From noreply at r-forge.r-project.org  Tue Apr  2 12:50:23 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  2 Apr 2013 12:50:23 +0200 (CEST)
Subject: [Pomp-commits] r842 - pkg/pomp
Message-ID: <20130402105023.6EEF618490D@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-02 12:50:23 +0200 (Tue, 02 Apr 2013)
New Revision: 842

Modified:
   pkg/pomp/DESCRIPTION
Log:


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-03-26 11:51:33 UTC (rev 841)
+++ pkg/pomp/DESCRIPTION	2013-04-02 10:50:23 UTC (rev 842)
@@ -7,8 +7,8 @@
 Contributor: Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman, Simon N. Wood
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Author at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
-	  person(given=c("Edward","L."),family="Ionides",role=c("ctb")),
-	  person(given=c("Carles"),family="Breto",role=c("ctb")),
+	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
+	  person(given=c("Carles"),family="Breto",role=c("aut")),
 	  person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
 	  person(given=c("Matthew","J."),family="Ferrari",role=c("ctb")),
 	  person(given=c("Bruce","E."),family="Kendall",role=c("ctb")),


From noreply at r-forge.r-project.org  Tue Apr 16 15:51:47 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 16 Apr 2013 15:51:47 +0200 (CEST)
Subject: [Pomp-commits] r843 - branches
Message-ID: <20130416135147.BBE84185164@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-16 15:51:47 +0200 (Tue, 16 Apr 2013)
New Revision: 843

Added:
   branches/premif2/
Log:
- branch for updates needed but prior to release of mif2



From noreply at r-forge.r-project.org  Tue Apr 16 16:21:36 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 16 Apr 2013 16:21:36 +0200 (CEST)
Subject: [Pomp-commits] r844 - in pkg/pomp: src tests
Message-ID: <20130416142136.C6487185155@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-16 16:21:36 +0200 (Tue, 16 Apr 2013)
New Revision: 844

Modified:
   pkg/pomp/src/SSA.f
   pkg/pomp/tests/ou2-mif.Rout.save
Log:
- modify fortran code to eliminate (false positive) bounds violation error when -fbounds-check flag is given to gfortran.


Modified: pkg/pomp/src/SSA.f
===================================================================
--- pkg/pomp/src/SSA.f	2013-04-16 13:51:47 UTC (rev 843)
+++ pkg/pomp/src/SSA.f	2013-04-16 14:21:36 UTC (rev 844)
@@ -123,18 +123,20 @@
 c     
 c Recording output at required time points
 c     
-         do while((icount.le.ntimes).and.(t.ge.times(icount)))
-            do i=1,n
-               xout(i,irep,icount)=y(i)
-            enddo
+         if (icount.le.ntimes) then
+            do while((icount.le.ntimes).and.(t.ge.times(icount)))
+               do i=1,n
+                  xout(i,irep,icount)=y(i)
+               enddo
 c===============================
 c     Set appropriate states to zero
 c===============================
-            do i=1,nzero
-               y(izero(i)+1)=0.0d0
+               do i=1,nzero
+                  y(izero(i)+1)=0.0d0
+               enddo
+               icount=icount+1
             enddo
-            icount=icount+1
-         enddo
+         endif
 
          if((mcov.gt.0).and.(t.le.tmax))then
             call tlook(lcov,mcov,tcov,cov,t,covars)

Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save	2013-04-16 13:51:47 UTC (rev 843)
+++ pkg/pomp/tests/ou2-mif.Rout.save	2013-04-16 14:21:36 UTC (rev 844)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -87,7 +86,7 @@
 > plot(mif1)
 > compare.mif(mif2)
 > try(compare.mif(mif1,mif2))
-Error in compare.mif(mif1, mif2) : unused argument(s) (mif2)
+Error in compare.mif(mif1, mif2) : unused argument (mif2)
 > compare.mif(list(mif1,mif2))
 > dev.off()
 null device 
@@ -283,4 +282,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 11.384   0.072  11.591 
+ 12.416   0.084  12.654 


From noreply at r-forge.r-project.org  Tue Apr 16 16:48:29 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 16 Apr 2013 16:48:29 +0200 (CEST)
Subject: [Pomp-commits] r845 - branches/premif2
Message-ID: <20130416144829.D561E1848BE@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-16 16:48:28 +0200 (Tue, 16 Apr 2013)
New Revision: 845

Removed:
   branches/premif2/DESCRIPTION
   branches/premif2/NAMESPACE
   branches/premif2/R/
   branches/premif2/data/
   branches/premif2/demo/
   branches/premif2/inst/
   branches/premif2/man/
   branches/premif2/src/
   branches/premif2/tests/
Log:
- start over


Deleted: branches/premif2/DESCRIPTION
===================================================================
--- branches/premif2/DESCRIPTION	2013-04-16 14:21:36 UTC (rev 844)
+++ branches/premif2/DESCRIPTION	2013-04-16 14:48:28 UTC (rev 845)
@@ -1,25 +0,0 @@
-Package: pomp
-Type: Package
-Title: Statistical inference for partially observed Markov processes
-Version: 0.44-1
-Date: 2013-01-09
-Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
-Maintainer: Aaron A. King <kingaa at umich.edu>
-URL: http://pomp.r-forge.r-project.org
-Description: Inference methods for partially-observed Markov processes
-Depends: R(>= 2.14.1), stats, methods, graphics, mvtnorm, subplex, deSolve
-License: GPL(>= 2)
-LazyLoad: true
-LazyData: false
-BuildVignettes: no
-Collate: aaa.R authors.R version.R eulermultinom.R plugins.R 
-	 parmat.R slice-design.R profile-design.R sobol.R bsplines.R sannbox.R
-	 pomp-fun.R pomp-class.R pomp.R pomp-methods.R 
-	 rmeasure-pomp.R rprocess-pomp.R init-state-pomp.R dmeasure-pomp.R dprocess-pomp.R skeleton-pomp.R 
-	 simulate-pomp.R trajectory-pomp.R plot-pomp.R 
-	 pfilter.R pfilter-methods.R traj-match.R bsmc.R
-	 mif-class.R particles-mif.R mif.R mif-methods.R compare-mif.R 
- 	 pmcmc.R pmcmc-methods.R compare-pmcmc.R
- 	 nlf-funcs.R nlf-guts.R nlf-objfun.R nlf.R 
-	 probe.R probe-match.R basic-probes.R spect.R spect-match.R
-	 builder.R example.R

Deleted: branches/premif2/NAMESPACE
===================================================================
--- branches/premif2/NAMESPACE	2013-04-16 14:21:36 UTC (rev 844)
+++ branches/premif2/NAMESPACE	2013-04-16 14:48:28 UTC (rev 845)
@@ -1,97 +0,0 @@
-useDynLib(			
-          pomp,
-          get_pomp_fun,
-          bspline_basis,
-          periodic_bspline_basis,
-          bspline_basis_function,
-          systematic_resampling,
-          euler_model_simulator,
-          euler_model_density,
-          lookup_in_table,
-          SSA_simulator,
-          R_Euler_Multinom,D_Euler_Multinom,R_GammaWN,
-          pfilter_computations,
-          simulation_computations,
-          iterate_map,traj_transp_and_copy,
-          apply_probe_data,apply_probe_sim,
-          probe_marginal_setup,probe_marginal_solve,
-          probe_acf,probe_ccf,
-          probe_nlar,
-          synth_loglik,
-          pomp_desolve_setup,pomp_desolve_takedown,
-          pomp_vf_eval,
-          do_partrans,
-          do_rprocess,
-          do_dprocess,
-          do_rmeasure,
-          do_dmeasure,
-          do_skeleton,
-          do_init_state
-          )
-
-importFrom(graphics,plot)		
-importFrom(stats,simulate,time,coef,logLik,window)
-importFrom(mvtnorm,dmvnorm,rmvnorm)
-importFrom(subplex,subplex)
-importFrom(deSolve,ode)
-
-exportClasses(
-              pomp,
-              pfilterd.pomp,
-              mif,
-              pmcmc,
-              traj.matched.pomp,
-              probed.pomp,probe.matched.pomp,
-              spect.pomp,spect.matched.pomp
-              )
-
-exportMethods(
-              pomp,
-              plot,show,print,coerce,summary,logLik,window,"$",
-              dprocess,rprocess,rmeasure,dmeasure,init.state,skeleton,
-              data.array,obs,partrans,coef,"coef<-",time,"time<-",timezero,"timezero<-",
-              simulate,pfilter,
-              eff.sample.size,cond.logLik,
-              particles,mif,continue,states,trajectory,
-              pred.mean,pred.var,filter.mean,conv.rec,
-              bsmc,
-              pmcmc,dprior,
-              spect,probe,
-              probe.match,traj.match
-              )
-
-export(
-       as.data.frame.pomp,
-       reulermultinom,
-       deulermultinom,
-       rgammawn,
-       euler.sim,
-       discrete.time.sim,
-       onestep.sim,
-       onestep.dens,
-       gillespie.sim,
-       sobol,
-       sobolDesign,
-       sliceDesign,
-       profileDesign,
-       bspline.basis,
-       periodic.bspline.basis,
-       compare.mif,
-       nlf,
-       parmat,
-       probe.mean,
-       probe.median,
-       probe.var,
-       probe.sd,
-       probe.period,
-       probe.quantile,
-       probe.acf,
-       probe.ccf,
-       probe.nlar,
-       probe.marginal,
-       sannbox,
-       spect.match,
-       traj.match.objfun,
-       pompBuilder,
-       pompExample
-       )


From noreply at r-forge.r-project.org  Tue Apr 16 16:49:42 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 16 Apr 2013 16:49:42 +0200 (CEST)
Subject: [Pomp-commits] r846 - branches
Message-ID: <20130416144942.7540B1848BE@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-16 16:49:41 +0200 (Tue, 16 Apr 2013)
New Revision: 846

Removed:
   branches/premif2/
Log:
- start over



From noreply at r-forge.r-project.org  Tue Apr 16 16:50:36 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 16 Apr 2013 16:50:36 +0200 (CEST)
Subject: [Pomp-commits] r847 - branches
Message-ID: <20130416145036.4EFF81848BE@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-16 16:50:35 +0200 (Tue, 16 Apr 2013)
New Revision: 847

Added:
   branches/premif2/
Log:
- branch for needed changes that must precede the release of the 'mif2' version



From noreply at r-forge.r-project.org  Tue Apr 16 18:27:03 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 16 Apr 2013 18:27:03 +0200 (CEST)
Subject: [Pomp-commits] r848 - in branches/premif2: . R src tests
Message-ID: <20130416162704.040751851AE@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-16 18:27:02 +0200 (Tue, 16 Apr 2013)
New Revision: 848

