[Pomp-commits] r848 - in branches/premif2: . R src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 16 18:27:03 CEST 2013
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
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