Make it possible to use different ode solvers

5 files changed, 47 insertions, 16 deletions

diff --git a/GNUmakefile b/GNUmakefile
index 255b97f3..cf5c845e 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -19,9 +19,13 @@ help:
 	@echo "  build                   Create the package"
 	@echo "  build-no-vignettes      Create the package without rebuilding vignettes"
 	@echo "  check                   Invoke build and then check the package"
+	@echo "  check-no-vignettes      Invoke build without rebuilding vignettes, and then check"
 	@echo "  install                 Invoke build and then install the result"
+	@echo "  install                 Invoke build without rebuilding vignettes and then install the result"
 	@echo "  test                    Install a new copy of the package and run it "
 	@echo "                          through the testsuite"
+	@echo "  test-no-vignettes       Invoke build without rebuilding vignettes, and then run it"
+	@echo "                          through the testsuite"
 	@echo ""
 	@echo "Packaging Tasks"
 	@echo "---------------"
@@ -44,15 +48,27 @@ build-no-vignettes:
 	cd ..;\
 		"$(RBIN)/R" CMD build $(PKGSRC) --no-build-vignettes
 
-install%: build%
+install: build
 	cd ..;\
 		"$(RBIN)/R" CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
 
-check%: build%
+install-no-vignettes: build-no-vignettes
+	cd ..;\
+		"$(RBIN)/R" CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
+
+check: build
+	cd ..;\
+		"$(RBIN)/R" CMD check --as-cran --no-tests $(PKGNAME)_$(PKGVERS).tar.gz
+
+check-no-vignettes: build-no-vignettes
 	cd ..;\
 		"$(RBIN)/R" CMD check --as-cran --no-tests $(PKGNAME)_$(PKGVERS).tar.gz
 
-test%: install%
+test: install
+	cd tests;\
+		"$(RBIN)/Rscript" doRUnit.R
+
+test-no-vignettes: install-no-vignettes
 	cd tests;\
 		"$(RBIN)/Rscript" doRUnit.R
 
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 3e47479f..749d7485 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -1,5 +1,3 @@
-# $Id$

-

 # Copyright (C) 2010-2013 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/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$diffs)
@@ -96,6 +97,7 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de
       times = outtimes,
       func = mkindiff, 
       parms = odeparms,
+      method = method.ode,
       atol = atol,
       rtol = rtol,
       ...
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 51e26ed5..0c5d76a9 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -20,6 +20,7 @@ mkinfit(mkinmod, observed,
   state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), 
   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, err = NULL, weight = "none", 
@@ -85,6 +86,11 @@ mkinfit(mkinmod, observed,
     dependence of degradation rates and metabolites). This argument is passed
     on to the helper function \code{\link{mkinpredict}}.
   }
+  \item{method.ode}{
+    The solution method passed via \code{\link{mkinpredict}} to
+    \code{\link{ode}} in case the solution type is "deSolve". The default
+    "lsoda" is performant, but sometimes fails to converge.
+  }
   \item{method.modFit}{
     The optimisation method passed to \code{\link{modFit}}. The default "Marq"
     is the Levenberg Marquardt algorithm \code{\link{nls.lm}} from the package
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index afb57e0b..97db90e3 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -10,7 +10,7 @@
 }
 \usage{
   mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
-	      map_output = TRUE, atol = 1e-08, rtol = 1e-10, ...)
+	      method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)
 }
 \arguments{
   \item{mkinmod}{
@@ -33,12 +33,13 @@
     The method that should be used for producing the predictions. This should
     generally be "analytical" if there is only one observed variable, and
     usually "deSolve" in the case of several observed variables. The third
-    possibility "eigen" is faster but produces results that the author believes
-    to be less accurate.
+    possibility "eigen" is faster but not applicable to some models e.g.
+    using FOMC for the parent compound.
   }
-  \item{map_output}{
-    Boolean to specify if the output should list values for the observed
-    variables (default) or for all state variables (if set to FALSE). 
+  \item{method.ode}{
+    The solution method passed via \code{\link{mkinpredict}} to
+    \code{\link{ode}} in case the solution type is "deSolve". The default
+    "lsoda" is performant, but sometimes fails to converge.
   }
   \item{atol}{
     Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
@@ -48,6 +49,10 @@
     Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10,
     much lower than in \code{\link{lsoda}}.
   }
+  \item{map_output}{
+    Boolean to specify if the output should list values for the observed
+    variables (default) or for all state variables (if set to FALSE). 
+  }
   \item{\dots}{
     Further arguments passed to the ode solver in case such a solver is used.
   }