Modified:
   branches/premif2/DESCRIPTION
   branches/premif2/R/authors.R
   branches/premif2/src/SSA.f
   branches/premif2/src/SSA_wrapper.c
   branches/premif2/src/blowfly.c
   branches/premif2/src/dprocess.c
   branches/premif2/src/partrans.c
   branches/premif2/src/pomp_fun.c
   branches/premif2/tests/bbs-trajmatch.Rout.save
   branches/premif2/tests/bbs.Rout.save
   branches/premif2/tests/blowflies.Rout.save
   branches/premif2/tests/dacca.Rout.save
   branches/premif2/tests/dimchecks.Rout.save
   branches/premif2/tests/fhn.Rout.save
   branches/premif2/tests/filtfail.Rout.save
   branches/premif2/tests/gillespie.Rout.save
   branches/premif2/tests/gompertz.Rout.save
   branches/premif2/tests/logistic.Rout.save
   branches/premif2/tests/ou2-bsmc.Rout.save
   branches/premif2/tests/ou2-forecast.Rout.save
   branches/premif2/tests/ou2-icfit.Rout.save
   branches/premif2/tests/ou2-kalman.Rout.save
   branches/premif2/tests/ou2-mif-fp.Rout.save
   branches/premif2/tests/ou2-mif.Rout.save
   branches/premif2/tests/ou2-nlf.Rout.save
   branches/premif2/tests/ou2-pmcmc.Rout.save
   branches/premif2/tests/ou2-probe.Rout.save
   branches/premif2/tests/ou2-procmeas.Rout.save
   branches/premif2/tests/ou2-simulate.Rout.save
   branches/premif2/tests/ou2-trajmatch.Rout.save
   branches/premif2/tests/partrans.Rout.save
   branches/premif2/tests/pfilter.Rout.save
   branches/premif2/tests/pomppomp.Rout.save
   branches/premif2/tests/ricker-bsmc.Rout.save
   branches/premif2/tests/ricker-probe.Rout.save
   branches/premif2/tests/ricker-spect.Rout.save
   branches/premif2/tests/ricker.Rout.save
   branches/premif2/tests/rw2.Rout.save
   branches/premif2/tests/sir.Rout.save
   branches/premif2/tests/skeleton.Rout.save
   branches/premif2/tests/steps.Rout.save
   branches/premif2/tests/synlik.Rout.save
   branches/premif2/tests/verhulst.Rout.save
Log:
- checkout revision 765, then merge changes in revisions 775, 780, 788, 816, 839, 844
- update author list
- modify fortran code to eliminate (false positive) bounds violation error when -fbounds-check flag is given to gfortran.
- fig bug in mif: non-constant Np was ignored
- cosmetic changes to code (indentation, etc.)
- more informative error message when pomp_fun handler fails
- update bibliography database



Modified: branches/premif2/DESCRIPTION
===================================================================
--- branches/premif2/DESCRIPTION	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/DESCRIPTION	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,10 +1,21 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.43-4
-Date: 2012-08-08
-Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
+Version: 0.43-8
+Date: 2013-04-16
+Author: Aaron A. King, Edward L. Ionides, Carles Breto
+Contributor: Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman, Simon N. Wood
 Maintainer: Aaron A. King <kingaa at umich.edu>
+Author at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
+	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
+	  person(given=c("Carles"),family="Breto",role=c("aut")),
+	  person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
+	  person(given=c("Matthew","J."),family="Ferrari",role=c("ctb")),
+	  person(given=c("Bruce","E."),family="Kendall",role=c("ctb")),
+	  person(given=c("Michael"),family="Lavine",role=c("ctb")),
+	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),
+	  person(given=c("Helen"),family="Wearing",role=c("ctb")),
+	  person(given=c("Simon","N."),family="Wood",role=c("ctb")))
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially-observed Markov processes
 Depends: R(>= 2.14.1), stats, methods, graphics, mvtnorm, subplex, deSolve

Modified: branches/premif2/R/authors.R
===================================================================
--- branches/premif2/R/authors.R	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/R/authors.R	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,9 +1,9 @@
 list(
      aak=person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
-     eli=person(given=c("Edward","L."),family="Ionides",role=c("aut"),email="ionides at umich.edu"),
-     cb=person(given=c("Carles"),family="Breto",role=c("aut")),
-     spe=person(given=c("Stephen","P."),family="Ellner",role=c("aut")),
-     bek=person(given=c("Bruce","E."),family="Kendall",role=c("aut")),
+     eli=person(given=c("Edward","L."),family="Ionides",role=c("ctb")),
+     cb=person(given=c("Carles"),family="Breto",role=c("ctb")),
+     spe=person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
+     bek=person(given=c("Bruce","E."),family="Kendall",role=c("ctb")),
      mf=person(given=c("Matthew","J."),family="Ferrari",role=c("ctb")),
      ml=person(given=c("Michael"),family="Lavine",role=c("ctb")),
      dcr=person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),

Modified: branches/premif2/src/SSA.f
===================================================================
--- branches/premif2/src/SSA.f	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/src/SSA.f	2013-04-16 16:27:02 UTC (rev 848)
@@ -123,18 +123,20 @@
 c     
 c Recording output at required time points
 c     
-         do while((icount.le.ntimes).and.(t.ge.times(icount)))
-            do i=1,n
-               xout(i,irep,icount)=y(i)
-            enddo
+         if (icount.le.ntimes) then
+            do while((icount.le.ntimes).and.(t.ge.times(icount)))
+               do i=1,n
+                  xout(i,irep,icount)=y(i)
+               enddo
 c===============================
 c     Set appropriate states to zero
 c===============================
-            do i=1,nzero
-               y(izero(i)+1)=0.0d0
+               do i=1,nzero
+                  y(izero(i)+1)=0.0d0
+               enddo
+               icount=icount+1
             enddo
-            icount=icount+1
-         enddo
+         endif
 
          if((mcov.gt.0).and.(t.le.tmax))then
             call tlook(lcov,mcov,tcov,cov,t,covars)

Modified: branches/premif2/src/SSA_wrapper.c
===================================================================
--- branches/premif2/src/SSA_wrapper.c	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/src/SSA_wrapper.c	2013-04-16 16:27:02 UTC (rev 848)
@@ -3,6 +3,10 @@
 #include "pomp_internal.h"
 #include <R_ext/Constants.h>
 
+typedef double (*_pomp_rxnrate) (const int *j, const double *t, const double *x, const double *p,
+			   int *stateindex, int *parindex, int *covarindex, 
+			   int *ncovar, double *covar);
+
 void F77_SUB(rndstart)(void) { GetRNGstate(); }
 void F77_SUB(rndend)(void) { PutRNGstate(); }
 double F77_SUB(unifrnd)(void) { return unif_rand(); }
@@ -11,7 +15,7 @@
 double F77_SUB(gammarnd)(double shape, double scale) { return rgamma(shape,scale); }
 void F77_SUB(multinomrnd)(int N, double *p, int ncat, int *ix) { rmultinom(N,p,ncat,ix); }
 
-void F77_NAME(driverssa)(void *fprob, int *nvar, int *nevent, int *npar, int *nreps, int *ntimes, 
+void F77_NAME(driverssa)(_pomp_rxnrate *fprob, int *nvar, int *nevent, int *npar, int *nreps, int *ntimes, 
 			 int *kflag, double *xstart, double *times, double *params, double *xout,
 			 double *e, double *v, double *d, int *nzero, int *izero, int *istate, 
 			 int *ipar, int *ncov, int *icov, int *lcov, int *mcov, double *tcov, double *cov);

Modified: branches/premif2/src/blowfly.c
===================================================================
--- branches/premif2/src/blowfly.c	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/src/blowfly.c	2013-04-16 16:27:02 UTC (rev 848)
@@ -5,7 +5,7 @@
 #include "pomp.h"
 
 #define P       (p[parindex[0]]) // growth rate
-#define NZERO   (p[parindex[1]]) // density-dependence parameter
+#define N0      (p[parindex[1]]) // density-dependence parameter
 #define DELTA   (p[parindex[2]]) // survival parameter
 #define SIGMAP  (p[parindex[3]]) // recruitment noise SD
 #define SIGMAD  (p[parindex[4]]) // survivorship noise SD
@@ -29,7 +29,7 @@
   double eps = rgammawn(SIGMAD,dt)/dt;
   int k;
 
-  R = rpois(P*N[tau]*exp(-N[tau]/NZERO)*dt*e);
+  R = rpois(P*N[tau]*exp(-N[tau]/N0)*dt*e);
   S = rbinom(N[0],exp(-DELTA*dt*eps));
   E = e;
   EPS = eps;
@@ -60,7 +60,7 @@
 #undef EPS
 
 #undef P
-#undef NZERO
+#undef N0
 #undef DELTA
 #undef SIGMAP
 #undef SIGMAD

Modified: branches/premif2/src/dprocess.c
===================================================================
--- branches/premif2/src/dprocess.c	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/src/dprocess.c	2013-04-16 16:27:02 UTC (rev 848)
@@ -12,7 +12,7 @@
   int nprotect = 0;
   int *xdim, npars, nvars, nreps, nrepsx, ntimes;
   SEXP X, fn, fcall, rho;
-  SEXP dimP, dimF;
+  SEXP dimF;
 
   ntimes = length(times);
   if (ntimes < 2)

Modified: branches/premif2/src/partrans.c
===================================================================
--- branches/premif2/src/partrans.c	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/src/partrans.c	2013-04-16 16:27:02 UTC (rev 848)
@@ -12,7 +12,7 @@
   int nprotect = 0;
   SEXP fn, fcall, rho, ans, nm;
   SEXP pdim, pvec;
-  SEXP tparams;
+  SEXP tparams = R_NilValue;
   int mode = -1;
   int qmat;
   int ndim[2], *dim, *idx;

Modified: branches/premif2/src/pomp_fun.c
===================================================================
--- branches/premif2/src/pomp_fun.c	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/src/pomp_fun.c	2013-04-16 16:27:02 UTC (rev 848)
@@ -33,7 +33,7 @@
     PROTECT(f = getListElement(nsi,"address")); nprotect++;
     break;
   default:
-    error("'pomp_fun_handler': invalid 'mode' value");
+    error("operation cannot be completed: some needed function has not been specified");
     break;
   }
 

Modified: branches/premif2/tests/bbs-trajmatch.Rout.save
===================================================================
--- branches/premif2/tests/bbs-trajmatch.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/bbs-trajmatch.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -68,4 +67,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.180   0.032   2.236 
+  2.180   0.068   2.271 

Modified: branches/premif2/tests/bbs.Rout.save
===================================================================
--- branches/premif2/tests/bbs.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/bbs.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -45,7 +44,7 @@
   Walker's alias method used: results are different from R < 2.2.0
 > signif(coef(fit1),3)
    gamma       mu     iota     beta  beta.sd      pop      rho    sigma 
-   0.333    0.000    0.000    3.460    0.000 1400.000    0.900    2.050 
+   0.333    0.000    0.000    3.220    0.000 1400.000    0.900    2.240 
      S.0      I.0      R.0 
    0.999    0.001    0.000 
 > 
@@ -58,4 +57,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.816   0.028   2.867 
+  2.884   0.060   2.969 

