[Pomp-commits] r1045 - in pkg/pomp: . R src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 7 00:08:16 CET 2015
Author: kingaa
Date: 2015-01-07 00:08:15 +0100 (Wed, 07 Jan 2015)
New Revision: 1045
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/trajectory-pomp.R
pkg/pomp/src/dmeasure.c
pkg/pomp/src/dprocess.c
pkg/pomp/src/initstate.c
pkg/pomp/src/pomp_internal.h
pkg/pomp/src/rmeasure.c
pkg/pomp/src/rprior.c
pkg/pomp/src/rprocess.c
pkg/pomp/src/skeleton.c
pkg/pomp/tests/bbs-trajmatch.Rout.save
pkg/pomp/tests/bbs.Rout.save
pkg/pomp/tests/blowflies.Rout.save
pkg/pomp/tests/dacca.Rout.save
pkg/pomp/tests/dimchecks.Rout.save
pkg/pomp/tests/fhn.Rout.save
pkg/pomp/tests/filtfail.Rout.save
pkg/pomp/tests/gillespie.Rout.save
pkg/pomp/tests/gompertz.Rout.save
pkg/pomp/tests/logistic.Rout.save
pkg/pomp/tests/ou2-abc.Rout.save
pkg/pomp/tests/ou2-bsmc.Rout.save
pkg/pomp/tests/ou2-bsmc2.Rout.save
pkg/pomp/tests/ou2-forecast.Rout.save
pkg/pomp/tests/ou2-kalman.Rout.save
pkg/pomp/tests/ou2-mif-fp.Rout.save
pkg/pomp/tests/ou2-mif.Rout.save
pkg/pomp/tests/ou2-mif2.Rout.save
pkg/pomp/tests/ou2-nlf.Rout.save
pkg/pomp/tests/ou2-pmcmc.Rout.save
pkg/pomp/tests/ou2-probe.Rout.save
pkg/pomp/tests/ou2-procmeas.R
pkg/pomp/tests/ou2-procmeas.Rout.save
pkg/pomp/tests/ou2-simulate.Rout.save
pkg/pomp/tests/ou2-trajmatch.Rout.save
pkg/pomp/tests/partrans.Rout.save
pkg/pomp/tests/pfilter.Rout.save
pkg/pomp/tests/pomppomp.Rout.save
pkg/pomp/tests/prior.Rout.save
pkg/pomp/tests/ricker-bsmc.Rout.save
pkg/pomp/tests/ricker-probe.Rout.save
pkg/pomp/tests/ricker-spect.Rout.save
pkg/pomp/tests/ricker.Rout.save
pkg/pomp/tests/rw2.Rout.save
pkg/pomp/tests/sir.Rout.save
pkg/pomp/tests/skeleton.Rout.save
pkg/pomp/tests/steps.Rout.save
pkg/pomp/tests/synlik.Rout.save
pkg/pomp/tests/verhulst.Rout.save
Log:
- use names on dimnames of arrays returned by basic pomp methods
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/DESCRIPTION 2015-01-06 23:08:15 UTC (rev 1045)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.57-1
-Date: 2015-01-02
+Version: 0.57-2
+Date: 2015-01-06
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")),
Modified: pkg/pomp/R/trajectory-pomp.R
===================================================================
--- pkg/pomp/R/trajectory-pomp.R 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/R/trajectory-pomp.R 2015-01-06 23:08:15 UTC (rev 1045)
@@ -91,6 +91,8 @@
}
+ dimnames(x) <- setNames(dimnames(x),c("variable","rep","time"))
+
if (as.data.frame) {
x <- lapply(
seq_len(ncol(x)),
Modified: pkg/pomp/src/dmeasure.c
===================================================================
--- pkg/pomp/src/dmeasure.c 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/dmeasure.c 2015-01-06 23:08:15 UTC (rev 1045)
@@ -129,7 +129,9 @@
// create array to store results
{
int dim[2] = {nreps, ntimes};
+ const char *dimnm[2] = {"rep","time"};
PROTECT(F = makearray(2,dim)); nprotect++;
+ fixdimnames(F,dimnm,2);
}
// now do computations
Modified: pkg/pomp/src/dprocess.c
===================================================================
--- pkg/pomp/src/dprocess.c 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/dprocess.c 2015-01-06 23:08:15 UTC (rev 1045)
@@ -109,7 +109,10 @@
UNPROTECT(nprotect);
error("dprocess error: user 'dprocess' must return a %d x %d array",nreps,ntimes-1);
}
-
+ {
+ const char *dimnms[2] = {"rep","time"};
+ fixdimnames(X,dimnms,2);
+ }
UNPROTECT(nprotect);
return X;
}
Modified: pkg/pomp/src/initstate.c
===================================================================
--- pkg/pomp/src/initstate.c 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/initstate.c 2015-01-06 23:08:15 UTC (rev 1045)
@@ -18,6 +18,7 @@
int npar, nrep, nvar;
int xdim[2], j, k;
double *p, *pp, *xp, *xpp;
+ const char *dimnms[2] = {"variable","rep"};
PROTECT(params = as_matrix(params)); nprotect++;
dim = INTEGER(GET_DIM(params));
@@ -76,6 +77,7 @@
xdim[0] = nvar; xdim[1] = nrep;
PROTECT(x = makearray(2,xdim)); nprotect++;
setrownames(x,statenames,2);
+ fixdimnames(x,dimnms,2);
xpp = REAL(x);
for (k = 0; k < nvar; k++) xpp[k] = xp[k];
Modified: pkg/pomp/src/pomp_internal.h
===================================================================
--- pkg/pomp/src/pomp_internal.h 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/pomp_internal.h 2015-01-06 23:08:15 UTC (rev 1045)
@@ -13,7 +13,6 @@
# define MATCHNAMES(X,N,W) (matchnames(GET_NAMES(X),(N),(W)))
# define MATCHROWNAMES(X,N,W) (matchnames(GET_ROWNAMES(GET_DIMNAMES(X)),(N),(W)))
# define MATCHCOLNAMES(X,N,W) (matchnames(GET_COLNAMES(GET_DIMNAMES(X)),(N),(W)))
-# define MATCH_CHAR_TO_ROWNAMES(X,N,A) (match_char_to_names(GET_ROWNAMES(GET_DIMNAMES(X)),(N),(A)))
// lookup-table structure, as used internally
typedef struct lookup_table {
@@ -77,27 +76,25 @@
void unset_pomp_userdata (void);
static R_INLINE SEXP makearray (int rank, int *dim) {
- int nprotect = 0;
int *dimp, k;
double *xp;
SEXP dimx, x;
- PROTECT(dimx = NEW_INTEGER(rank)); nprotect++;
+ PROTECT(dimx = NEW_INTEGER(rank));
dimp = INTEGER(dimx);
for (k = 0; k < rank; k++) dimp[k] = dim[k];
- PROTECT(x = allocArray(REALSXP,dimx)); nprotect++;
+ PROTECT(x = allocArray(REALSXP,dimx));
xp = REAL(x);
for (k = 0; k < length(x); k++) xp[k] = NA_REAL;
- UNPROTECT(nprotect);
+ UNPROTECT(2);
return x;
}
static R_INLINE SEXP matchnames (SEXP x, SEXP names, const char *where) {
- int nprotect = 0;
int n = length(names);
int *idx, k;
SEXP index, nm;
- PROTECT(nm = AS_CHARACTER(names)); nprotect++;
- PROTECT(index = match(x,names,0)); nprotect++;
+ PROTECT(nm = AS_CHARACTER(names));
+ PROTECT(index = match(x,names,0));
idx = INTEGER(index);
for (k = 0; k < n; k++) {
if (idx[k]==0)
@@ -106,31 +103,10 @@
where);
idx[k] -= 1;
}
- UNPROTECT(nprotect);
+ UNPROTECT(2);
return index;
}
-static R_INLINE SEXP match_char_to_names (SEXP x, int n, char **names) {
- int nprotect = 0;
- int *idx, k;
- SEXP index, nm;
- PROTECT(nm = NEW_CHARACTER(n)); nprotect++;
- for (k = 0; k < n; k++) {
- SET_STRING_ELT(nm,k,mkChar(names[k]));
- }
- PROTECT(index = match(x,nm,0)); nprotect++;
- idx = INTEGER(index);
- for (k = 0; k < n; k++) {
- if (idx[k]==0) {
- UNPROTECT(nprotect);
- error("variable %s not specified",names[k]);
- }
- idx[k] -= 1;
- }
- UNPROTECT(nprotect);
- return index;
-}
-
static R_INLINE SEXP name_index (SEXP names, SEXP object, const char *slot) {
SEXP slotnames, index;
PROTECT(slotnames = GET_SLOT(object,install(slot)));
@@ -144,12 +120,27 @@
}
static R_INLINE void setrownames (SEXP x, SEXP names, int n) {
- int nprotect = 0;
SEXP dimnms, nm;
- PROTECT(nm = AS_CHARACTER(names)); nprotect++;
- PROTECT(dimnms = allocVector(VECSXP,n)); nprotect++;
+ PROTECT(nm = AS_CHARACTER(names));
+ PROTECT(dimnms = allocVector(VECSXP,n));
SET_ELEMENT(dimnms,0,nm); // set row names
SET_DIMNAMES(x,dimnms);
+ UNPROTECT(2);
+}
+
+static R_INLINE void fixdimnames (SEXP x, const char **names, int n) {
+ int nprotect = 0;
+ int i;
+ SEXP dimnames, nm;
+ PROTECT(dimnames = GET_DIMNAMES(x)); nprotect++;
+ if (isNull(dimnames)) {
+ PROTECT(dimnames = allocVector(VECSXP,n)); nprotect++;
+ }
