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limits for scale_y_percent - Licence update

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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
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6
R/ab_property.R
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@ -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
R/abname.R
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@ -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
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@ -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
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@ -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
R/count.R
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@ -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
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@ -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
R/deprecated.R
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@ -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
R/eucast_rules.R
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@ -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
R/first_isolate.R
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@ -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
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@ -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
R/g.test.R
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@ -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
R/get_locale.R
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@ -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

15
R/ggplot_rsi.R
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@ -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
R/globals.R
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@ -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(".",

18
R/join_microorganisms.R
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@ -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
R/key_antibiotics.R
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
R/mo_property.R
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@ -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
R/p.symbol.R
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@ -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
R/portion.R
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@ -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
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@ -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
R/resistance_predict.R
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@ -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
View File

@ -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
R/rsi_calc.R
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@ -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
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@ -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
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@ -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: