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limits for scale_y_percent - Licence update
This commit is contained in:
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' Property of an antibiotic
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|
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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||||
# This program is free software; you can redistribute it and/or modify #
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# This package is free software; you can redistribute it and/or modify #
|
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' Name of an antibiotic
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58
R/age.R
58
R/age.R
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
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||||
# This package is free software; you can redistribute it and/or modify #
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||||
# it under the terms of the GNU General Public License version 2.0, #
|
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# This R package is distributed in the hope that it will be useful, #
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||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' Age in years of individuals
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@ -49,7 +49,7 @@ age <- function(x, y = Sys.Date()) {
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ages
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}
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#' Split ages in age groups
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#' Split ages into age groups
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#'
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#' Splits ages into groups defined by the \code{split} parameter.
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#' @param x age, e.g. calculated with \code{\link{age}}
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@ -61,33 +61,36 @@ age <- function(x, y = Sys.Date()) {
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#' \item{A character:}
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#' \itemize{
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#' \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+.}
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#' \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+.}
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#' \item{\code{"fives"}, equivalent: of \code{1:20 * 5}. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.}
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#' \item{\code{"tens"}, equivalent: of \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29 and so forth.}
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#' \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+.}
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#' \item{\code{"fives"}, equivalent of: \code{1:20 * 5}. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.}
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#' \item{\code{"tens"}, equivalent of: \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29 and so forth.}
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#' }
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#' }
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#' @keywords age_group age
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#' @return Ordered \code{\link{factor}}
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#' @seealso age
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#' @export
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#' @examples
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#' ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
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#'
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#' # split on 0-49 and 50+
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#' # split into 0-49 and 50+
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#' age_groups(ages, 50)
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#'
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#' # split on 0-20, 21-49 and 50+
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#' age_groups(ages, c(21, 50))
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#' # split into 0-19, 20-49 and 50+
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#' age_groups(ages, c(20, 50))
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#'
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#' # split on every ten years
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#' # split into groups of ten years
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#' age_groups(ages, 1:10 * 10)
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#' age_groups(ages, "tens")
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#' age_groups(ages, split_at = "tens")
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#'
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#' # split on every five years
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#' # split into groups of five years
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#' age_groups(ages, 1:20 * 5)
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#' age_groups(ages, "fives")
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#' age_groups(ages, split_at = "fives")
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#'
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#' # split on children
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#' # split specifically for children
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#' age_groups(ages, "children")
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#' # same:
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#' age_groups(ages, c(1, 2, 4, 6, 13, 17))
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#'
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#' # resistance of ciprofloxacine per age group
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#' library(dplyr)
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@ -101,20 +104,18 @@ age <- function(x, y = Sys.Date()) {
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#' ggplot_rsi(x = "age_group")
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age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
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if (is.character(split_at)) {
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split_at <- split_at[1]
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split_at <- split_at[1L]
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if (split_at %like% "^child") {
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split_at <- c(0, 1, 2, 4, 6, 13, 18)
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}
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if (split_at %like% "^elder" | split_at %like% "^senior") {
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} else if (split_at %like% "^(elder|senior)") {
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split_at <- c(65, 75, 85, 95)
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}
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if (split_at %like% "fives") {
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} else if (split_at %like% "^five") {
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split_at <- 1:20 * 5
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}
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if (split_at %like% "^tens") {
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} else if (split_at %like% "^ten") {
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split_at <- 1:10 * 10
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}
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}
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split_at <- as.integer(split_at)
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if (!is.numeric(x) | !is.numeric(split_at)) {
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stop("`x` and `split_at` must both be numeric.")