Modified: branches/premif2/tests/blowflies.Rout.save
===================================================================
--- branches/premif2/tests/blowflies.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/blowflies.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.14.2 (2012-02-29)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -68,3 +67,6 @@
 > logLik(f2)
 [1] -1471.781
 > 
+> proc.time()
+   user  system elapsed 
+  1.268   0.036   1.319 

Modified: branches/premif2/tests/dacca.Rout.save
===================================================================
--- branches/premif2/tests/dacca.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/dacca.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -50,4 +49,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.428   0.052   3.501 
+  3.392   0.056   3.472 

Modified: branches/premif2/tests/dimchecks.Rout.save
===================================================================
--- branches/premif2/tests/dimchecks.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/dimchecks.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -160,4 +159,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.436   0.044   0.494 
+  0.516   0.056   0.588 

Modified: branches/premif2/tests/fhn.Rout.save
===================================================================
--- branches/premif2/tests/fhn.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/fhn.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -93,4 +92,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.016   0.044   1.198 
+  1.000   0.056   1.187 

Modified: branches/premif2/tests/filtfail.Rout.save
===================================================================
--- branches/premif2/tests/filtfail.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/filtfail.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -119,4 +118,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.424   0.040   0.475 
+  0.492   0.052   0.558 

Modified: branches/premif2/tests/gillespie.Rout.save
===================================================================
--- branches/premif2/tests/gillespie.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/gillespie.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -131,4 +130,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.248   0.044   2.308 
+  2.576   0.044   2.641 

Modified: branches/premif2/tests/gompertz.Rout.save
===================================================================
--- branches/premif2/tests/gompertz.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/gompertz.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -131,4 +130,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.496   0.056   1.567 
+  1.572   0.048   1.640 

Modified: branches/premif2/tests/logistic.Rout.save
===================================================================
--- branches/premif2/tests/logistic.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/logistic.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -124,4 +123,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.800   0.052   0.937 
+  0.932   0.032   1.152 

Modified: branches/premif2/tests/ou2-bsmc.Rout.save
===================================================================
--- branches/premif2/tests/ou2-bsmc.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-bsmc.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -62,7 +61,7 @@
 > post <- smc$post
 > 
 > print(etime <- toc-tic)
-Time difference of 3.02021 secs
+Time difference of 3.065297 secs
 > 
 > print(
 +       cbind(
@@ -74,8 +73,8 @@
 +       )
         prior.mean posterior.mean truth       2.5%        50%      97.5%
 alpha.1  0.8000000      0.8000000   0.8  0.8000000  0.8000000  0.8000000
-alpha.2 -0.4999287     -0.4853833  -0.5 -0.5353593 -0.4881214 -0.4521997
-alpha.3  0.2996065      0.3186368   0.3  0.2933113  0.3120256  0.3476582
+alpha.2 -0.4999287     -0.5105023  -0.5 -0.5402483 -0.4993459 -0.4536930
+alpha.3  0.2996065      0.3148637   0.3  0.2823821  0.3260754  0.3388949
 alpha.4  0.9000000      0.9000000   0.9  0.9000000  0.9000000  0.9000000
 sigma.1  3.0000000      3.0000000   3.0  3.0000000  3.0000000  3.0000000
 sigma.2 -0.5000000     -0.5000000  -0.5 -0.5000000 -0.5000000 -0.5000000
@@ -85,9 +84,9 @@
 x2.0     4.0000000      4.0000000   4.0  4.0000000  4.0000000  4.0000000
 > 
 > print(min(smc$eff.sample.size))
-[1] 40.66176
+[1] 22.94863
 > print(smc$log.evidence)
-[1] 44.55899
+[1] 45.47584
 > 
 > smc <- bsmc(ou2,ntries=5,Np=5000,smooth=0.1,est=estnames,seed=648651945L)
 > print(smc$eff.sample.size)
@@ -98,4 +97,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  4.848   0.040   4.912 
+  5.044   0.064   5.138 

Modified: branches/premif2/tests/ou2-forecast.Rout.save
===================================================================
--- branches/premif2/tests/ou2-forecast.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-forecast.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -61,4 +60,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.492   0.048   1.691 
+  1.656   0.052   1.834 

Modified: branches/premif2/tests/ou2-icfit.Rout.save
===================================================================
--- branches/premif2/tests/ou2-icfit.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-icfit.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -107,4 +106,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 16.365   0.056  16.483 
+ 17.725   0.052  17.851 

Modified: branches/premif2/tests/ou2-kalman.Rout.save
===================================================================
--- branches/premif2/tests/ou2-kalman.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-kalman.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -164,7 +163,7 @@
     117 function evaluations used
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 5.289137 secs
+Time difference of 3.744109 secs
 > tic <- Sys.time()
 > print(loglik.mle <- -kalm.fit1$value,digits=4)
 [1] -477.2
@@ -188,4 +187,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  5.776   0.040   5.861 
+  4.296   0.056   4.385 

Modified: branches/premif2/tests/ou2-mif-fp.Rout.save
===================================================================
--- branches/premif2/tests/ou2-mif-fp.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-mif-fp.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -68,4 +67,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 19.521   0.056  19.776 
+ 20.673   0.060  20.945 

Modified: branches/premif2/tests/ou2-mif.Rout.save
===================================================================
--- branches/premif2/tests/ou2-mif.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-mif.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -80,7 +79,7 @@
 > plot(mif1)
 > compare.mif(mif2)
 > try(compare.mif(mif1,mif2))
-Error in compare.mif(mif1, mif2) : unused argument(s) (mif2)
+Error in compare.mif(mif1, mif2) : unused argument (mif2)
 > compare.mif(list(mif1,mif2))
 > dev.off()
 null device 
@@ -267,4 +266,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 13.728   0.036  13.921 
+ 13.704   0.044  13.926 

Modified: branches/premif2/tests/ou2-nlf.Rout.save
===================================================================
--- branches/premif2/tests/ou2-nlf.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-nlf.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -220,4 +219,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  8.256   0.040   8.334 
+  8.472   0.028   8.558 

Modified: branches/premif2/tests/ou2-pmcmc.Rout.save
===================================================================
--- branches/premif2/tests/ou2-pmcmc.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-pmcmc.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -85,4 +84,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.744   0.040   3.037 
+  2.872   0.052   3.187 

Modified: branches/premif2/tests/ou2-probe.Rout.save
===================================================================
--- branches/premif2/tests/ou2-probe.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-probe.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -294,4 +293,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.320   0.040   1.484 
+  1.368   0.060   1.491 

Modified: branches/premif2/tests/ou2-procmeas.Rout.save
===================================================================
--- branches/premif2/tests/ou2-procmeas.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-procmeas.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -54,4 +53,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.432   0.040   0.480 
+  0.480   0.040   0.537 

Modified: branches/premif2/tests/ou2-simulate.Rout.save
===================================================================
--- branches/premif2/tests/ou2-simulate.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-simulate.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -35,7 +34,7 @@
 > ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.01002026 secs
+Time difference of 0.009061098 secs
 > 
 > coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
 > 
@@ -46,4 +45,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.432   0.048   0.493 
+  0.480   0.064   0.558 

Modified: branches/premif2/tests/ou2-trajmatch.Rout.save
===================================================================
--- branches/premif2/tests/ou2-trajmatch.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ou2-trajmatch.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -184,4 +183,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.244   0.044   2.311 
+  1.656   0.044   1.720 

Modified: branches/premif2/tests/partrans.Rout.save
===================================================================
--- branches/premif2/tests/partrans.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/partrans.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -52,4 +51,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.424   0.036   0.472 
+  0.492   0.052   0.560 

Modified: branches/premif2/tests/pfilter.Rout.save
===================================================================
--- branches/premif2/tests/pfilter.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/pfilter.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -66,4 +65,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  6.224   0.048   6.307 
+  6.124   0.056   6.215 

Modified: branches/premif2/tests/pomppomp.Rout.save
===================================================================
--- branches/premif2/tests/pomppomp.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/pomppomp.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.0 (2012-03-30)
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -41,4 +40,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.432   0.036   0.491 
+  0.508   0.060   0.588 

Modified: branches/premif2/tests/ricker-bsmc.Rout.save
===================================================================
--- branches/premif2/tests/ricker-bsmc.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ricker-bsmc.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -53,4 +52,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 23.861   0.076  24.137 
+ 23.553   0.072  23.855 

Modified: branches/premif2/tests/ricker-probe.Rout.save
===================================================================
--- branches/premif2/tests/ricker-probe.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ricker-probe.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -296,4 +295,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 12.404   0.060  12.659 
+ 12.588   0.080  12.896 

Modified: branches/premif2/tests/ricker-spect.Rout.save
===================================================================
--- branches/premif2/tests/ricker-spect.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ricker-spect.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -70,4 +69,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.264   0.064   2.509 
+  2.376   0.068   2.613 

Modified: branches/premif2/tests/ricker.Rout.save
===================================================================
--- branches/premif2/tests/ricker.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/ricker.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -83,4 +82,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.508   0.028   0.665 
+  0.640   0.052   0.829 

Modified: branches/premif2/tests/rw2.Rout.save
===================================================================
--- branches/premif2/tests/rw2.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/rw2.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -260,7 +259,7 @@
     }
     y
 }
-<environment: 0x216d088>
+<environment: 0x38d5698>
 measurement model density, dmeasure = 
 function (y, x, t, params, log, covars, ...) 
 {
@@ -273,11 +272,11 @@
         f
     else exp(f)
 }
-<environment: 0x216d088>
+<environment: 0x38d5698>
 skeleton ( map ) = 
 function (x, t, params, covars, ...) 
 stop(sQuote("skeleton"), " not specified")
-<environment: 0x2181870>
+<environment: 0x38e74e8>
 initializer = 
 function (params, t0, ...) 
 {
@@ -433,4 +432,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.876   0.048   0.940 
+  0.964   0.044   1.024 

Modified: branches/premif2/tests/sir.Rout.save
===================================================================
--- branches/premif2/tests/sir.Rout.save	2013-04-16 14:50:35 UTC (rev 847)
+++ branches/premif2/tests/sir.Rout.save	2013-04-16 16:27:02 UTC (rev 848)
@@ -1,7 +1,6 @@
 
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 848

From noreply at r-forge.r-project.org  Tue Apr 16 19:00:00 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 16 Apr 2013 19:00:00 +0200 (CEST)
Subject: [Pomp-commits] r849 - pkg/pomp
Message-ID: <20130416170001.63DBB18513C@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-16 19:00:00 +0200 (Tue, 16 Apr 2013)
New Revision: 849