+ PROTECT(nm = allocVector(VECSXP,n)); nprotect++;
+ for (i = 0; i < n; i++)
+ SET_ELEMENT(nm,i,mkChar(names[i]));
+ SET_NAMES(dimnames,nm);
+ SET_DIMNAMES(x,dimnames);
UNPROTECT(nprotect);
}
Modified: pkg/pomp/src/rmeasure.c
===================================================================
--- pkg/pomp/src/rmeasure.c 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/rmeasure.c 2015-01-06 23:08:15 UTC (rev 1045)
@@ -61,8 +61,10 @@
{
int dim[3] = {nobs, nreps, ntimes};
+ const char *dimnm[3] = {"variable","rep","time"};
PROTECT(Y = makearray(3,dim)); nprotect++;
setrownames(Y,Onames,3);
+ fixdimnames(Y,dimnm,3);
}
// extract the user-defined function
Modified: pkg/pomp/src/rprior.c
===================================================================
--- pkg/pomp/src/rprior.c 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/rprior.c 2015-01-06 23:08:15 UTC (rev 1045)
@@ -20,6 +20,7 @@
SEXP Pnames, P, fn, fcall;
SEXP pompfun;
int *dim;
+ const char *dimnms[2] = {"variable","rep"};
PROTECT(params = as_matrix(params)); nprotect++;
dim = INTEGER(GET_DIM(params));
@@ -144,5 +145,6 @@
}
UNPROTECT(nprotect);
+ fixdimnames(P,dimnms,2);
return P;
}
Modified: pkg/pomp/src/rprocess.c
===================================================================
--- pkg/pomp/src/rprocess.c 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/rprocess.c 2015-01-06 23:08:15 UTC (rev 1045)
@@ -14,6 +14,7 @@
int *xdim, nvars, npars, nreps, nrepsx, ntimes, off;
SEXP X, Xoff, copy, fn, fcall, rho;
SEXP dimXstart, dimP, dimX;
+ const char *dimnm[3] = {"variable","rep","time"};
PROTECT(gnsi = duplicate(gnsi)); nprotect++;
@@ -113,10 +114,12 @@
xdim[2] -= off;
PROTECT(Xoff = makearray(3,xdim)); nprotect++;
setrownames(Xoff,GET_ROWNAMES(GET_DIMNAMES(X)),3);
+ fixdimnames(Xoff,dimnm,3);
memcpy(REAL(Xoff),REAL(X)+off*nvars*nreps,(ntimes-off)*nvars*nreps*sizeof(double));
UNPROTECT(nprotect);
return Xoff;
} else {
+ fixdimnames(X,dimnm,3);
UNPROTECT(nprotect);
return X;
}
Modified: pkg/pomp/src/skeleton.c
===================================================================
--- pkg/pomp/src/skeleton.c 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/src/skeleton.c 2015-01-06 23:08:15 UTC (rev 1045)
@@ -131,8 +131,10 @@
// set up the array to hold results
{
int dim[3] = {nvars, nreps, ntimes};
+ const char *dimnms[3] = {"variable","rep","time"};
PROTECT(F = makearray(3,dim)); nprotect++;
setrownames(F,Snames,3);
+ fixdimnames(F,dimnms,3);
}
// first do setup
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -80,4 +80,4 @@
>
> proc.time()
user system elapsed
- 2.725 0.017 2.733
+ 2.480 0.052 2.555
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/bbs.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -69,4 +69,4 @@
>
> proc.time()
user system elapsed
- 7.769 0.051 7.832
+ 7.008 0.076 7.124
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/blowflies.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -24,45 +24,47 @@
blowflies1 blowflies2
>
> init.state(blowflies1)
- [,1]
-N1 397.0
-N2 450.5
-N3 504.0
-N4 590.0
-N5 676.0
-N6 738.5
-N7 801.0
-N8 829.5
-N9 858.0
-N10 884.5
-N11 911.0
-N12 926.5
-N13 942.0
-N14 945.0
-N15 948.0
-R 0.0
-S 0.0
-e 0.0
-eps 0.0
+ rep
+variable [,1]
+ N1 397.0
+ N2 450.5
+ N3 504.0
+ N4 590.0
+ N5 676.0
+ N6 738.5
+ N7 801.0
+ N8 829.5
+ N9 858.0
+ N10 884.5
+ N11 911.0
+ N12 926.5
+ N13 942.0
+ N14 945.0
+ N15 948.0
+ R 0.0
+ S 0.0
+ e 0.0
+ eps 0.0
> x1 <- simulate(blowflies1)
> f1 <- pfilter(blowflies1,Np=1000,seed=599688L)
> logLik(f1)
[1] -1466.694
>
