions # helper function for dates
to_date_4D <- function(x) { to_date_4D <- function(x) {
date_regular <- as.Date(x, format = "%d-%m-%y") date_regular <- as.Date(x, format = "%d-%m-%y")
posixlt <- as.POSIXlt(date_regular) 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 posixlt[date_regular > Sys.Date() & !is.na(posixlt)]$year <- posixlt[date_regular > Sys.Date() & !is.na(posixlt)]$year - 100
as.Date(posixlt) 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) { if (info == TRUE) {
message("OK\nTransforming column names... ", appendLF = FALSE) 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) data_4D$date_received <- to_date_4D(data_4D$date_received)
} }
if ("age" %in% colnames(data_4D)) { 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)) { if ("gender" %in% colnames(data_4D)) {
data_4D$gender[data_4D$gender == "V"] <- "F" data_4D$gender[data_4D$gender == "V"] <- "F"

6
R/resistance_predict.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' Predict antimicrobial resistance

6
R/rsi.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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' #' Class 'rsi'

6
R/rsi_calc.R
View File

@ -6,14 +6,14 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all

18
R/skewness.R
View File

@ -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 #' 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. #' @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
View File

@ -6,21 +6,21 @@
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# # # #
# LICENCE # # 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, # # it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. # # 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 # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # 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 #' The \code{AMR} Package
#' #'
#' Welcome to the \code{AMR} package. This page gives some additional contact information about the authors. #' Welcome to the \code{AMR} package. This page gives some additional contact information about the authors.
#' @details #' @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). #' 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: #' @section Authors:

18
inst/rstudio/addins.dcf
View File

@ -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% Name: Insert %in%
Binding: addin_insert_in Binding: addin_insert_in
Interactive: false Interactive: false

2
man/AMR.Rd
View File

@ -7,7 +7,7 @@
Welcome to the \code{AMR} package. This page gives some additional contact information about the authors. Welcome to the \code{AMR} package. This page gives some additional contact information about the authors.
} }
\details{ \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). 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).
} }

28
man/age_groups.Rd
View File

@ -2,7 +2,7 @@
% Please edit documentation in R/age.R % Please edit documentation in R/age.R
\name{age_groups} \name{age_groups}
\alias{age_groups} \alias{age_groups}
\title{Split ages in age groups} \title{Split ages into age groups}
\usage{ \usage{
age_groups(x, split_at = c(12, 25, 55, 75)) age_groups(x, split_at = c(12, 25, 55, 75))
} }
@ -25,31 +25,33 @@ To split ages, the input can be:
\item{A character:} \item{A character:}
\itemize{ \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{"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{"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{"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{"tens"}, equivalent of: \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29 and so forth.}
} }
} }
} }
\examples{ \examples{
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21) 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) age_groups(ages, 50)
# split on 0-20, 21-49 and 50+ # split into 0-19, 20-49 and 50+
age_groups(ages, c(21, 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, 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, 1:20 * 5)
age_groups(ages, "fives") age_groups(ages, split_at = "fives")
# split on children # split specifically for children
age_groups(ages, "children") age_groups(ages, "children")
# same:
age_groups(ages, c(1, 2, 4, 6, 13, 17))
# resistance of ciprofloxacine per age group # resistance of ciprofloxacine per age group
library(dplyr) library(dplyr)
@ -65,3 +67,5 @@ septic_patients \%>\%
\seealso{ \seealso{
age age
} }
\keyword{age}
\keyword{age_group}

8
man/ggplot_rsi.Rd
View File

@ -12,8 +12,8 @@
\usage{ \usage{
ggplot_rsi(data, position = NULL, x = "Antibiotic", ggplot_rsi(data, position = NULL, x = "Antibiotic",
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1), fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
translate_ab = "official", fun = count_df, nrow = NULL, limits = NULL, translate_ab = "official", fun = count_df,
datalabels = TRUE, datalabels.size = 3, nrow = NULL, datalabels = TRUE, datalabels.size = 3,
datalabels.colour = "grey15", ...) datalabels.colour = "grey15", ...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"), 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) 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() scale_rsi_colours()
@ -44,6 +44,8 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
\item{breaks}{numeric vector of positions} \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{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}}} \item{fun}{function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}}

2
man/read.4D.Rd
View File

@ -117,7 +117,7 @@ read.4D(file, info = interactive(), header = TRUE, row.names = NULL,
} }
} }
\description{ \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{ \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. 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.

