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quasiquotation, alpha for geom_rsi

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dr. M.S. (Matthijs) Berends
2018-08-23 00:40:36 +02:00
parent 43ba16f8ed
commit da5379c881
18 changed files with 304 additions and 235 deletions
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41
R/count.R
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@ -18,7 +18,7 @@
#' Count isolates
#'
#' @description These functions can be used to count resistant/susceptible microbial isolates. All functions can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
#' @description These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
#'
#' \code{count_R} and \code{count_IR} can be used to count resistant isolates, \code{count_S} and \code{count_SI} can be used to count susceptible isolates.\cr
#' @inheritParams portion
@ -87,11 +87,9 @@
#' group_by(hospital_id) %>%
#' count_df(translate = FALSE)
#'
count_R <- function(ab1,
ab2 = NULL) {
rsi_calc(type = "R",
ab1 = ab1,
ab2 = ab2,
count_R <- function(...) {
rsi_calc(...,
type = "R",
include_I = FALSE,
minimum = 0,
as_percent = FALSE,
@ -100,11 +98,9 @@ count_R <- function(ab1,
#' @rdname count
#' @export
count_IR <- function(ab1,
ab2 = NULL) {
rsi_calc(type = "R",
ab1 = ab1,
ab2 = ab2,
count_IR <- function(...) {
rsi_calc(...,
type = "R",
include_I = TRUE,
minimum = 0,
as_percent = FALSE,
@ -113,10 +109,9 @@ count_IR <- function(ab1,
#' @rdname count
#' @export
count_I <- function(ab1) {
rsi_calc(type = "I",
ab1 = ab1,
ab2 = NULL,
count_I <- function(...) {
rsi_calc(...,
type = "I",
include_I = FALSE,
minimum = 0,
as_percent = FALSE,
@ -125,11 +120,9 @@ count_I <- function(ab1) {
#' @rdname count
#' @export
count_SI <- function(ab1,
ab2 = NULL) {
rsi_calc(type = "S",
ab1 = ab1,
ab2 = ab2,
count_SI <- function(...) {
rsi_calc(...,
type = "S",
include_I = TRUE,
minimum = 0,
as_percent = FALSE,
@ -138,11 +131,9 @@ count_SI <- function(ab1,
#' @rdname count
#' @export
count_S <- function(ab1,
ab2 = NULL) {
rsi_calc(type = "S",
ab1 = ab1,
ab2 = ab2,
count_S <- function(...) {
rsi_calc(...,
type = "S",
include_I = FALSE,
minimum = 0,
as_percent = FALSE,