> init.state(blowflies2)
- [,1]
-N1 397
-N2 504
-N3 676
-N4 801
-N5 858
-N6 911
-N7 942
-N8 948
-R 0
-S 0
-e 0
-eps 0
+ rep
+variable [,1]
+ N1 397
+ N2 504
+ N3 676
+ N4 801
+ N5 858
+ N6 911
+ N7 942
+ N8 948
+ R 0
+ S 0
+ e 0
+ eps 0
> x2 <- simulate(blowflies2)
> f2 <- pfilter(blowflies2,Np=1000,seed=599688L)
> logLik(f2)
@@ -70,4 +72,4 @@
>
> proc.time()
user system elapsed
- 1.493 0.039 1.519
+ 1.304 0.044 1.380
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/dacca.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -107,4 +107,4 @@
>
> proc.time()
user system elapsed
- 14.817 0.035 14.853
+ 10.852 0.064 10.968
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/dimchecks.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -29,19 +29,22 @@
> pars <- coef(po)
> xstart <- init.state(po,params=pars)
> rprocess(po,xstart,times=0:5,params=pars)[,1,]
- [,1] [,2] [,3] [,4] [,5] [,6]
-N 7 0.4578051 11.78599703 0.004766933 0.2732487 14.6301023
-e 0 0.4727782 -0.09397106 0.173032749 0.2534460 0.4537029
+ time
+variable [,1] [,2] [,3] [,4] [,5] [,6]
+ N 7 0.4578051 11.78599703 0.004766933 0.2732487 14.6301023
+ e 0 0.4727782 -0.09397106 0.173032749 0.2534460 0.4537029
>
> rprocess(po,xstart=parmat(xstart,5),times=0:5,params=pars)[,3,]
- [,1] [,2] [,3] [,4] [,5] [,6]
-N 7 0.1788532 8.0265735 0.11906954 4.1101032 4.7809853
-e 0 -0.4671001 0.1828009 0.01576817 -0.1394347 0.4613017
+ time
+variable [,1] [,2] [,3] [,4] [,5] [,6]
+ N 7 0.1788532 8.0265735 0.11906954 4.1101032 4.7809853
+ e 0 -0.4671001 0.1828009 0.01576817 -0.1394347 0.4613017
>
> rprocess(po,xstart=xstart,times=0:5,params=parmat(pars,3))[,3,]
- [,1] [,2] [,3] [,4] [,5] [,6]
-N 7 0.3200483 7.9793435 0.1061246 6.3880659 0.5943893
-e 0 0.1148066 -0.2638123 -0.1406537 0.4036972 0.2134135
+ time
+variable [,1] [,2] [,3] [,4] [,5] [,6]
+ N 7 0.3200483 7.9793435 0.1061246 6.3880659 0.5943893
+ e 0 0.1148066 -0.2638123 -0.1406537 0.4036972 0.2134135
>
> try(
+ rprocess(po,xstart=parmat(xstart,2),times=0:5,params=parmat(pars,3))[,,3]
@@ -50,9 +53,10 @@
rprocess error: larger number of replicates is not a multiple of smaller
>
> rprocess(po,xstart=parmat(xstart,2),times=0:5,params=parmat(pars,6))[,,3]
- [,1] [,2] [,3] [,4] [,5] [,6]
-N 11.4232929 11.3881039 4.8636396 7.1427117 9.4874566 9.65359657
-e 0.1987878 0.2241485 -0.5425199 -0.1655866 0.2008968 -0.09235699
+ rep
+variable [,1] [,2] [,3] [,4] [,5] [,6]
+ N 11.4232929 11.3881039 4.8636396 7.1427117 9.4874566 9.65359657
+ e 0.1987878 0.2241485 -0.5425199 -0.1655866 0.2008968 -0.09235699
>
> x <- rprocess(po,xstart=parmat(xstart,2),times=0:5,params=parmat(pars,8))
>
@@ -68,72 +72,85 @@
> rmeasure(po,x=x,params=parmat(pars,4),times=0:5)
, , 1
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y 95 77 70 84 75 65 55 73
+ rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+ y 95 77 70 84 75 65 55 73
, , 2
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y 6 2 4 9 3 1 2 1
+ rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+ y 6 2 4 9 3 1 2 1
, , 3
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y 107 67 95 99 74 54 36 74
+ rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+ y 107 67 95 99 74 54 36 74
, , 4
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y 0 7 0 0 1 4 10 5
+ rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+ y 0 7 0 0 1 4 10 5
, , 5
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y 7 178 14 1 82 190 200 88
+ rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+ y 7 178 14 1 82 190 200 88
, , 6
