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#' Plotting method for \code{fitTK} objects
#'
#' This is the generic \code{plot} S3 method for the
#' \code{fitTK}. It plots the fit obtained for each
#' variable in the original dataset.
#'
#' @param x And object returned by fitTK
#' @param time_interp A vector with additional time point to interpolate.
#' Time point of the original data set are conserved.
#' @param \dots Additional arguments
#'
#' @return a plot of class \code{ggplot}
#'
#' @export
#'
#' @import ggplot2
#'
plot.fitTK <- function(x, time_interp = NULL, ...){
if(is.null(time_interp)){
fit <- x
df <- .df_for_plot(fit)
# HACK TO BE > 0
df$q50 <- ifelse(df$q50<0,0,df$q50)
df$qinf95 <- ifelse(df$qinf95<0,0,df$qinf95)
df$qsup95 <- ifelse(df$qsup95<0,0,df$qsup95)
plt <- ggplot(data = df) +
theme_classic() +
labs(x = "Time", y = "Concentration") +
# scale_y_continuous(limits = c(0,NA)) +
geom_ribbon(
aes_string(x = 'time', ymin = 'qinf95', ymax = 'qsup95'), fill = "grey80") +
geom_line(aes_string(x = 'time', y = 'q50'), color = "orange") +
geom_point(aes_string(x = 'time', y = 'observation' )) +
facet_wrap(~variable, scales = "free")
return(plt)
} else{
object <- x
data <- x$stanTKdata$origin_data
predict_TKstan <- predict_stan(object, data, time_interp = time_interp, ...)
plt <- plot(predict_TKstan, add_data = TRUE)
return(plt)
}
}
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