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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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12
R/resistance_predict.R
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@ -44,7 +44,7 @@
#' @param main title of the plot
#' @param ribbon a [logical] to indicate whether a ribbon should be shown (default) or error bars
#' @param ... arguments passed on to functions
#' @inheritSection as.rsi Interpretation of R and S/I
#' @inheritSection as.sir Interpretation of SIR
#' @inheritParams first_isolate
#' @inheritParams graphics::plot
#' @details Valid options for the statistical model (argument `model`) are:
@ -76,7 +76,7 @@
#' plot(x)
#' \donttest{
#' if (require("ggplot2")) {
#' ggplot_rsi_predict(x)
#' ggplot_sir_predict(x)
#' }
#'
#' # using dplyr:
@ -156,7 +156,7 @@ resistance_predict <- function(x,
}
df <- x
df[, col_ab] <- droplevels(as.rsi(df[, col_ab, drop = TRUE]))
df[, col_ab] <- droplevels(as.sir(df[, col_ab, drop = TRUE]))
if (I_as_S == TRUE) {
# then I as S
df[, col_ab] <- gsub("I", "S", df[, col_ab, drop = TRUE], fixed = TRUE)
@ -286,7 +286,7 @@ resistance_predict <- function(x,
#' @rdname resistance_predict
#' @export
rsi_predict <- resistance_predict
sir_predict <- resistance_predict
#' @method plot resistance_predict
#' @export
@ -341,7 +341,7 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
#' @rdname resistance_predict
#' @export
ggplot_rsi_predict <- function(x,
ggplot_sir_predict <- function(x,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
...) {
@ -402,7 +402,7 @@ autoplot.resistance_predict <- function(object,
x_name <- paste0(ab_name(attributes(object)$ab), " (", attributes(object)$ab, ")")
meet_criteria(main, allow_class = "character", has_length = 1)
meet_criteria(ribbon, allow_class = "logical", has_length = 1)
ggplot_rsi_predict(x = object, main = main, ribbon = ribbon, ...)
ggplot_sir_predict(x = object, main = main, ribbon = ribbon, ...)
}
#' @method fortify resistance_predict