R/mkinparplot.R

In mkin: Kinetic Evaluation of Chemical Degradation Data

#' Function to plot the confidence intervals obtained using mkinfit
#' 
#' This function plots the confidence intervals for the parameters fitted using
#' \code{\link{mkinfit}}.
#' 
#' @param object A fit represented in an \code{\link{mkinfit}} object.
#' @return Nothing is returned by this function, as it is called for its side
#'   effect, namely to produce a plot.
#' @author Johannes Ranke
#' @examples
#' 
#' \dontrun{
#' model <- mkinmod(
#'   T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE),
#'   phenol = mkinsub("SFO", to = c("anisole")),
#'   anisole = mkinsub("SFO"), use_of_ff = "max")
#' fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#' mkinparplot(fit)
#' }
#' @export
mkinparplot <- function(object) {
  state.optim = rownames(subset(object$start, type == "state"))
  deparms.optim = rownames(subset(object$start, type == "deparm"))
  fractions.optim = grep("^f_", deparms.optim, value = TRUE)
  N.optim = grep("^N_", deparms.optim, value = TRUE)
  if ("g" %in% deparms.optim) fractions.optim <- c("g", fractions.optim)
  rates.optim.unsorted = setdiff(deparms.optim, union(fractions.optim, N.optim))
  rates.optim <- rownames(object$start[rates.optim.unsorted, ])
  n.plot <- c(state.optim = length(state.optim),
              rates.optim = length(rates.optim),
	      N.optim = length(N.optim),
              fractions.optim = length(fractions.optim))
  n.plot <- n.plot[n.plot > 0]

  oldpar <- par(no.readonly = TRUE)
  on.exit(par(oldpar, no.readonly = TRUE))
  layout(matrix(1:length(n.plot), ncol = 1), heights = n.plot + 1)

  s <- summary(object)
  bpar <- data.frame(t(s$bpar[, c("Estimate", "Lower", "Upper")]))
  par(mar = c(2.1, 2.1, 0.1, 2.1))
  par(cex = 1)
  for (type in names(n.plot)) {
    parnames <- get(type)
    values <- bpar[parnames]
    values_with_confints <- data.frame(t(subset(data.frame(t(values)), !is.na("Lower"))))
    xlim = switch(type,
                  state.optim = range(c(0, unlist(values)),
                                      na.rm = TRUE, finite = TRUE),
                  rates.optim = range(c(0, unlist(values)),
                                      na.rm = TRUE, finite = TRUE),
                  N.optim = range(c(0, 1, unlist(values)),
                                      na.rm = TRUE, finite = TRUE),
                  fractions.optim = range(c(0, 1, unlist(values)),
                                          na.rm = TRUE, finite = TRUE))
    parname_index <- length(parnames):1 # Reverse order for strip chart

    stripchart(values["Estimate", ][parname_index],
               xlim = xlim,
               ylim = c(0.5, length(get(type)) + 0.5),
               yaxt = "n")
    if (type %in% c("rates.optim", "fractions.optim")) abline(v = 0, lty = 2)
    if (type %in% c("N.optim", "fractions.optim")) abline(v = 1, lty = 2)
    position <- ifelse(values["Estimate", ] < mean(xlim), "right", "left")
    text(ifelse(position == "left", min(xlim), max(xlim)),
         parname_index, parnames,
         pos = ifelse(position == "left", 4, 2))

    values.upper.nonInf <- ifelse(values["Upper", ] == Inf, 1.5 * xlim[[2]], values["Upper", ])
    # Suppress warnings for non-existing arrow lengths
    suppressWarnings(arrows(as.numeric(values["Lower", ]), parname_index,
	   as.numeric(values.upper.nonInf), parname_index,
	   code = 3, angle = 90, length = 0.05))
  }
}