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-y 216 0 190 106 1 0 0 0
+ rep
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+ y 216 0 190 106 1 0 0 0
>
> x <- rprocess(po,xstart=xstart,times=0:5,params=pars)
> rmeasure(po,x=x,params=parmat(pars,2),times=0:5)
, , 1
- [,1] [,2]
-y 79 73
+ rep
+variable [,1] [,2]
+ y 79 73
, , 2
- [,1] [,2]
-y 1 1
+ rep
+variable [,1] [,2]
+ y 1 1
, , 3
- [,1] [,2]
-y 73 51
+ rep
+variable [,1] [,2]
+ y 73 51
, , 4
- [,1] [,2]
-y 10 12
+ rep
+variable [,1] [,2]
+ y 10 12
, , 5
- [,1] [,2]
-y 193 186
+ rep
+variable [,1] [,2]
+ y 193 186
, , 6
- [,1] [,2]
-y 0 0
+ rep
+variable [,1] [,2]
+ y 0 0
>
> y <- rmeasure(po,x=x,params=parmat(pars,4),times=0:5)
> dmeasure(po,x=x,y=y[,2,,drop=F],params=pars,times=0:5)
- [,1] [,2] [,3] [,4] [,5] [,6]
-[1,] 0.002350788 0.268881 0.04825714 0.1309304 0.02090266 0.9998435
+ time
+rep [,1] [,2] [,3] [,4] [,5] [,6]
+ [1,] 0.002350788 0.268881 0.04825714 0.1309304 0.02090266 0.9998435
>
> x <- rprocess(po,xstart=parmat(xstart,3),times=0:5,params=pars)
> y <- rmeasure(po,x=x,params=pars,times=0:5)
@@ -162,4 +179,4 @@
>
> proc.time()
user system elapsed
- 0.489 0.041 0.517
+ 0.560 0.092 0.677
Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/fhn.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -44,15 +44,17 @@
> skeleton(fhn,x,t=c(0,3),params=params)
, , 1
- [,1] [,2]
-V -0.40 -6.666667
-R -0.05 0.100000
+ rep
+variable [,1] [,2]
+ V -0.40 -6.666667
+ R -0.05 0.100000
, , 2
- [,1] [,2]
-V 0.9333333 5.0
-R 0.4500000 0.2
+ rep
+variable [,1] [,2]
+ V 0.9333333 5.0
+ R 0.4500000 0.2
> y <- trajectory(fhn,params=params,hmax=0.1)
> invisible(y[,,599:601])
@@ -91,4 +93,4 @@
>
> proc.time()
user system elapsed
- 0.927 0.060 0.950
+ 1.084 0.064 1.285
Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/filtfail.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -116,4 +116,4 @@
>
> proc.time()
user system elapsed
- 0.489 0.053 0.529
+ 0.576 0.068 0.660
Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/gillespie.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -131,4 +131,4 @@
>
> proc.time()
user system elapsed
- 2.565 0.041 2.592
+ 2.564 0.048 2.635
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/gompertz.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -133,4 +133,4 @@
>
> proc.time()
user system elapsed
- 1.797 0.038 1.822
+ 1.576 0.052 1.652
Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/logistic.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -76,8 +76,9 @@
+ ),
+ digits=4
+ )
- [,1] [,2] [,3] [,4] [,5]
-[1,] 0.001204 0.0005132 0.0005411 0.0007547 0.0005974
+ time
+rep [,1] [,2] [,3] [,4] [,5]
+ [1,] 0.001204 0.0005132 0.0005411 0.0007547 0.0005974
>
> print(
+ dmeasure(
@@ -90,8 +91,9 @@
+ ),
+ digits=4
+ )
- [,1] [,2] [,3] [,4] [,5] [,6]
-[1,] -7.915 -8.896 -7.992 -8.196 -11.12 -7.946
+ time
+rep [,1] [,2] [,3] [,4] [,5] [,6]
+ [1,] -7.915 -8.896 -7.992 -8.196 -11.12 -7.946
>
> print(
+ drop(
@@ -122,4 +124,4 @@
>
> proc.time()
user system elapsed
- 0.874 0.030 0.887
+ 0.976 0.052 1.175
Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-abc.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -131,4 +131,4 @@
>
> proc.time()
user system elapsed
- 11.085 0.055 11.138
+ 9.612 0.100 9.906
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -59,7 +59,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 3.430529 secs
+Time difference of 2.789886 secs
>
> print(
+ cbind(
@@ -101,4 +101,4 @@
>
> proc.time()
user system elapsed
- 5.498 0.064 5.527
+ 4.688 0.064 4.785