Modified:
   pkg/pomp/DESCRIPTION
Log:
- fix DESCRIPTION file


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-04-16 16:27:02 UTC (rev 848)
+++ pkg/pomp/DESCRIPTION	2013-04-16 17:00:00 UTC (rev 849)
@@ -1,12 +1,10 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.44-3
-Date: 2013-03-21
-Author: Aaron A. King, Edward L. Ionides, Carles Breto
-Contributor: Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman, Simon N. Wood
+Version: 0.44-4
+Date: 2013-04-16
 Maintainer: Aaron A. King <kingaa at umich.edu>
-Author at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
+Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
 	  person(given=c("Carles"),family="Breto",role=c("aut")),
 	  person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
@@ -15,7 +13,8 @@
 	  person(given=c("Michael"),family="Lavine",role=c("ctb")),
 	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),
 	  person(given=c("Helen"),family="Wearing",role=c("ctb")),
-	  person(given=c("Simon","N."),family="Wood",role=c("ctb")))
+	  person(given=c("Simon","N."),family="Wood",role=c("ctb")),
+	  person(given="Dao",family="Nguyen",role=c("ctb"))	)
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially-observed Markov processes
 Depends: R(>= 2.14.1), stats, methods, graphics, mvtnorm, subplex, deSolve


From noreply at r-forge.r-project.org  Tue Apr 16 19:00:23 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 16 Apr 2013 19:00:23 +0200 (CEST)
Subject: [Pomp-commits] r850 - branches/premif2
Message-ID: <20130416170024.1803718513C@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-16 19:00:22 +0200 (Tue, 16 Apr 2013)
New Revision: 850

Modified:
   branches/premif2/DESCRIPTION
Log:
- fix DESCRIPTION file


Modified: branches/premif2/DESCRIPTION
===================================================================
--- branches/premif2/DESCRIPTION	2013-04-16 17:00:00 UTC (rev 849)
+++ branches/premif2/DESCRIPTION	2013-04-16 17:00:22 UTC (rev 850)
@@ -3,10 +3,8 @@
 Title: Statistical inference for partially observed Markov processes
 Version: 0.43-8
 Date: 2013-04-16
-Author: Aaron A. King, Edward L. Ionides, Carles Breto
-Contributor: Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman, Simon N. Wood
 Maintainer: Aaron A. King <kingaa at umich.edu>
-Author at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
+Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
 	  person(given=c("Carles"),family="Breto",role=c("aut")),
 	  person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),


From noreply at r-forge.r-project.org  Wed Apr 17 13:27:55 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 17 Apr 2013 13:27:55 +0200 (CEST)
Subject: [Pomp-commits] r851 - branches/premif2/src
Message-ID: <20130417112755.8F5A8184BA3@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-17 13:27:55 +0200 (Wed, 17 Apr 2013)
New Revision: 851

Added:
   branches/premif2/src/SSA.f90
Removed:
   branches/premif2/src/SSA.f
Modified:
   branches/premif2/src/SSA_wrapper.c
Log:
- fix the fortran90 in SSA.f and designate this file as fortran90
- fix minor inconsistency in SSA_wrapper.c


Deleted: branches/premif2/src/SSA.f
===================================================================
--- branches/premif2/src/SSA.f	2013-04-16 17:00:22 UTC (rev 850)
+++ branches/premif2/src/SSA.f	2013-04-17 11:27:55 UTC (rev 851)
@@ -1,354 +0,0 @@
-      subroutine driverSSA(fprob,nvar,nevent,npar,nreps,ntimes,kflag,
-     &     xstart,times,params,xout,e,v,d,nzero,izero,istate,ipar,
-     &     ncovar,icovar,lcov,mcov,tcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension xstart(nvar,nreps), times(ntimes)
-      dimension params(npar,nreps), par(npar)
-      dimension xout(nvar,nreps,ntimes)
-      dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
-      dimension izero(nzero)
-      dimension istate(nvar), ipar(npar), icovar(ncovar)
-      dimension tcov(lcov), cov(lcov,mcov)
-      dimension covars(mcov)
-      external fprob
-      ntreeh=1+int(log(nevent*1.0)/log(2.0)+1)
-      do irep=1,nreps
-         call SSA(fprob,irep,nvar,nevent,ntreeh,npar,nreps,
-     &        ntimes,kflag,xstart,times,params,xout,e,v,d,
-     &        nzero,izero,istate,ipar,ncovar,icovar,lcov,mcov,
-     &        tcov,cov)
-      enddo
-      return
-      end
-
-      subroutine SSA(fprob,irep,nvar,nevent,ntreeh,npar,nreps,
-     &     ntimes,kflag,xstart,times,params,xout,e,v,d,nzero,
-     &     izero,istate,ipar,ncovar,icovar,lcov,mcov,tcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension xstart(nvar,nreps), times(ntimes)
-      dimension params(npar,nreps), par(npar)
-      dimension xout(nvar,nreps,ntimes)
-      dimension y(nvar),f(nevent,ntreeh),k(nevent)
-      dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
-      dimension izero(nzero)
-      dimension istate(nvar), ipar(npar), icovar(ncovar)
-      dimension tcov(lcov), cov(lcov,mcov)
-      dimension covars(mcov)
-      external gillespie,kleap,fprob
-      n=nvar
-      m=nevent
-c================
-c Initialisation
-c================
-      t=times(1)
-      tmax=times(ntimes)
-      iflag=0
-      icount=2
-      do i=1,npar
-         par(i)=params(i,irep)
-      enddo
-      do i=1,n
-         y(i)=xstart(i,irep)
-      enddo
-c Set appropriate states to zero
-      do i=1,nzero
-         y(izero(i)+1)=0.0d0
-      enddo
-c Copy initial states into xout
-      do i=1,n
-         xout(i,irep,1)=y(i)
-      enddo
-c Initialize the covariate vector
-      if(mcov.gt.0)then
-         call tlook(lcov,mcov,tcov,cov,t,covars)
-      endif
-c========================================
-c Initialise propensity functions & tree
-c========================================
-      do j=1,m
-         f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,covars)
-      enddo
-      jdum=m
-      do itree=2,ntreeh
-         jend=int((jdum+1)/2)
-         do j=1,jend
-            if(2*j.le.jdum)then
-               f(j,itree)=f(2*j-1,itree-1)+f(2*j,itree-1)
-            else
-               f(j,itree)=f(2*j-1,itree-1)         
-            endif
-         enddo
-         jdum=jend
-      enddo
-c=====
-      do while(icount.le.ntimes)
-         call rchkusr
-         if(kflag.eq.0)then
-            call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,
-     &           jevent,iflag,istate,ipar,ncovar,icovar,
-     &           mcov,covars)
-            if(iflag.eq.1)goto 100
-         else                   !if(kflag.eq.1)then
-c=================
-c Determine kappa (most accurate but slowest method)
-c=================
-            dum=10d8
-            do i=1,n
-               dum=min(e(i)*y(i),dum)
-               if(dum.le.1.0)goto 50
-            enddo
- 50         kappa=max(dum,1.0d0)
-            if(kappa.eq.1)then
-               call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,
-     &              jevent,iflag,istate,ipar,ncovar,icovar,
-     &              mcov,covars)
-               if(iflag.eq.1)goto 100
-            else
-               call kleap(fprob,kappa,t,f,y,v,d,par,n,m,ntreeh,npar,
-     &              k,iflag,istate,ipar,ncovar,icovar,
-     &              mcov,covars)
-               if(iflag.eq.1)goto 100
-            endif
-c         else
-c===============
-c Determine tau (need to add code to avoid negative #s & determine tau)
-c===============
-c            tau=e(1)
-c            call tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,
-c     &           k,iflag)
-c            if(iflag.eq.1)goto 100
-         endif
-c     
-c Recording output at required time points
-c     
-         if (icount.le.ntimes) then
-            do while((icount.le.ntimes).and.(t.ge.times(icount)))
-               do i=1,n
-                  xout(i,irep,icount)=y(i)
-               enddo
-c===============================
-c     Set appropriate states to zero
-c===============================
-               do i=1,nzero
-                  y(izero(i)+1)=0.0d0
-               enddo
-               icount=icount+1
-            enddo
-         endif
-
-         if((mcov.gt.0).and.(t.le.tmax))then
-            call tlook(lcov,mcov,tcov,cov,t,covars)
-         endif
-c     
-      enddo
-c=====
- 100  return
-      end
-      
-      subroutine gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,jevent,
-     &     iflag,istate,ipar,ncovar,icovar,mcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension y(n),f(m,ntreeh),v(n,m),d(n,m),par(npar),ichangey(n)
-      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
-      external unifrnd,fprob
-c=================================
-c Generate uniform random numbers
-c=================================
-      p1=unifrnd()
-      p2=unifrnd()
-c=========================================
-c Determine time interval and update time
-c=========================================
-      fsum=f(1,ntreeh)
-      if(fsum.gt.0.0)then
-         tstep=-log(p1)/fsum
-         t=t+tstep
-      else
-         iflag=1
-         goto 500
-      endif
-c=========================================
-c Determine event, update pops & events
-c=========================================
-      jtree=1
-      temp=p2*fsum
-      do itree=ntreeh-1,1,-1
-         if(itree.eq.1)then
-            if(temp.lt.f(jtree,itree))then
-               jevent=jtree
-            else 
-               jevent=jtree+1
-            endif
-         else
-            if(temp.lt.f(jtree,itree))then
-               jtree=2*jtree-1
-            else
-               temp=temp-f(jtree,itree)
-               jtree=2*jtree+1
-            endif
-         endif
-      enddo 
-      do i=1,n
-         ichangey(i)=0
-      enddo
-      do i = 1,n
-         if(v(i,jevent).ne.0)then
-            y(i) = y(i) + v(i,jevent)
-            ichangey(i)=1
-         endif
-      enddo
-c
-c only updating events & tree entries that have changed
-c
-      do j=1,m
-         do i=1,n
-            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
-               fold=f(j,1)
-               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
-               diff=f(j,1)-fold
-               jdum=int((j+1)/2)
-               do itree=2,ntreeh
-                  f(jdum,itree)=f(jdum,itree)+diff
-                  jdum=int((jdum+1)/2)
-               enddo
-               goto 400
-            endif
-         enddo
- 400     continue
-      enddo
- 500  return
-      end
-
-      subroutine kleap(fprob,kappa,t,f,y,v,d,par,n,m,ntreeh,npar,k,
-     &     iflag,istate,ipar,ncovar,icovar,mcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension y(n),f(m,ntreeh),p(m),v(n,m),d(n,m),par(npar)
-      dimension k(m),ichangey(n)
-      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
-      external gammarnd,fprob
-c=========================================
-c Determine time interval and update time
-c=========================================
-      fsum=f(1,ntreeh)
-      if(fsum.gt.0.0d0)then
-         tstep=gammarnd(kappa,fsum)
-         t=t+tstep
-      else
-         iflag=1
-         goto 500
-      endif
-c=====================================================
-c Determine frequency of events, update pops & events
-c=====================================================
-      do j=1,m
-         p(j)=f(j,1)/fsum
-      enddo
-      call multinomrnd(kappa,p,m,k)
-c
-c some matrix-vector multiplication but only where necessary
-c
-      do i=1,n
-         ichangey(i)=0
-      enddo
-      do j=1,m
-         if(k(j).ne.0)then
-            temp=k(j)
-            do i = 1,n
-               if(v(i,j).ne.0)then
-                  y(i) = y(i) + temp*v(i,j)
-                  ichangey(i)=1
-               endif
-            enddo
-         endif
-      enddo
-c
-c only updating events & tree entries that have changed
-c
-      do j=1,m
-         do i=1,n
-            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
-               fold=f(j,1)
-               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
-               diff=f(j,1)-fold
-               jdum=int((j+1)/2)
-               do itree=2,ntreeh
-                  f(jdum,itree)=f(jdum,itree)+diff
-                  jdum=int((jdum+1)/2)
-               enddo
-               goto 400
-            endif
-         enddo
- 400     continue
-      enddo
- 500  return
-      end
-
-      subroutine tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,k,
-     &     iflag,istate,ipar,ncovar,icovar,mcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension y(n),f(m,ntreeh),k(m),v(n,m),d(n,m),par(npar)
-      dimension ichangey(n)
-      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
-      external poisrnd,fprob
-c======================================================================
-c Generate Poisson random variables (number of event firings in t+tau)
-c======================================================================
-      fsum=f(1,ntreeh)
-      if(fsum.gt.0.0d0)then
-         do j=1,m
-            k(j)=poisrnd(f(j,1)*tau)
-         enddo
-      else
-         iflag=1
-         goto 500
-      endif
-c==========
-c Update t
-c==========
-      t=t+tau
-c================================================
-c Compute changes in population numbers & events
-c================================================
-c
-c some matrix-vector multiplication but only where necessary
-c
-      do i=1,n
-         ichangey(i)=0
-      enddo
-      do j=1,m
-         if(k(j).ne.0)then
-            temp=k(j)
-            do i = 1,n
-               if(v(i,j).ne.0)then
-                  y(i) = y(i) + temp*v(i,j)
-                  ichangey(i)=1
-               endif
-            enddo
-         endif
-      enddo
-c
-c only updating events & tree entries that have changed
-c
-      do j=1,m
-         do i=1,n
-            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
-               fold=f(j,1)
-               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
-               diff=f(j,1)-fold
-               jdum=int((j+1)/2)
-               do itree=2,ntreeh
-                  f(jdum,itree)=f(jdum,itree)+diff
-                  jdum=int((jdum+1)/2)
-               enddo
-               goto 400
-            endif
-         enddo
- 400     continue
-      enddo
- 500  return
-      end

