#' 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))
}
}