18
tests/testthat.R
View File

@ -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(testthat)
library(AMR) library(AMR)

18
tests/testthat/test-ab_property.R
View File

@ -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") context("ab_property.R")
test_that("ab_property works", { test_that("ab_property works", {

18
tests/testthat/test-abname.R
View File

@ -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") context("abname.R")
test_that("abname works", { test_that("abname works", {

30
tests/testthat/test-age.R
View File

@ -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", { test_that("age works", {
expect_equal(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"), expect_equal(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
@ -22,8 +40,16 @@ test_that("age_groups works", {
2) 2)
expect_equal(length(unique(age_groups(ages, c(50, 60)))), expect_equal(length(unique(age_groups(ages, c(50, 60)))),
3) 3)
expect_identical(class(age_groups(ages)), expect_identical(class(age_groups(ages, "child")),
c("ordered", "factor")) 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"))
}) })

18
tests/testthat/test-atc.R
View File

@ -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") context("atc.R")
# test_that("atc_property works", { # test_that("atc_property works", {

18
tests/testthat/test-count.R
View File

@ -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") context("count.R")
test_that("counts work", { test_that("counts work", {

18
tests/testthat/test-data.R
View File

@ -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") context("data.R")
test_that("data sets are valid", { test_that("data sets are valid", {

18
tests/testthat/test-deprecated.R
View File

@ -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") context("deprecated.R")
test_that("deprecated functions work", { test_that("deprecated functions work", {

18
tests/testthat/test-eucast_rules.R
View File

@ -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") context("eucast_rules.R")
test_that("EUCAST rules work", { test_that("EUCAST rules work", {

18
tests/testthat/test-first_isolate.R
View File

@ -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") context("first_isolate.R")
test_that("first isolates work", { test_that("first isolates work", {

18
tests/testthat/test-freq.R
View File

@ -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") context("freq.R")
test_that("frequency table works", { test_that("frequency table works", {

18
tests/testthat/test-g.test.R
View File

@ -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") context("g.test.R")
test_that("G-test works", { test_that("G-test works", {

18
tests/testthat/test-get_locale.R
View File

@ -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") context("get_locale.R")
test_that("get_locale works", { test_that("get_locale works", {

18
tests/testthat/test-ggplot_rsi.R
View File

@ -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") context("ggplot_rsi.R")
test_that("ggplot_rsi works", { test_that("ggplot_rsi works", {

18
tests/testthat/test-join_microorganisms.R
View File

@ -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") context("join_microorganisms.R")
test_that("joins work", { test_that("joins work", {

18
tests/testthat/test-key_antibiotics.R
View File

@ -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") context("key_antibiotics.R")
test_that("keyantibiotics work", { test_that("keyantibiotics work", {

18
tests/testthat/test-kurtosis.R
View File

@ -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") context("kurtosis.R")
test_that("kurtosis works", { test_that("kurtosis works", {

18
tests/testthat/test-like.R
View File

@ -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") context("like.R")
test_that("`like` works", { test_that("`like` works", {

19
tests/testthat/test-mdro.R
View File

@ -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", { test_that("mdro works", {
library(dplyr) library(dplyr)

18
tests/testthat/test-mic.R
View File

@ -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") context("mic.R")
test_that("mic works", { test_that("mic works", {

18
tests/testthat/test-misc.R
View File

@ -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") context("misc.R")
test_that("percentages works", { test_that("percentages works", {

18
tests/testthat/test-mo.R
View File

@ -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") context("mo.R")
test_that("as.mo works", { test_that("as.mo works", {

18
tests/testthat/test-mo_property.R
View File

@ -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") context("mo_property.R")
test_that("mo_property works", { test_that("mo_property works", {

18
tests/testthat/test-p.symbol.R
View File

@ -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") context("p.symbol.R")
test_that("P symbol works", { test_that("P symbol works", {

18
tests/testthat/test-portion.R
View File

@ -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") context("portion.R")
test_that("portions works", { test_that("portions works", {

18
tests/testthat/test-read.4d.R
View File

@ -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") context("read.4d.R")
test_that("read 4D works", { test_that("read 4D works", {

18
tests/testthat/test-rsi.R
View File

@ -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") context("rsi.R")
test_that("rsi works", { test_that("rsi works", {

18
tests/testthat/test-skewness.R
View File

@ -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") context("skewness.R")
test_that("skewness works", { test_that("skewness works", {