Copied: branches/premif2/src/SSA.f90 (from rev 850, branches/premif2/src/SSA.f)
===================================================================
--- branches/premif2/src/SSA.f90	                        (rev 0)
+++ branches/premif2/src/SSA.f90	2013-04-17 11:27:55 UTC (rev 851)
@@ -0,0 +1,352 @@
+      subroutine driverSSA(fprob,nvar,nevent,npar,nreps,ntimes,kflag,&
+           xstart,times,params,xout,e,v,d,nzero,izero,istate,ipar,ncovar,&
+           icovar,lcov,mcov,tcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension xstart(nvar,nreps), times(ntimes)
+      dimension params(npar,nreps)
+      dimension xout(nvar,nreps,ntimes)
+      dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
+      dimension izero(nzero)
+      dimension istate(nvar), ipar(npar), icovar(ncovar)
+      dimension tcov(lcov), cov(lcov,mcov)
+      external fprob
+      ntreeh=1+int(log(nevent*1.0)/log(2.0)+1)
+      do irep=1,nreps
+         call SSA(fprob,irep,nvar,nevent,ntreeh,npar,nreps,&
+              ntimes,kflag,xstart,times,params,xout,e,v,d,&
+              nzero,izero,istate,ipar,ncovar,icovar,lcov,mcov,&
+              tcov,cov)
+      enddo
+      return
+      end
+
+      subroutine SSA(fprob,irep,nvar,nevent,ntreeh,npar,nreps,&
+           ntimes,kflag,xstart,times,params,xout,e,v,d,nzero,&
+           izero,istate,ipar,ncovar,icovar,lcov,mcov,tcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension xstart(nvar,nreps), times(ntimes)
+      dimension params(npar,nreps), par(npar)
+      dimension xout(nvar,nreps,ntimes)
+      dimension y(nvar),f(nevent,ntreeh),k(nevent)
+      dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
+      dimension izero(nzero)
+      dimension istate(nvar), ipar(npar), icovar(ncovar)
+      dimension tcov(lcov), cov(lcov,mcov)
+      dimension covars(mcov)
+      external gillespie,kleap,fprob
+      n=nvar
+      m=nevent
+!================
+! Initialisation
+!================
+      t=times(1)
+      tmax=times(ntimes)
+      iflag=0
+      icount=2
+      do i=1,npar
+         par(i)=params(i,irep)
+      enddo
+      do i=1,n
+         y(i)=xstart(i,irep)
+      enddo
+! Set appropriate states to zero
+      do i=1,nzero
+         y(izero(i)+1)=0.0d0
+      enddo
+! Copy initial states into xout
+      do i=1,n
+         xout(i,irep,1)=y(i)
+      enddo
+! Initialize the covariate vector
+      if(mcov.gt.0)then
+         call tlook(lcov,mcov,tcov,cov,t,covars)
+      endif
+!========================================
+! Initialise propensity functions & tree
+!========================================
+      do j=1,m
+         f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,covars)
+      enddo
+      jdum=m
+      do itree=2,ntreeh
+         jend=int((jdum+1)/2)
+         do j=1,jend
+            if(2*j.le.jdum)then
+               f(j,itree)=f(2*j-1,itree-1)+f(2*j,itree-1)
+            else
+               f(j,itree)=f(2*j-1,itree-1)         
+            endif
+         enddo
+         jdum=jend
+      enddo
+!=====
+      do while(icount.le.ntimes)
+         call rchkusr
+         if(kflag.eq.0)then
+            call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,&
+                 jevent,iflag,istate,ipar,ncovar,icovar,&
+                 mcov,covars)
+            if(iflag.eq.1)goto 100
+         else                   !if(kflag.eq.1)then
+!=================
+! Determine kappa (most accurate but slowest method)
+!=================
+            dum=10d8
+            do i=1,n
+               dum=min(e(i)*y(i),dum)
+               if(dum.le.1.0)goto 50
+            enddo
+ 50         kappa=int(max(dum,1.0d0))
+            if(kappa.eq.1)then
+               call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,&
+                    jevent,iflag,istate,ipar,ncovar,icovar,&
+                    mcov,covars)
+               if(iflag.eq.1)goto 100
+            else
+               call kleap(fprob,kappa,t,f,y,v,d,par,n,m,ntreeh,npar,&
+                    k,iflag,istate,ipar,ncovar,icovar,&
+                    mcov,covars)
+               if(iflag.eq.1)goto 100
+            endif
+!         else
+!===============
+! Determine tau (need to add code to avoid negative #s & determine tau)
+!===============
+!            tau=e(1)
+!            call tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,&
+!                         k,iflag)
+!            if(iflag.eq.1)goto 100
+         endif
+!     
+! Recording output at required time points
+!     
+         do while ((icount.le.ntimes).and.(t.ge.times(icount)))
+            do i=1,n
+               xout(i,irep,icount)=y(i)
+            enddo
+!===============================
+!     Set appropriate states to zero
+!===============================
+            do i=1,nzero
+               y(izero(i)+1)=0.0d0
+            enddo
+            icount=icount+1
+            if (icount.gt.ntimes) exit
+         enddo
+
+         if((mcov.gt.0).and.(t.le.tmax))then
+            call tlook(lcov,mcov,tcov,cov,t,covars)
+         endif
+!     
+      enddo
+!=====
+ 100  return
+      end
+      
+      subroutine gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,jevent,&
+           iflag,istate,ipar,ncovar,icovar,mcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension y(n),f(m,ntreeh),v(n,m),d(n,m),par(npar),ichangey(n)
+      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
+      external unifrnd,fprob
+!=================================
+! Generate uniform random numbers
+!=================================
+      p1=unifrnd()
+      p2=unifrnd()
+!=========================================
+! Determine time interval and update time
+!=========================================
+      fsum=f(1,ntreeh)
+      if(fsum.gt.0.0)then
+         tstep=-log(p1)/fsum
+         t=t+tstep
+      else
+         iflag=1
+         goto 500
+      endif
+!=========================================
+! Determine event, update pops & events
+!=========================================
+      jtree=1
+      temp=p2*fsum
+      do itree=ntreeh-1,1,-1
+         if(itree.eq.1)then
+            if(temp.lt.f(jtree,itree))then
+               jevent=jtree
+            else 
+               jevent=jtree+1
+            endif
+         else
+            if(temp.lt.f(jtree,itree))then
+               jtree=2*jtree-1
+            else
+               temp=temp-f(jtree,itree)
+               jtree=2*jtree+1
+            endif
+         endif
+      enddo 
+      do i=1,n
+         ichangey(i)=0
+      enddo
+      do i = 1,n
+         if(v(i,jevent).ne.0)then
+            y(i) = y(i) + v(i,jevent)
+            ichangey(i)=1
+         endif
+      enddo
+!
+! only updating events & tree entries that have changed
+!
+      do j=1,m
+         do i=1,n
+            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
+               fold=f(j,1)
+               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
+               diff=f(j,1)-fold
+               jdum=int((j+1)/2)
+               do itree=2,ntreeh
+                  f(jdum,itree)=f(jdum,itree)+diff
+                  jdum=int((jdum+1)/2)
+               enddo
+               goto 400
+            endif
+         enddo
+ 400     continue
+      enddo
+ 500  return
+      end
+
+      subroutine kleap(fprob,kappa,t,f,y,v,d,par,n,m,ntreeh,npar,k,&
+           iflag,istate,ipar,ncovar,icovar,mcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension y(n),f(m,ntreeh),p(m),v(n,m),d(n,m),par(npar)
+      dimension k(m),ichangey(n)
+      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
+      external gammarnd,fprob
+!=========================================
+! Determine time interval and update time
+!=========================================
+      fsum=f(1,ntreeh)
+      if(fsum.gt.0.0d0)then
+         tstep=gammarnd(kappa,fsum)
+         t=t+tstep
+      else
+         iflag=1
+         goto 500
+      endif
+!=====================================================
+! Determine frequency of events, update pops & events
+!=====================================================
+      do j=1,m
+         p(j)=f(j,1)/fsum
+      enddo
+      call multinomrnd(kappa,p,m,k)
+!
+! some matrix-vector multiplication but only where necessary
+!
+      do i=1,n
+         ichangey(i)=0
+      enddo
+      do j=1,m
+         if(k(j).ne.0)then
+            temp=k(j)
+            do i = 1,n
+               if(v(i,j).ne.0)then
+                  y(i) = y(i) + temp*v(i,j)
+                  ichangey(i)=1
+               endif
+            enddo
+         endif
+      enddo
+!
+! only updating events & tree entries that have changed
+!
+      do j=1,m
+         do i=1,n
+            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
+               fold=f(j,1)
+               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
+               diff=f(j,1)-fold
+               jdum=int((j+1)/2)
+               do itree=2,ntreeh
+                  f(jdum,itree)=f(jdum,itree)+diff
+                  jdum=int((jdum+1)/2)
+               enddo
+               goto 400
+            endif
+         enddo
+ 400     continue
+      enddo
+ 500  return
+      end
+
+      subroutine tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,k,&
+           iflag,istate,ipar,ncovar,icovar,mcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension y(n),f(m,ntreeh),k(m),v(n,m),d(n,m),par(npar)
+      dimension ichangey(n)
+      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
+      external poisrnd,fprob
+!======================================================================
+! Generate Poisson random variables (number of event firings in t+tau)
+!======================================================================
+      fsum=f(1,ntreeh)
+      if(fsum.gt.0.0d0)then
+         do j=1,m
+            k(j)=int(poisrnd(f(j,1)*tau))
+         enddo
+      else
+         iflag=1
+         goto 500
+      endif
+!==========
+! Update t
+!==========
+      t=t+tau
+!================================================
+! Compute changes in population numbers & events
+!================================================
+!
+! some matrix-vector multiplication but only where necessary
+!
+      do i=1,n
+         ichangey(i)=0
+      enddo
+      do j=1,m
+         if(k(j).ne.0)then
+            temp=k(j)
+            do i = 1,n
+               if(v(i,j).ne.0)then
+                  y(i) = y(i) + temp*v(i,j)
+                  ichangey(i)=1
+               endif
+            enddo
+         endif
+      enddo
+!
+! only updating events & tree entries that have changed
+!
+      do j=1,m
+         do i=1,n
+            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
+               fold=f(j,1)
+               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
+               diff=f(j,1)-fold
+               jdum=int((j+1)/2)
+               do itree=2,ntreeh
+                  f(jdum,itree)=f(jdum,itree)+diff
+                  jdum=int((jdum+1)/2)
+               enddo
+               goto 400
+            endif
+         enddo
+ 400     continue
+      enddo
+ 500  return
+      end

