[Pomp-commits] r839 - in pkg/pomp: . R src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 21 15:35:11 CET 2013
Author: kingaa
Date: 2013-03-21 15:35:10 +0100 (Thu, 21 Mar 2013)
New Revision: 839
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/authors.R
pkg/pomp/src/SSA_wrapper.c
pkg/pomp/src/blowfly.c
pkg/pomp/src/dprocess.c
pkg/pomp/src/partrans.c
Log:
- update author list
- fix some warnings generated by clang
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2013-03-20 19:41:25 UTC (rev 838)
+++ pkg/pomp/DESCRIPTION 2013-03-21 14:35:10 UTC (rev 839)
@@ -1,10 +1,21 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.44-2
-Date: 2013-03-11
-Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
+Version: 0.44-3
+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
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("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: pkg/pomp/R/authors.R
===================================================================
--- pkg/pomp/R/authors.R 2013-03-20 19:41:25 UTC (rev 838)
+++ pkg/pomp/R/authors.R 2013-03-21 14:35:10 UTC (rev 839)
@@ -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: pkg/pomp/src/SSA_wrapper.c
===================================================================
--- pkg/pomp/src/SSA_wrapper.c 2013-03-20 19:41:25 UTC (rev 838)
+++ pkg/pomp/src/SSA_wrapper.c 2013-03-21 14:35:10 UTC (rev 839)
@@ -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: pkg/pomp/src/blowfly.c
===================================================================
--- pkg/pomp/src/blowfly.c 2013-03-20 19:41:25 UTC (rev 838)
+++ pkg/pomp/src/blowfly.c 2013-03-21 14:35:10 UTC (rev 839)
@@ -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: pkg/pomp/src/dprocess.c
===================================================================
--- pkg/pomp/src/dprocess.c 2013-03-20 19:41:25 UTC (rev 838)
+++ pkg/pomp/src/dprocess.c 2013-03-21 14:35:10 UTC (rev 839)
@@ -12,7 +12,7 @@
int nprotect = 0;
int *xdim, npars, nvars, nreps, nrepsx, ntimes;
SEXP X, fn, fcall, rho;
- SEXP dimP, dimF;
+ SEXP dimF;
PROTECT(gnsi = duplicate(gnsi)); nprotect++;
Modified: pkg/pomp/src/partrans.c
===================================================================
--- pkg/pomp/src/partrans.c 2013-03-20 19:41:25 UTC (rev 838)
+++ pkg/pomp/src/partrans.c 2013-03-21 14:35:10 UTC (rev 839)
@@ -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;
char direc;
int qmat;
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