Nothing
#' IsothermalGrowth class
#'
#' @description
#' `r lifecycle::badge("superseded")`
#'
#' The class [IsothermalGrowth] has been superseded by the top-level
#' class [GrowthPrediction], which provides a unified approach for growth modelling.
#'
#' Still, it is still returned if the superseded [predict_isothermal_growth()] is called.
#'
#' It is a subclass of list with the items:
#' \itemize{
#' \item simulation: A tibble with the model simulation.
#' \item model: The name of the model used for the predictions.
#' \item pars: A list with the values of the model parameters.
#' }
#'
#' @name IsothermalGrowth
#'
NULL
#' @describeIn IsothermalGrowth print of the model
#'
#' @param x An instance of `IsothermalGrowth`.
#' @param ... ignored
#'
#' @export
#'
print.IsothermalGrowth <- function(x, ...) {
cat("Growth prediction based on primary models\n\n")
cat(paste("Growth model:", x$model, "\n\n"))
cat("Parameters of the primary model:\n")
print(unlist(x$pars))
logbase <- x$logbase_mu
if ( abs(logbase - exp(1)) < .1 ) {
logbase <- "e"
}
cat("\n")
cat(paste0("Parameter mu defined in log-", logbase, " scale"))
}
#' @describeIn IsothermalGrowth plot of the predicted growth curve.
#'
#' @param x The object of class [IsothermalGrowth] to plot.
#' @param y ignored
#' @param ... ignored.
#' @param line_col Aesthetic parameter to change the colour of the line,
#' see: [geom_line()]
#' @param line_size Aesthetic parameter to change the thickness of the line,
#' see: [geom_line()]
#' @param line_type Aesthetic parameter to change the type of the line,
#' takes numbers (1-6) or strings ("solid") see: [geom_line()]
#' @param label_x Title of the x-axis
#' @param label_y Title of the y-axis
#' @param ylims Two-dimensional numeric vector with the limits of the y-axis
#' (or `NULL`, which is the default)
#'
#' @export
#'
#' @importFrom ggplot2 ggplot geom_line
#' @importFrom rlang .data
#' @importFrom cowplot theme_cowplot
#'
plot.IsothermalGrowth <- function(x, y=NULL, ...,
line_col = "black",
line_size = 1,
line_type = "solid",
ylims = NULL,
label_y = NULL,
label_x = "time") {
ggplot(x$simulation) +
geom_line(aes(x = .data$time, y = .data$logN),
col = line_col,
size = line_size,
linetype = line_type) +
scale_y_continuous(limits = ylims,
name = label_y) +
xlab(label_x) +
theme_cowplot()
}
#' @describeIn IsothermalGrowth coefficients of the model
#'
#' @param object an instance of [IsothermalGrowth]
#' @param ... ignored
#'
#' @export
#'
coef.IsothermalGrowth <- function(object, ...) {
unlist(object$pars)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.