Modified: pkg/pomp/tests/ou2-bsmc2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc2.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-bsmc2.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -56,7 +56,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 2.234756 secs
+Time difference of 2.022153 secs
>
> print(
+ cbind(
@@ -98,4 +98,4 @@
>
> proc.time()
user system elapsed
- 3.846 0.045 3.881
+ 3.588 0.084 3.697
Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-forecast.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -61,4 +61,4 @@
>
> proc.time()
user system elapsed
- 1.376 0.042 1.402
+ 1.420 0.036 1.559
Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-kalman.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -164,7 +164,7 @@
117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 3.235065 secs
+Time difference of 3.309699 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
@@ -188,4 +188,4 @@
>
> proc.time()
user system elapsed
- 3.769 0.026 3.787
+ 3.960 0.044 4.036
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -70,4 +70,4 @@
>
> proc.time()
user system elapsed
- 24.537 0.066 24.614
+ 19.413 0.056 19.690
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -281,4 +281,4 @@
>
> proc.time()
user system elapsed
- 13.791 0.053 13.848
+ 11.452 0.064 11.704
Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-mif2.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -135,4 +135,4 @@
>
> proc.time()
user system elapsed
- 62.157 0.075 62.274
+ 49.355 0.040 49.763
Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-nlf.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -85,4 +85,4 @@
>
> proc.time()
user system elapsed
- 5.003 0.037 5.037
+ 4.380 0.092 6.425
Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -114,4 +114,4 @@
>
> proc.time()
user system elapsed
- 26.822 0.042 26.880
+ 24.125 0.068 24.493
Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-probe.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -340,4 +340,4 @@
>
> proc.time()
user system elapsed
- 8.501 0.048 8.545
+ 7.892 0.092 8.187
Modified: pkg/pomp/tests/ou2-procmeas.R
===================================================================
--- pkg/pomp/tests/ou2-procmeas.R 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-procmeas.R 2015-01-06 23:08:15 UTC (rev 1045)
@@ -23,8 +23,8 @@
x <- simulate(po,states=T,params=coef(po))
dp2 <- dprocess(po,x=x,times=time(po),params=coef(po),log=T)
dp3 <- dprocess(po,x=x,times=time(po),params=pmat,log=T)
-stopifnot(identical(rbind(dp2,dp2,dp2),dp3))
+stopifnot(identical(rbind(dp2,dp2,dp2),unname(dp3)))
dm2 <- dmeasure(po,x=x,y=obs(po),times=time(po),params=coef(po),log=T)
dm3 <- dmeasure(po,x=x,y=obs(po),times=time(po),params=pmat,log=T)
-stopifnot(identical(rbind(dm2,dm2,dm2),dm3))
+stopifnot(identical(rbind(dm2,dm2,dm2),unname(dm3)))
Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -46,12 +46,12 @@
> x <- simulate(po,states=T,params=coef(po))
> dp2 <- dprocess(po,x=x,times=time(po),params=coef(po),log=T)
> dp3 <- dprocess(po,x=x,times=time(po),params=pmat,log=T)
-> stopifnot(identical(rbind(dp2,dp2,dp2),dp3))
+> stopifnot(identical(rbind(dp2,dp2,dp2),unname(dp3)))
>
> dm2 <- dmeasure(po,x=x,y=obs(po),times=time(po),params=coef(po),log=T)
> dm3 <- dmeasure(po,x=x,y=obs(po),times=time(po),params=pmat,log=T)
-> stopifnot(identical(rbind(dm2,dm2,dm2),dm3))
+> stopifnot(identical(rbind(dm2,dm2,dm2),unname(dm3)))
>
> proc.time()
user system elapsed
- 0.493 0.037 0.495
+ 0.408 0.048 0.479
Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-simulate.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -35,7 +35,7 @@
> ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.007747889 secs
+Time difference of 0.006910086 secs
>
> coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
>
@@ -46,4 +46,4 @@
>
> proc.time()
user system elapsed
- 0.501 0.022 0.507
+ 0.508 0.040 0.572
Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -175,4 +175,4 @@
>
> proc.time()
user system elapsed
- 1.740 0.048 1.765
+ 1.712 0.060 1.801
Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/partrans.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -52,4 +52,4 @@
>
> proc.time()
user system elapsed
- 0.492 0.020 0.494
+ 0.600 0.060 0.678
Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/pfilter.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -77,4 +77,4 @@
>
> proc.time()
user system elapsed
- 9.887 0.037 9.924
+ 8.448 0.080 8.699
Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/pomppomp.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -55,4 +55,4 @@
>
> proc.time()
user system elapsed
- 0.489 0.030 0.504
+ 0.580 0.064 0.663
Modified: pkg/pomp/tests/prior.Rout.save
===================================================================
--- pkg/pomp/tests/prior.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/prior.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -53,18 +53,19 @@
>
> stopifnot(all.equal(mean(dprior(po,params=parmat(coef(po),3))),dnorm(x=0,mean=0,sd=5)^4))
> rprior(po,params=coef(po))
- [,1]
-alpha.1 -2.2417803
-alpha.2 0.7708391
-alpha.3 -3.2398829
-alpha.4 9.9993334
-sigma.1 3.0000000
-sigma.2 -0.5000000
-sigma.3 2.0000000
-tau 1.0000000
-x1.0 -3.0000000
-x2.0 4.0000000
-alpha.sd 5.0000000
+ rep
+variable [,1]
+ alpha.1 -2.2417803
+ alpha.2 0.7708391
+ alpha.3 -3.2398829
+ alpha.4 9.9993334
+ sigma.1 3.0000000
+ sigma.2 -0.5000000
+ sigma.3 2.0000000
+ tau 1.0000000
+ x1.0 -3.0000000
+ x2.0 4.0000000
+ alpha.sd 5.0000000
>
> coef(po,"alpha.sd") <- 1
> mean(dprior(po,params=rprior(po,params=parmat(coef(po),10000)),log=TRUE))+0.5*(1+log(2*pi))*4
@@ -72,4 +73,4 @@
>
> proc.time()
user system elapsed
- 0.683 0.025 0.694
+ 0.736 0.056 0.809
Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -54,4 +54,4 @@
>
> proc.time()
user system elapsed
- 2.571 0.057 2.614
+ 2.604 0.072 2.860
Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ricker-probe.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -297,4 +297,4 @@
>
> proc.time()
user system elapsed
- 13.643 0.070 13.713
+ 11.976 0.072 12.278
Modified: pkg/pomp/tests/ricker-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-spect.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ricker-spect.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -70,4 +70,4 @@
>
> proc.time()
user system elapsed
- 2.504 0.018 2.511
+ 2.284 0.084 3.241
Modified: pkg/pomp/tests/ricker.Rout.save
===================================================================
--- pkg/pomp/tests/ricker.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/ricker.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -83,4 +83,4 @@
>
> proc.time()
user system elapsed
- 0.554 0.038 0.579
+ 0.704 0.048 0.884
Modified: pkg/pomp/tests/rw2.Rout.save
===================================================================
--- pkg/pomp/tests/rw2.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/rw2.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -164,7 +164,7 @@
}
y
}
-<environment: 0x1c9a9f8>
+<environment: 0x24441b8>
measurement model density, dmeasure =
function (y, x, t, params, log, covars, ...)