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}
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@ -129,19 +130,14 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
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# turn input values to 'split_at' indices
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y <- x
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labs <- split_at
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for (i in 1:length(split_at)) {
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y[x >= split_at[i]] <- i
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# create labels
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# when age group consists of only one age
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labs[i - 1] <- paste0(unique(c(split_at[i - 1], split_at[i] - 1)), collapse = "-")
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}
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# create labels
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labs <- split_at
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for (i in 2:length(labs)) {
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if (split_at[i - 1] == split_at[i] - 1) {
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labs[i - 1] <- split_at[i - 1]
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} else {
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labs[i - 1] <- paste0(split_at[i - 1], "-", split_at[i] - 1)
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}
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}
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# last category
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labs[length(labs)] <- paste0(split_at[length(split_at)], "+")
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6
R/atc.R
6
R/atc.R
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
|
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# This program is free software; you can redistribute it and/or modify #
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# This package is free software; you can redistribute it and/or modify #
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||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
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||||
# This program is distributed in the hope that it will be useful, #
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||||
# 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. #
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# ==================================================================== #
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|
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
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||||
# This package is free software; you can redistribute it and/or modify #
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||||
# it under the terms of the GNU General Public License version 2.0, #
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||||
# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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||||
# This R package is distributed in the hope that it will be useful, #
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||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' Count isolates
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6
R/data.R
6
R/data.R
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
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||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
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||||
# #
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||||
# This program is distributed in the hope that it will be useful, #
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||||
# 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 #
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||||
# GNU General Public License for more details. #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' Data set with 423 antibiotics
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@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
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||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
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# #
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||||
# This program is distributed in the hope that it will be useful, #
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||||
# 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 #
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# GNU General Public License for more details. #
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||||
# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' Deprecated functions
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|
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
|
||||
# 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. #
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# #
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||||
# This program is distributed in the hope that it will be useful, #
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||||
# 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 #
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# GNU General Public License for more details. #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' EUCAST rules
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|
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
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# #
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# LICENCE #
|
||||
# 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. #
|
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# #
|
||||
# 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. #
|
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' Determine first (weighted) isolates
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|
6
R/freq.R
6
R/freq.R
@ -6,14 +6,14 @@
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
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# #
|
||||
# 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. #
|
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# ==================================================================== #
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#' Frequency table
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|
@ -6,14 +6,14 @@
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# 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. #
|
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# ==================================================================== #
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#' \emph{G}-test for Count Data
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@ -6,14 +6,14 @@
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# 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
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|
@ -6,14 +6,14 @@
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# 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}
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@ -24,6 +24,7 @@
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#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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#' @param breaks numeric vector of positions
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#' @param limits numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum
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#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
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#' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.
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#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
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@ -150,6 +151,7 @@ ggplot_rsi <- function(data,
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# params = list(),
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facet = NULL,
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breaks = seq(0, 1, 0.1),
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limits = NULL,
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translate_ab = "official",
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fun = count_df,
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nrow = NULL,
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@ -203,7 +205,7 @@ ggplot_rsi <- function(data,
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if (fun_name == "portion_df"
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| (fun_name == "count_df" & position == "fill")) {
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# portions, so use y scale with percentage
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p <- p + scale_y_percent(breaks = breaks)
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p <- p + scale_y_percent(breaks = breaks, limits = limits)
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}
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if (fun_name == "count_df" & datalabels == TRUE) {
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@ -295,9 +297,10 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
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#' @rdname ggplot_rsi
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||||
#' @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,
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||||
labels = percent(breaks))
|
||||
labels = percent(breaks),
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||||
limits = limits)
|
||||
}
|
||||
|
||||
#' @rdname ggplot_rsi
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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(".",
|
||||
|
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Join a table with \code{microorganisms}
|
||||
#'
|
||||
#' Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Key antibiotics for first \emph{weighted} isolates
|
||||
|
18
R/kurtosis.R
18
R/kurtosis.R
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Kurtosis of the sample
|
||||
#'
|
||||
#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.
