From e959fde98f95f3595e01490b67892678bbcd1b27 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 7 May 2014 14:47:28 +0200
Subject: Fork the gmkin GUI from mkin. See ChangeLog for details

---
 R/mkinpredict.R | 121 --------------------------------------------------------
 1 file changed, 121 deletions(-)
 delete mode 100644 R/mkinpredict.R

(limited to 'R/mkinpredict.R')

diff --git a/R/mkinpredict.R b/R/mkinpredict.R
deleted file mode 100644
index 14efc56..0000000
--- a/R/mkinpredict.R
+++ /dev/null
@@ -1,121 +0,0 @@
-# Copyright (C) 2010-2014 Johannes Ranke
-# Some lines in this code are copyright (C) 2013 Eurofins Regulatory AG
-# 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/>
-
-mkinpredict <- function(mkinmod, odeparms, odeini, 
-			outtimes, solution_type = "deSolve", 
-			method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
-			map_output = TRUE, ...) {
-
-  # Get the names of the state variables in the model
-  mod_vars <- names(mkinmod$diffs)
-
-  # Order the inital values for state variables if they are named
-  if (!is.null(names(odeini))) {
-    odeini <- odeini[mod_vars]
-  }
-
-  # Create function for evaluation of expressions with ode parameters and initial values
-  evalparse <- function(string)
-  {
-    eval(parse(text=string), as.list(c(odeparms, odeini)))
-  }
-
-  # Create a function calculating the differentials specified by the model
-  # if necessary
-  if (solution_type == "analytical") {
-    parent.type = names(mkinmod$map[[1]])[1]  
-    parent.name = names(mkinmod$diffs)[[1]]
-    o <- switch(parent.type,
-      SFO = SFO.solution(outtimes, 
-          evalparse(parent.name),
-          ifelse(mkinmod$use_of_ff == "min", 
-	    evalparse(paste("k", parent.name, "sink", sep="_")),
-	    evalparse(paste("k", parent.name, sep="_")))),
-      FOMC = FOMC.solution(outtimes,
-          evalparse(parent.name),
-          evalparse("alpha"), evalparse("beta")),
-      DFOP = DFOP.solution(outtimes,
-          evalparse(parent.name),
-          evalparse("k1"), evalparse("k2"),
-          evalparse("g")),
-      HS = HS.solution(outtimes,
-          evalparse(parent.name),
-          evalparse("k1"), evalparse("k2"),
-          evalparse("tb")),
-      SFORB = SFORB.solution(outtimes,
-          evalparse(parent.name),
-          evalparse(paste("k", parent.name, "bound", sep="_")),
-          evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")),
-          evalparse(paste("k", parent.name, "sink", sep="_")))
-    )
-    out <- data.frame(outtimes, o)
-    names(out) <- c("time", sub("_free", "", parent.name))
-  }
-  if (solution_type == "eigen") {
-    coefmat.num <- matrix(sapply(as.vector(mkinmod$coefmat), evalparse), 
-      nrow = length(mod_vars))
-    e <- eigen(coefmat.num)
-    c <- solve(e$vectors, odeini)
-    f.out <- function(t) {
-      e$vectors %*% diag(exp(e$values * t), nrow=length(mod_vars)) %*% c
-    }
-    o <- matrix(mapply(f.out, outtimes), 
-      nrow = length(mod_vars), ncol = length(outtimes))
-    out <- data.frame(outtimes, t(o))
-    names(out) <- c("time", mod_vars)
-  } 
-  if (solution_type == "deSolve") {
-    mkindiff <- function(t, state, parms) {
-
-      time <- t
-      diffs <- vector()
-      for (box in names(mkinmod$diffs))
-      {
-        diffname <- paste("d", box, sep="_")      
-        diffs[diffname] <- with(as.list(c(time, state, parms)),
-          eval(parse(text=mkinmod$diffs[[box]])))
-      }
-      return(list(c(diffs)))
-    } 
-    out <- ode(
-      y = odeini,
-      times = outtimes,
-      func = mkindiff, 
-      parms = odeparms,
-      method = method.ode,
-      atol = atol,
-      rtol = rtol,
-      ...
-    )
-  }
-  if (map_output) {
-    # Output transformation for models with unobserved compartments like SFORB
-    out_mapped <- data.frame(time = out[,"time"])
-    for (var in names(mkinmod$map)) {
-      if((length(mkinmod$map[[var]]) == 1) || solution_type == "analytical") {
-        out_mapped[var] <- out[, var]
-      } else {
-        out_mapped[var] <- rowSums(out[, mkinmod$map[[var]]])
-      }
-    }
-    return(out_mapped) 
-  } else {
-    return(out)
-  }
-}
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