# Copyright (C) 2014 Johannes Ranke
# Contact: jranke@uni-bremen.de

# This file is part of the R package mkin

# mkin is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.

# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
# details.

# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
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)
  if ("g" %in% deparms.optim) fractions.optim <- c("g", fractions.optim)
  rates.optim = setdiff(deparms.optim, fractions.optim)
  n.plot <- c(state.optim = length(state.optim), 
              rates.optim = length(rates.optim), 
              fractions.optim = length(fractions.optim))
  n.plot <- n.plot[n.plot > 0]

  layout(matrix(1:length(n.plot), ncol = 1), heights = n.plot + 1)

  s <- summary(object)
  bpar <- data.frame(t(s$bpar))
  oldpars <- par(no.readonly = TRUE)
  par(mar = c(2.1, 2.1, 0.1, 2.1))
  for (type in names(n.plot)) {
    parnames <- get(type)
    values <- bpar[parnames]
    xlim = switch(type,
                  state.optim = range(c(0, unlist(values)), 
                                      na.rm = TRUE, finite = TRUE),
                  rates.optim = range(unlist(values), 
                                      na.rm = TRUE, finite = TRUE),
                  fractions.optim = range(c(0, 1, unlist(values)), 
                                          na.rm = TRUE, finite = TRUE))
    stripchart(bpar[get(type)], xlim = xlim,
               yaxt = "n", ylim = c(0.5, length(get(type)) + 0.5))
    text(mean(xlim), 1:length(parnames), parnames, pos = 3, offset = 1)
    arrows(as.numeric(values["Lower", ]), 1:length(parnames), 
           as.numeric(values["Upper", ]), 1:length(parnames), 
           code = 3, angle = 90, length = 0.1)
  }
  par(oldpars)
}