R/plot_fit.R

In rbioacc: Inference and Prediction of ToxicoKinetic (TK) Models

#' 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)
  }
}