Modified: branches/premif2/src/SSA_wrapper.c
===================================================================
--- branches/premif2/src/SSA_wrapper.c	2013-04-16 17:00:22 UTC (rev 850)
+++ branches/premif2/src/SSA_wrapper.c	2013-04-17 11:27:55 UTC (rev 851)
@@ -15,7 +15,7 @@
 double F77_SUB(gammarnd)(double shape, double scale) { return rgamma(shape,scale); }
 void F77_SUB(multinomrnd)(int N, double *p, int ncat, int *ix) { rmultinom(N,p,ncat,ix); }
 
-void F77_NAME(driverssa)(_pomp_rxnrate *fprob, int *nvar, int *nevent, int *npar, int *nreps, int *ntimes, 
+void F77_NAME(driverssa)(_pomp_rxnrate fprob, int *nvar, int *nevent, int *npar, int *nreps, int *ntimes, 
 			 int *kflag, double *xstart, double *times, double *params, double *xout,
 			 double *e, double *v, double *d, int *nzero, int *izero, int *istate, 
 			 int *ipar, int *ncov, int *icov, int *lcov, int *mcov, double *tcov, double *cov);


From noreply at r-forge.r-project.org  Wed Apr 17 14:14:12 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 17 Apr 2013 14:14:12 +0200 (CEST)
Subject: [Pomp-commits] r852 - pkg/pomp/src
Message-ID: <20130417121412.5CA8318501D@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-17 14:14:11 +0200 (Wed, 17 Apr 2013)
New Revision: 852

Added:
   pkg/pomp/src/SSA.f90
Removed:
   pkg/pomp/src/SSA.f
Modified:
   pkg/pomp/src/SSA_wrapper.c
Log:
- fix the fortran90 in SSA.f and designate this file as fortran90
- fix minor inconsistency in SSA_wrapper.c



Deleted: pkg/pomp/src/SSA.f
===================================================================
--- pkg/pomp/src/SSA.f	2013-04-17 11:27:55 UTC (rev 851)
+++ pkg/pomp/src/SSA.f	2013-04-17 12:14:11 UTC (rev 852)
@@ -1,354 +0,0 @@
-      subroutine driverSSA(fprob,nvar,nevent,npar,nreps,ntimes,kflag,
-     &     xstart,times,params,xout,e,v,d,nzero,izero,istate,ipar,
-     &     ncovar,icovar,lcov,mcov,tcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension xstart(nvar,nreps), times(ntimes)
-      dimension params(npar,nreps), par(npar)
-      dimension xout(nvar,nreps,ntimes)
-      dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
-      dimension izero(nzero)
-      dimension istate(nvar), ipar(npar), icovar(ncovar)
-      dimension tcov(lcov), cov(lcov,mcov)
-      dimension covars(mcov)
-      external fprob
-      ntreeh=1+int(log(nevent*1.0)/log(2.0)+1)
-      do irep=1,nreps
-         call SSA(fprob,irep,nvar,nevent,ntreeh,npar,nreps,
-     &        ntimes,kflag,xstart,times,params,xout,e,v,d,
-     &        nzero,izero,istate,ipar,ncovar,icovar,lcov,mcov,
-     &        tcov,cov)
-      enddo
-      return
-      end
-
-      subroutine SSA(fprob,irep,nvar,nevent,ntreeh,npar,nreps,
-     &     ntimes,kflag,xstart,times,params,xout,e,v,d,nzero,
-     &     izero,istate,ipar,ncovar,icovar,lcov,mcov,tcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension xstart(nvar,nreps), times(ntimes)
-      dimension params(npar,nreps), par(npar)
-      dimension xout(nvar,nreps,ntimes)
-      dimension y(nvar),f(nevent,ntreeh),k(nevent)
-      dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
-      dimension izero(nzero)
-      dimension istate(nvar), ipar(npar), icovar(ncovar)
-      dimension tcov(lcov), cov(lcov,mcov)
-      dimension covars(mcov)
-      external gillespie,kleap,fprob
-      n=nvar
-      m=nevent
-c================
-c Initialisation
-c================
-      t=times(1)
-      tmax=times(ntimes)
-      iflag=0
-      icount=2
-      do i=1,npar
-         par(i)=params(i,irep)
-      enddo
-      do i=1,n
-         y(i)=xstart(i,irep)
-      enddo
-c Set appropriate states to zero
-      do i=1,nzero
-         y(izero(i)+1)=0.0d0
-      enddo
-c Copy initial states into xout
-      do i=1,n
-         xout(i,irep,1)=y(i)
-      enddo
-c Initialize the covariate vector
-      if(mcov.gt.0)then
-         call tlook(lcov,mcov,tcov,cov,t,covars)
-      endif
-c========================================
-c Initialise propensity functions & tree
-c========================================
-      do j=1,m
-         f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,covars)
-      enddo
-      jdum=m
-      do itree=2,ntreeh
-         jend=int((jdum+1)/2)
-         do j=1,jend
-            if(2*j.le.jdum)then
-               f(j,itree)=f(2*j-1,itree-1)+f(2*j,itree-1)
-            else
-               f(j,itree)=f(2*j-1,itree-1)         
-            endif
-         enddo
-         jdum=jend
-      enddo
-c=====
-      do while(icount.le.ntimes)
-         call rchkusr
-         if(kflag.eq.0)then
-            call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,
-     &           jevent,iflag,istate,ipar,ncovar,icovar,
-     &           mcov,covars)
-            if(iflag.eq.1)goto 100
-         else                   !if(kflag.eq.1)then
-c=================
-c Determine kappa (most accurate but slowest method)
-c=================
-            dum=10d8
-            do i=1,n
-               dum=min(e(i)*y(i),dum)
-               if(dum.le.1.0)goto 50
-            enddo
- 50         kappa=max(dum,1.0d0)
-            if(kappa.eq.1)then
-               call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,
-     &              jevent,iflag,istate,ipar,ncovar,icovar,
-     &              mcov,covars)
-               if(iflag.eq.1)goto 100
-            else
-               call kleap(fprob,kappa,t,f,y,v,d,par,n,m,ntreeh,npar,
-     &              k,iflag,istate,ipar,ncovar,icovar,
-     &              mcov,covars)
-               if(iflag.eq.1)goto 100
-            endif
-c         else
-c===============
-c Determine tau (need to add code to avoid negative #s & determine tau)
-c===============
-c            tau=e(1)
-c            call tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,
-c     &           k,iflag)
-c            if(iflag.eq.1)goto 100
-         endif
-c     
-c Recording output at required time points
-c     
-         if (icount.le.ntimes) then
-            do while((icount.le.ntimes).and.(t.ge.times(icount)))
-               do i=1,n
-                  xout(i,irep,icount)=y(i)
-               enddo
-c===============================
-c     Set appropriate states to zero
-c===============================
-               do i=1,nzero
-                  y(izero(i)+1)=0.0d0
-               enddo
-               icount=icount+1
-            enddo
-         endif
-
-         if((mcov.gt.0).and.(t.le.tmax))then
-            call tlook(lcov,mcov,tcov,cov,t,covars)
-         endif
-c     
-      enddo
-c=====
- 100  return
-      end
-      
-      subroutine gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,jevent,
-     &     iflag,istate,ipar,ncovar,icovar,mcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension y(n),f(m,ntreeh),v(n,m),d(n,m),par(npar),ichangey(n)
-      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
-      external unifrnd,fprob
-c=================================
-c Generate uniform random numbers
-c=================================
-      p1=unifrnd()
-      p2=unifrnd()
-c=========================================
-c Determine time interval and update time
-c=========================================
-      fsum=f(1,ntreeh)
-      if(fsum.gt.0.0)then
-         tstep=-log(p1)/fsum
-         t=t+tstep
-      else
-         iflag=1
-         goto 500
-      endif
-c=========================================
-c Determine event, update pops & events
-c=========================================
-      jtree=1
-      temp=p2*fsum
-      do itree=ntreeh-1,1,-1
-         if(itree.eq.1)then
-            if(temp.lt.f(jtree,itree))then
-               jevent=jtree
-            else 
-               jevent=jtree+1
-            endif
-         else
-            if(temp.lt.f(jtree,itree))then
-               jtree=2*jtree-1
-            else
-               temp=temp-f(jtree,itree)
-               jtree=2*jtree+1
-            endif
-         endif
-      enddo 
-      do i=1,n
-         ichangey(i)=0
-      enddo
-      do i = 1,n
-         if(v(i,jevent).ne.0)then
-            y(i) = y(i) + v(i,jevent)
-            ichangey(i)=1
-         endif
-      enddo
-c
-c only updating events & tree entries that have changed
-c
-      do j=1,m
-         do i=1,n
-            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
-               fold=f(j,1)
-               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
-               diff=f(j,1)-fold
-               jdum=int((j+1)/2)
-               do itree=2,ntreeh
-                  f(jdum,itree)=f(jdum,itree)+diff
-                  jdum=int((jdum+1)/2)
-               enddo
-               goto 400
-            endif
-         enddo
- 400     continue
-      enddo
- 500  return
-      end
-
-      subroutine kleap(fprob,kappa,t,f,y,v,d,par,n,m,ntreeh,npar,k,
-     &     iflag,istate,ipar,ncovar,icovar,mcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension y(n),f(m,ntreeh),p(m),v(n,m),d(n,m),par(npar)
-      dimension k(m),ichangey(n)
-      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
-      external gammarnd,fprob
-c=========================================
-c Determine time interval and update time
-c=========================================
-      fsum=f(1,ntreeh)
-      if(fsum.gt.0.0d0)then
-         tstep=gammarnd(kappa,fsum)
-         t=t+tstep
-      else
-         iflag=1
-         goto 500
-      endif
-c=====================================================
-c Determine frequency of events, update pops & events
-c=====================================================
-      do j=1,m
-         p(j)=f(j,1)/fsum
-      enddo
-      call multinomrnd(kappa,p,m,k)
-c
-c some matrix-vector multiplication but only where necessary
-c
-      do i=1,n
-         ichangey(i)=0
-      enddo
-      do j=1,m
-         if(k(j).ne.0)then
-            temp=k(j)
-            do i = 1,n
-               if(v(i,j).ne.0)then
-                  y(i) = y(i) + temp*v(i,j)
-                  ichangey(i)=1
-               endif
-            enddo
-         endif
-      enddo
-c
-c only updating events & tree entries that have changed
-c
-      do j=1,m
-         do i=1,n
-            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
-               fold=f(j,1)
-               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
-               diff=f(j,1)-fold
-               jdum=int((j+1)/2)
-               do itree=2,ntreeh
-                  f(jdum,itree)=f(jdum,itree)+diff
-                  jdum=int((jdum+1)/2)
-               enddo
-               goto 400
-            endif
-         enddo
- 400     continue
-      enddo
- 500  return
-      end
-
-      subroutine tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,k,
-     &     iflag,istate,ipar,ncovar,icovar,mcov,cov)
-      implicit integer (i-n)
-      implicit double precision (a-h,o-z)
-      dimension y(n),f(m,ntreeh),k(m),v(n,m),d(n,m),par(npar)
-      dimension ichangey(n)
-      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
-      external poisrnd,fprob
-c======================================================================
-c Generate Poisson random variables (number of event firings in t+tau)
-c======================================================================
-      fsum=f(1,ntreeh)
-      if(fsum.gt.0.0d0)then
-         do j=1,m
-            k(j)=poisrnd(f(j,1)*tau)
-         enddo
-      else
-         iflag=1
-         goto 500
-      endif
-c==========
-c Update t
-c==========
-      t=t+tau
-c================================================
-c Compute changes in population numbers & events
-c================================================
-c
-c some matrix-vector multiplication but only where necessary
-c
-      do i=1,n
-         ichangey(i)=0
-      enddo
-      do j=1,m
-         if(k(j).ne.0)then
-            temp=k(j)
-            do i = 1,n
-               if(v(i,j).ne.0)then
-                  y(i) = y(i) + temp*v(i,j)
-                  ichangey(i)=1
-               endif
-            enddo
-         endif
-      enddo
-c
-c only updating events & tree entries that have changed
-c
-      do j=1,m
-         do i=1,n
-            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
-               fold=f(j,1)
-               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
-               diff=f(j,1)-fold
-               jdum=int((j+1)/2)
-               do itree=2,ntreeh
-                  f(jdum,itree)=f(jdum,itree)+diff
-                  jdum=int((jdum+1)/2)
-               enddo
-               goto 400
-            endif
-         enddo
- 400     continue
-      enddo
- 500  return
-      end