{
@@ -177,7 +177,7 @@
f
else exp(f)
}
-<environment: 0x1c9a9f8>
+<environment: 0x24441b8>
prior simulator, rprior =
function not specified
prior density, dprior =
@@ -342,4 +342,4 @@
>
> proc.time()
user system elapsed
- 0.879 0.041 0.908
+ 0.992 0.040 1.052
Modified: pkg/pomp/tests/sir.Rout.save
===================================================================
--- pkg/pomp/tests/sir.Rout.save 2015-01-06 23:07:54 UTC (rev 1044)
+++ pkg/pomp/tests/sir.Rout.save 2015-01-06 23:08:15 UTC (rev 1045)
@@ -192,7 +192,7 @@
method = 0L, zeronames = zeronames, tcovar = tcovar,
covar = covar, args = pairlist(...), gnsi = .getnativesymbolinfo)
}
-<environment: 0x151f968>
+<environment: 0x24f3bf8>
process model density, dprocess =
function (x, times, params, ..., tcovar, covar, log = FALSE,
.getnativesymbolinfo = TRUE)
@@ -201,7 +201,7 @@
params = params, tcovar = tcovar, covar = covar, log = log,
args = pairlist(...), gnsi = .getnativesymbolinfo)
}
-<environment: 0x1272bc8>
+<environment: 0x228d048>
measurement model simulator, rmeasure =
function (x, t, params, covars, ...)
{
@@ -274,7 +274,7 @@
> x <- simulate(po,nsim=3)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.9468338 secs
+Time difference of 0.8555272 secs
>
> pdf(file='sir.pdf')
>
@@ -291,7 +291,7 @@
> X3 <- trajectory(po,times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.560688 secs
+Time difference of 0.5343869 secs
> plot(t3,X3['I',1,],type='l')
>
> f1 <- dprocess(
@@ -322,14 +322,16 @@
+ params=params
+ )
> print(h1[c("S","I","R"),,],digits=4)
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
-S 32161.6 31582.4 32142.21 31758.36 31639.0 32006 31953.5 31666
-I -318.4 -218.9 -88.93 21.52 128.7 218 309.2 403
-R -31855.2 -31375.0 -32064.98 -31792.40 -31780.0 -32236 -32276.8 -32083
- [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
-S 31017.5 29782.5 29443.9 28916.7 27997.1 27494 26434 25448
-I 518.5 675.3 768.6 868.8 996.8 1074 1187 1278
-R -31549.7 -30472.3 -30226.0 -29798.8 -29007.2 -28580 -27634 -26740
+ time
+variable [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+ S 32161.6 31582.4 32142.21 31758.36 31639.0 32006 31953.5 31666
+ I -318.4 -218.9 -88.93 21.52 128.7 218 309.2 403
+ R -31855.2 -31375.0 -32064.98 -31792.40 -31780.0 -32236 -32276.8 -32083
+ time
+variable [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
+ S 31017.5 29782.5 29443.9 28916.7 27997.1 27494 26434 25448
+ I 518.5 675.3 768.6 868.8 996.8 1074 1187 1278
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1045
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