Merge branch 'master' of https://github.com/jranke/mkin

Conflicts:
	DESCRIPTION
	R/mkinfit.R

3 files changed, 13 insertions, 20 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index fd536277..6c976a37 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -1,5 +1,3 @@
-# $Id$

-

 # Copyright (C) 2010-2014 Johannes Ranke

 # Contact: jranke@uni-bremen.de

 # The summary function is an adapted and extended version of summary.modFit

@@ -28,6 +26,7 @@ mkinfit <- function(mkinmod, observed,
   fixed_parms = NULL,

   fixed_initials = names(mkinmod$diffs)[-1],

   solution_type = "auto",

+  method.ode = "lsoda",

   method.modFit = "Marq",

   control.modFit = list(),

   plot = FALSE, quiet = FALSE,

@@ -161,6 +160,7 @@ mkinfit <- function(mkinmod, observed,
     # Solve the system with current transformed parameter values

     out <- mkinpredict(mkinmod, parms, odeini, outtimes, 

                        solution_type = solution_type, 

+                       method.ode = method.ode,

                        atol = atol, rtol = rtol, ...)

 

     assign("out_predicted", out, inherits=TRUE)

@@ -177,7 +177,9 @@ mkinfit <- function(mkinmod, observed,
         outtimes_plot = seq(min(observed$time), max(observed$time), length.out=100)

 

         out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 

-          solution_type = solution_type, atol = atol, rtol = rtol, ...)

+                                solution_type = solution_type, 

+                                method.ode = method.ode,

+                                atol = atol, rtol = rtol, ...)

 

         plot(0, type="n", 

           xlim = range(observed$time), ylim = range(observed$value, na.rm=TRUE),

diff --git a/R/mkinmod.R b/R/mkinmod.R
index c743777b..2bc6ae35 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -1,6 +1,4 @@
-# $Id$

-

-# Copyright (C) 2010-2012 Johannes Ranke {{{

+# Copyright (C) 2010-2013 Johannes Ranke {{{

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -46,19 +44,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
   # fractions

   if(spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {

     mat = FALSE 

-    if(!is.null(spec[[1]]$to)) {

-      message <- paste(

-        "Only constant formation fractions over time are implemented.",

-        "Depending on the reason for the time dependence of degradation",

-        "this may be unrealistic. You may want to consider using the",

-        "SFORB model",

-        sep="\n")

-      warning(message)

-    } else message <- "ok"

   } else mat = TRUE

   #}}}

 

-  # Establish list of differential equations as well as map from observed {{{

+  # Establish a list of differential equations as well as a map from observed {{{

   # compartments to differential equations

   for (varname in obs_vars)

   {

diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index 7ce26caf..07c1a819 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -1,6 +1,4 @@
-# $Id$
-
-# Copyright (C) 2010-2012 Johannes Ranke
+# Copyright (C) 2010-2013 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -18,7 +16,10 @@
 # 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", map_output = TRUE, atol = 1e-8, rtol = 1e-10, ...) {
+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)
@@ -96,6 +97,7 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de
       times = outtimes,
       func = mkindiff, 
       parms = odeparms,
+      method = method.ode,
       atol = atol,
       rtol = rtol,
       ...