Copied: pkg/pomp/src/SSA.f90 (from rev 850, pkg/pomp/src/SSA.f)
===================================================================
--- pkg/pomp/src/SSA.f90	                        (rev 0)
+++ pkg/pomp/src/SSA.f90	2013-04-17 12:14:11 UTC (rev 852)
@@ -0,0 +1,352 @@
+      subroutine driverSSA(fprob,nvar,nevent,npar,nreps,ntimes,kflag,&
+           xstart,times,params,xout,e,v,d,nzero,izero,istate,ipar,ncovar,&
+           icovar,lcov,mcov,tcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension xstart(nvar,nreps), times(ntimes)
+      dimension params(npar,nreps)
+      dimension xout(nvar,nreps,ntimes)
+      dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
+      dimension izero(nzero)
+      dimension istate(nvar), ipar(npar), icovar(ncovar)
+      dimension tcov(lcov), cov(lcov,mcov)
+      external fprob
+      ntreeh=1+int(log(nevent*1.0)/log(2.0)+1)
+      do irep=1,nreps
+         call SSA(fprob,irep,nvar,nevent,ntreeh,npar,nreps,&
+              ntimes,kflag,xstart,times,params,xout,e,v,d,&
+              nzero,izero,istate,ipar,ncovar,icovar,lcov,mcov,&
+              tcov,cov)
+      enddo
+      return
+      end
+
+      subroutine SSA(fprob,irep,nvar,nevent,ntreeh,npar,nreps,&
+           ntimes,kflag,xstart,times,params,xout,e,v,d,nzero,&
+           izero,istate,ipar,ncovar,icovar,lcov,mcov,tcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension xstart(nvar,nreps), times(ntimes)
+      dimension params(npar,nreps), par(npar)
+      dimension xout(nvar,nreps,ntimes)
+      dimension y(nvar),f(nevent,ntreeh),k(nevent)
+      dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
+      dimension izero(nzero)
+      dimension istate(nvar), ipar(npar), icovar(ncovar)
+      dimension tcov(lcov), cov(lcov,mcov)
+      dimension covars(mcov)
+      external gillespie,kleap,fprob
+      n=nvar
+      m=nevent
+!================
+! Initialisation
+!================
+      t=times(1)
+      tmax=times(ntimes)
+      iflag=0
+      icount=2
+      do i=1,npar
+         par(i)=params(i,irep)
+      enddo
+      do i=1,n
+         y(i)=xstart(i,irep)
+      enddo
+! Set appropriate states to zero
+      do i=1,nzero
+         y(izero(i)+1)=0.0d0
+      enddo
+! Copy initial states into xout
+      do i=1,n
+         xout(i,irep,1)=y(i)
+      enddo
+! Initialize the covariate vector
+      if(mcov.gt.0)then
+         call tlook(lcov,mcov,tcov,cov,t,covars)
+      endif
+!========================================
+! Initialise propensity functions & tree
+!========================================
+      do j=1,m
+         f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,covars)
+      enddo
+      jdum=m
+      do itree=2,ntreeh
+         jend=int((jdum+1)/2)
+         do j=1,jend
+            if(2*j.le.jdum)then
+               f(j,itree)=f(2*j-1,itree-1)+f(2*j,itree-1)
+            else
+               f(j,itree)=f(2*j-1,itree-1)         
+            endif
+         enddo
+         jdum=jend
+      enddo
+!=====
+      do while(icount.le.ntimes)
+         call rchkusr
+         if(kflag.eq.0)then
+            call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,&
+                 jevent,iflag,istate,ipar,ncovar,icovar,&
+                 mcov,covars)
+            if(iflag.eq.1)goto 100
+         else                   !if(kflag.eq.1)then
+!=================
+! Determine kappa (most accurate but slowest method)
+!=================
+            dum=10d8
+            do i=1,n
+               dum=min(e(i)*y(i),dum)
+               if(dum.le.1.0)goto 50
+            enddo
+ 50         kappa=int(max(dum,1.0d0))
+            if(kappa.eq.1)then
+               call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,&
+                    jevent,iflag,istate,ipar,ncovar,icovar,&
+                    mcov,covars)
+               if(iflag.eq.1)goto 100
+            else
+               call kleap(fprob,kappa,t,f,y,v,d,par,n,m,ntreeh,npar,&
+                    k,iflag,istate,ipar,ncovar,icovar,&
+                    mcov,covars)
+               if(iflag.eq.1)goto 100
+            endif
+!         else
+!===============
+! Determine tau (need to add code to avoid negative #s & determine tau)
+!===============
+!            tau=e(1)
+!            call tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,&
+!                         k,iflag)
+!            if(iflag.eq.1)goto 100
+         endif
+!     
+! Recording output at required time points
+!     
+         do while ((icount.le.ntimes).and.(t.ge.times(icount)))
+            do i=1,n
+               xout(i,irep,icount)=y(i)
+            enddo
+!===============================
+!     Set appropriate states to zero
+!===============================
+            do i=1,nzero
+               y(izero(i)+1)=0.0d0
+            enddo
+            icount=icount+1
+            if (icount.gt.ntimes) exit
+         enddo
+
+         if((mcov.gt.0).and.(t.le.tmax))then
+            call tlook(lcov,mcov,tcov,cov,t,covars)
+         endif
+!     
+      enddo
+!=====
+ 100  return
+      end
+      
+      subroutine gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,jevent,&
+           iflag,istate,ipar,ncovar,icovar,mcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension y(n),f(m,ntreeh),v(n,m),d(n,m),par(npar),ichangey(n)
+      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
+      external unifrnd,fprob
+!=================================
+! Generate uniform random numbers
+!=================================
+      p1=unifrnd()
+      p2=unifrnd()
+!=========================================
+! Determine time interval and update time
+!=========================================
+      fsum=f(1,ntreeh)
+      if(fsum.gt.0.0)then
+         tstep=-log(p1)/fsum
+         t=t+tstep
+      else
+         iflag=1
+         goto 500
+      endif
+!=========================================
+! Determine event, update pops & events
+!=========================================
+      jtree=1
+      temp=p2*fsum
+      do itree=ntreeh-1,1,-1
+         if(itree.eq.1)then
+            if(temp.lt.f(jtree,itree))then
+               jevent=jtree
+            else 
+               jevent=jtree+1
+            endif
+         else
+            if(temp.lt.f(jtree,itree))then
+               jtree=2*jtree-1
+            else
+               temp=temp-f(jtree,itree)
+               jtree=2*jtree+1
+            endif
+         endif
+      enddo 
+      do i=1,n
+         ichangey(i)=0
+      enddo
+      do i = 1,n
+         if(v(i,jevent).ne.0)then
+            y(i) = y(i) + v(i,jevent)
+            ichangey(i)=1
+         endif
+      enddo
+!
+! only updating events & tree entries that have changed
+!
+      do j=1,m
+         do i=1,n
+            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
+               fold=f(j,1)
+               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
+               diff=f(j,1)-fold
+               jdum=int((j+1)/2)
+               do itree=2,ntreeh
+                  f(jdum,itree)=f(jdum,itree)+diff
+                  jdum=int((jdum+1)/2)
+               enddo
+               goto 400
+            endif
+         enddo
+ 400     continue
+      enddo
+ 500  return
+      end
+
+      subroutine kleap(fprob,kappa,t,f,y,v,d,par,n,m,ntreeh,npar,k,&
+           iflag,istate,ipar,ncovar,icovar,mcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension y(n),f(m,ntreeh),p(m),v(n,m),d(n,m),par(npar)
+      dimension k(m),ichangey(n)
+      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
+      external gammarnd,fprob
+!=========================================
+! Determine time interval and update time
+!=========================================
+      fsum=f(1,ntreeh)
+      if(fsum.gt.0.0d0)then
+         tstep=gammarnd(kappa,fsum)
+         t=t+tstep
+      else
+         iflag=1
+         goto 500
+      endif
+!=====================================================
+! Determine frequency of events, update pops & events
+!=====================================================
+      do j=1,m
+         p(j)=f(j,1)/fsum
+      enddo
+      call multinomrnd(kappa,p,m,k)
+!
+! some matrix-vector multiplication but only where necessary
+!
+      do i=1,n
+         ichangey(i)=0
+      enddo
+      do j=1,m
+         if(k(j).ne.0)then
+            temp=k(j)
+            do i = 1,n
+               if(v(i,j).ne.0)then
+                  y(i) = y(i) + temp*v(i,j)
+                  ichangey(i)=1
+               endif
+            enddo
+         endif
+      enddo
+!
+! only updating events & tree entries that have changed
+!
+      do j=1,m
+         do i=1,n
+            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
+               fold=f(j,1)
+               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
+               diff=f(j,1)-fold
+               jdum=int((j+1)/2)
+               do itree=2,ntreeh
+                  f(jdum,itree)=f(jdum,itree)+diff
+                  jdum=int((jdum+1)/2)
+               enddo
+               goto 400
+            endif
+         enddo
+ 400     continue
+      enddo
+ 500  return
+      end
+
+      subroutine tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,k,&
+           iflag,istate,ipar,ncovar,icovar,mcov,cov)
+      implicit integer (i-n)
+      implicit double precision (a-h,o-z)
+      dimension y(n),f(m,ntreeh),k(m),v(n,m),d(n,m),par(npar)
+      dimension ichangey(n)
+      dimension istate(n),ipar(npar),icovar(ncovar),cov(mcov)
+      external poisrnd,fprob
+!======================================================================
+! Generate Poisson random variables (number of event firings in t+tau)
+!======================================================================
+      fsum=f(1,ntreeh)
+      if(fsum.gt.0.0d0)then
+         do j=1,m
+            k(j)=int(poisrnd(f(j,1)*tau))
+         enddo
+      else
+         iflag=1
+         goto 500
+      endif
+!==========
+! Update t
+!==========
+      t=t+tau
+!================================================
+! Compute changes in population numbers & events
+!================================================
+!
+! some matrix-vector multiplication but only where necessary
+!
+      do i=1,n
+         ichangey(i)=0
+      enddo
+      do j=1,m
+         if(k(j).ne.0)then
+            temp=k(j)
+            do i = 1,n
+               if(v(i,j).ne.0)then
+                  y(i) = y(i) + temp*v(i,j)
+                  ichangey(i)=1
+               endif
+            enddo
+         endif
+      enddo
+!
+! only updating events & tree entries that have changed
+!
+      do j=1,m
+         do i=1,n
+            if(ichangey(i).ne.0.and.d(i,j).ne.0)then
+               fold=f(j,1)
+               f(j,1)=fprob(j,t,y,par,istate,ipar,icovar,mcov,cov)
+               diff=f(j,1)-fold
+               jdum=int((j+1)/2)
+               do itree=2,ntreeh
+                  f(jdum,itree)=f(jdum,itree)+diff
+                  jdum=int((jdum+1)/2)
+               enddo
+               goto 400
+            endif
+         enddo
+ 400     continue
+      enddo
+ 500  return
+      end

