From 3d6b4b4b8293a4a4ab6f06805e1380600373796c Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 18 Oct 2017 11:18:07 +0200
Subject: Version 2.0

---
 CakeOlsFit.R | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

(limited to 'CakeOlsFit.R')

diff --git a/CakeOlsFit.R b/CakeOlsFit.R
index 75ac471..626a595 100644
--- a/CakeOlsFit.R
+++ b/CakeOlsFit.R
@@ -7,11 +7,11 @@
 # from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn
 # inspired by summary.nls.lm
 
-#$Id: CakeOlsFit.R 216 2011-07-05 14:35:03Z nelr $
+#$Id$
 # This version has been modified to expect SFO parameterised as k and flow fractions
 # Modifications developed by Tessella Plc for Syngenta: Copyright (C) 2011  Syngenta
-# Authors: Rob Nelson, Richard Smith
-# Tessella Project Reference: 6245
+# Authors: Rob Nelson, Richard Smith, Tamar Christina
+# Tessella Project Reference: 6245, 7247
 
 #    This program is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
@@ -36,6 +36,8 @@ CakeOlsFit <- function(mkinmod, observed,
   plot = FALSE, quiet = FALSE,
   err = NULL, weight = "none", scaleVar = FALSE,
   atol = 1e-6,
+  sannMaxIter = 10000,
+  useSolnp = FALSE, method='L-BFGS-B',
   ...)
 {
   mod_vars <- names(mkinmod$diffs)
@@ -294,20 +296,23 @@ CakeOlsFit <- function(mkinmod, observed,
   fit$fixed$type = c(rep("state", length(state.ini.fixed)), rep("deparm", length(parms.fixed)))
 
 #  # Calculate chi2 error levels according to FOCUS (2006)
-  fit$errmin <- CakeChi2(observed, predicted_long, obs_vars, parms.optim, state.ini.optim)
+  fit$errmin <- CakeChi2(mkinmod, observed, predicted_long, obs_vars, parms.optim, state.ini.optim, state.ini, parms.ini)
 
   # Calculate dissipation times DT50 and DT90 and formation fractions
   parms.all = c(fit$par, parms.fixed)
   fit$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)), DT90 = rep(NA, length(obs_vars)), 
     row.names = obs_vars)
+  fit$extraDT50<- data.frame(DT50 = rep(NA, 2), row.names = c("k1", "k2"))   
+        
   fit$ff <- vector()
   fit$SFORB <- vector()
   for (obs_var in obs_vars) {
     type = names(mkinmod$map[[obs_var]])[1]  
 
-    fit$distimes[obs_var, ] = CakeDT(type,obs_var,parms.all)
+    fit$distimes[obs_var, ] = CakeDT(type,obs_var,parms.all,sannMaxIter)
   }
 
+  fit$extraDT50[ ,c("DT50")] = CakeExtraDT(type,parms.all)  
   fit$penalties <- CakePenaltiesLong(parms.all, out_predicted, observed)
   
   # Collect observed, predicted and residuals
-- 
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