|
||||
|
6
R/like.R
6
R/like.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Pattern Matching
|
||||
|
6
R/mdro.R
6
R/mdro.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Determine multidrug-resistant organisms (MDRO)
|
||||
|
6
R/mic.R
6
R/mic.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Class 'mic'
|
||||
|
6
R/misc.R
6
R/misc.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
# No export, no Rd
|
||||
|
6
R/mo.R
6
R/mo.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Transform to microorganism ID
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Property of a microorganism
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Symbol of a p value
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Calculate resistance of isolates
|
||||
|
22
R/read.4d.R
22
R/read.4d.R
@ -6,19 +6,19 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Read data from 4D database
|
||||
#'
|
||||
#' This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
|
||||
#' This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
|
||||
#' @inheritParams utils::read.table
|
||||
#' @param info a logical to indicate whether info about the import should be printed, defaults to \code{TRUE} in interactive sessions
|
||||
#' @details Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.
|
||||
@ -59,7 +59,7 @@ read.4D <- function(file,
|
||||
fileEncoding = fileEncoding,
|
||||
encoding = encoding)
|
||||
|
||||
# helper functions
|
||||
# helper function for dates
|
||||
to_date_4D <- function(x) {
|
||||
date_regular <- as.Date(x, format = "%d-%m-%y")
|
||||
posixlt <- as.POSIXlt(date_regular)
|
||||
@ -68,16 +68,6 @@ read.4D <- function(file,
|
||||
posixlt[date_regular > Sys.Date() & !is.na(posixlt)]$year <- posixlt[date_regular > Sys.Date() & !is.na(posixlt)]$year - 100
|
||||
as.Date(posixlt)
|
||||
}
|
||||
to_age_4D <- function(from, to) {
|
||||
from_lt = as.POSIXlt(from)
|
||||
to_lt = as.POSIXlt(to)
|
||||
|
||||
age = to_lt$year - from_lt$year
|
||||
|
||||
ifelse(to_lt$mon < from_lt$mon |
|
||||
(to_lt$mon == from_lt$mon & to_lt$mday < from_lt$mday),
|
||||
age - 1, age)
|
||||
}
|
||||
|
||||
if (info == TRUE) {
|
||||
message("OK\nTransforming column names... ", appendLF = FALSE)
|
||||
@ -136,7 +126,7 @@ read.4D <- function(file,
|
||||
data_4D$date_received <- to_date_4D(data_4D$date_received)
|
||||
}
|
||||
if ("age" %in% colnames(data_4D)) {
|
||||
data_4D$age <- to_age_4D(data_4D$date_birth, data_4D$date_received)
|
||||
data_4D$age <- age(data_4D$date_birth, data_4D$date_received)
|
||||
}
|
||||
if ("gender" %in% colnames(data_4D)) {
|
||||
data_4D$gender[data_4D$gender == "V"] <- "F"
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Predict antimicrobial resistance
|
||||
|
6
R/rsi.R
6
R/rsi.R
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Class 'rsi'
|
||||
|
@ -6,14 +6,14 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all
|
||||
|
18
R/skewness.R
18
R/skewness.R
@ -1,3 +1,21 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# AUTHORS #
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Skewness of the sample
|
||||
#'
|
||||
#' @description Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
|
||||
|
8
R/zzz.R
8
R/zzz.R
@ -6,21 +6,21 @@
|
||||
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# LICENCE #
|
||||
# This program is free software; you can redistribute it and/or modify #
|
||||
# This package is free software; you can redistribute it and/or modify #
|
||||
# it under the terms of the GNU General Public License version 2.0, #
|
||||
# as published by the Free Software Foundation. #
|
||||
# #
|
||||
# This program is distributed in the hope that it will be useful, #
|
||||
# This R package is distributed in the hope that it will be useful, #
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
||||
# GNU General Public License for more details. #
|
||||
# GNU General Public License version 2.0 for more details. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' The \code{AMR} Package
|
||||
#'
|
||||
#' Welcome to the \code{AMR} package. This page gives some additional contact information about the authors.
|
||||
#' @details
|
||||
#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
|
||||
#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and ti work with antibiotic properties by using evidence-based methods.
|
||||
#'
|
||||
#' This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
|
||||
#' @section Authors:
|
||||
|
Reference in New Issue
Block a user