Modified: pkg/pomp/src/SSA_wrapper.c
===================================================================
--- pkg/pomp/src/SSA_wrapper.c	2013-04-17 11:27:55 UTC (rev 851)
+++ pkg/pomp/src/SSA_wrapper.c	2013-04-17 12:14:11 UTC (rev 852)
@@ -15,7 +15,7 @@
 double F77_SUB(gammarnd)(double shape, double scale) { return rgamma(shape,scale); }
 void F77_SUB(multinomrnd)(int N, double *p, int ncat, int *ix) { rmultinom(N,p,ncat,ix); }
 
-void F77_NAME(driverssa)(_pomp_rxnrate *fprob, int *nvar, int *nevent, int *npar, int *nreps, int *ntimes, 
+void F77_NAME(driverssa)(_pomp_rxnrate fprob, int *nvar, int *nevent, int *npar, int *nreps, int *ntimes, 
 			 int *kflag, double *xstart, double *times, double *params, double *xout,
 			 double *e, double *v, double *d, int *nzero, int *izero, int *istate, 
 			 int *ipar, int *ncov, int *icov, int *lcov, int *mcov, double *tcov, double *cov);


From noreply at r-forge.r-project.org  Wed Apr 17 14:21:19 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 17 Apr 2013 14:21:19 +0200 (CEST)
Subject: [Pomp-commits] r853 - pkg/pomp
Message-ID: <20130417122119.3823B18465C@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-17 14:21:18 +0200 (Wed, 17 Apr 2013)
New Revision: 853

Modified:
   pkg/pomp/DESCRIPTION
Log:
- update DESCRIPTION file


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-04-17 12:14:11 UTC (rev 852)
+++ pkg/pomp/DESCRIPTION	2013-04-17 12:21:18 UTC (rev 853)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.44-4
-Date: 2013-04-16
+Date: 2013-04-17
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),


From noreply at r-forge.r-project.org  Mon Apr 22 14:02:38 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 22 Apr 2013 14:02:38 +0200 (CEST)
Subject: [Pomp-commits] r854 - in pkg/pompExamples: . man tests
Message-ID: <20130422120238.F3BA9184988@r-forge.r-project.org>

Author: kingaa
Date: 2013-04-22 14:02:38 +0200 (Mon, 22 Apr 2013)
New Revision: 854

Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/man/budmoth.Rd
   pkg/pompExamples/man/pertussis.Rd
   pkg/pompExamples/tests/budmoth.R
   pkg/pompExamples/tests/pertussis.R
Log:
- update DESCRIPTION file
- fix errors in man pages


Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2013-04-17 12:21:18 UTC (rev 853)
+++ pkg/pompExamples/DESCRIPTION	2013-04-22 12:02:38 UTC (rev 854)
@@ -2,11 +2,20 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.21-1
-Date: 2013-01-13
-Author: NCEAS Working Group on Inference for Mechanistic Models: Aaron King, Steve Ellner, Bruce Kendall, Daniel C. Reuman, Matt Ferrari, Ed Ionides, Helen Wearing
+Date: 2013-04-22
 Maintainer: Aaron A. King <kingaa at umich.edu>
-Description: Inference methods for partially-observed Markov processes
-Depends: R(>= 2.14.2), stats, methods, graphics, pomp(>= 0.42-2)
+Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
+	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
+	  person(given=c("Carles"),family="Breto",role=c("aut")),
+	  person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
+	  person(given=c("Matthew","J."),family="Ferrari",role=c("ctb")),
+	  person(given=c("Bruce","E."),family="Kendall",role=c("ctb")),
+	  person(given=c("Michael"),family="Lavine",role=c("ctb")),
+	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),
+	  person(given=c("Helen"),family="Wearing",role=c("ctb")))
+URL: http://pomp.r-forge.r-project.org
+Description: More 'pomp' examples.
+Depends: R(>= 3.0.0), stats, methods, graphics, pomp(>= 0.43-8)
 License: GPL (>= 2)
 LazyLoad: true
 LazyData: false

Modified: pkg/pompExamples/man/budmoth.Rd
===================================================================
--- pkg/pompExamples/man/budmoth.Rd	2013-04-17 12:21:18 UTC (rev 853)
+++ pkg/pompExamples/man/budmoth.Rd	2013-04-22 12:02:38 UTC (rev 854)
@@ -22,5 +22,5 @@
 plot(budmoth.sim(para2))
 plot(budmoth.sim(tri))
 }
-\seealso{the dQuote{budmoth-model} vignette}
+\seealso{the \dQuote{budmoth-model} vignette}
 \keyword{datasets}

Modified: pkg/pompExamples/man/pertussis.Rd
===================================================================
--- pkg/pompExamples/man/pertussis.Rd	2013-04-17 12:21:18 UTC (rev 853)
+++ pkg/pompExamples/man/pertussis.Rd	2013-04-22 12:02:38 UTC (rev 854)
@@ -20,5 +20,5 @@
 plot(pertussis.sim(SEIRR.small))
 plot(pertussis.sim(full.big))
 }
-\seealso{the dQuote{pertussis-model} vignette}
+\seealso{the \dQuote{pertussis-model} vignette}
 \keyword{datasets}

Modified: pkg/pompExamples/tests/budmoth.R
===================================================================
--- pkg/pompExamples/tests/budmoth.R	2013-04-17 12:21:18 UTC (rev 853)
+++ pkg/pompExamples/tests/budmoth.R	2013-04-22 12:02:38 UTC (rev 854)
@@ -1,4 +1,4 @@
-require(pompExamples)
+library(pompExamples)
 
 all <- c("food","para1","para2","tri")
 

Modified: pkg/pompExamples/tests/pertussis.R
===================================================================
--- pkg/pompExamples/tests/pertussis.R	2013-04-17 12:21:18 UTC (rev 853)
+++ pkg/pompExamples/tests/pertussis.R	2013-04-22 12:02:38 UTC (rev 854)
@@ -1,4 +1,4 @@
-require(pompExamples)
+library(pompExamples)
 
 all <- c("SEIR.small","SEIR.big","SEIRS.small","SEIRS.big","SEIRR.small","SEIRR.big","full.small","full.big")