[Pomp-commits] r1207 - in pkg/pomp: R src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 17 14:56:36 CEST 2015
Author: kingaa
Date: 2015-06-17 14:56:36 +0200 (Wed, 17 Jun 2015)
New Revision: 1207
Modified:
pkg/pomp/R/abc.R
pkg/pomp/R/bsmc2.R
pkg/pomp/R/mif2.R
pkg/pomp/R/pfilter.R
pkg/pomp/R/profile-design.R
pkg/pomp/R/sannbox.R
pkg/pomp/R/simulate-pomp.R
pkg/pomp/src/cholmodel.c
pkg/pomp/src/dprior.c
pkg/pomp/src/initstate.c
pkg/pomp/src/pomp_fun.c
pkg/pomp/src/rprior.c
pkg/pomp/src/simulate.c
Log:
- minor edits to purge unused variables and obviate certain compiler warnings
Modified: pkg/pomp/R/abc.R
===================================================================
--- pkg/pomp/R/abc.R 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/R/abc.R 2015-06-17 12:56:36 UTC (rev 1207)
@@ -65,8 +65,6 @@
if (!all(sapply(probes,function(f)length(formals(f))==1)))
stop("each probe must be a function of a single argument")
- ntimes <- length(time(object))
-
if (verbose) {
cat("performing",Nabc,"ABC iteration(s)\n")
}
Modified: pkg/pomp/R/bsmc2.R
===================================================================
--- pkg/pomp/R/bsmc2.R 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/R/bsmc2.R 2015-06-17 12:56:36 UTC (rev 1207)
@@ -82,7 +82,6 @@
params
}
)
- statenames <- rownames(xstart)
nvars <- nrow(xstart)
ptsi.for <- FALSE
Modified: pkg/pomp/R/mif2.R
===================================================================
--- pkg/pomp/R/mif2.R 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/R/mif2.R 2015-06-17 12:56:36 UTC (rev 1207)
@@ -59,10 +59,6 @@
times <- time(object,t0=TRUE)
ntimes <- length(times)-1
- paramnames <- rownames(params)
- npars <- nrow(params)
- rwnames <- rownames(rw.sd)
-
loglik <- rep(NA,ntimes)
eff.sample.size <- numeric(ntimes)
nfail <- 0
Modified: pkg/pomp/R/pfilter.R
===================================================================
--- pkg/pomp/R/pfilter.R 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/R/pfilter.R 2015-06-17 12:56:36 UTC (rev 1207)
@@ -46,7 +46,7 @@
pompLoad(object)
- ptsi.inv <- ptsi.for <- gnsi.rproc <- gnsi.dmeas <- as.logical(.getnativesymbolinfo)
+ ptsi.for <- gnsi.rproc <- gnsi.dmeas <- as.logical(.getnativesymbolinfo)
mif2 <- as.logical(.mif2)
transform <- as.logical(.transform)
Modified: pkg/pomp/R/profile-design.R
===================================================================
--- pkg/pomp/R/profile-design.R 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/R/profile-design.R 2015-06-17 12:56:36 UTC (rev 1207)
@@ -7,7 +7,6 @@
ovars <- names(lower)
if (!all(sort(ovars)==sort(names(upper))))
stop(sQuote("profileDesign"),": names of ",sQuote("lower")," and ",sQuote("upper")," must match!")
- vars <- ovars[!(ovars%in%pvars)]
x <- expand.grid(...,stringsAsFactors=stringsAsFactors)
y <- sobolDesign(lower=lower,upper=upper,nseq=nprof)
z <- vector(mode='list',length=nrow(x)*nprof)
Modified: pkg/pomp/R/sannbox.R
===================================================================
--- pkg/pomp/R/sannbox.R 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/R/sannbox.R 2015-06-17 12:56:36 UTC (rev 1207)
@@ -57,7 +57,6 @@
control$upper <- rep(control$upper,npar)
## initialization for the algorithm
- laststep <- 0
thetabest <- thetacurrent <- par
ycurrent <- fn(thetacurrent,...)/control$fnscale
if (!is.finite(ycurrent)) ycurrent <- big
Modified: pkg/pomp/R/simulate-pomp.R
===================================================================
--- pkg/pomp/R/simulate-pomp.R 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/R/simulate-pomp.R 2015-06-17 12:56:36 UTC (rev 1207)
@@ -68,7 +68,6 @@
if (obs && states) {
dm <- dim(retval$obs)
nsim <- dm[2L]
- ntimes <- dm[3L]
nm <- rownames(retval$obs)
dim(retval$obs) <- c(dm[1L],prod(dm[-1L]))
rownames(retval$obs) <- nm
@@ -86,7 +85,6 @@
} else if (obs || states) {
dm <- dim(retval)
nsim <- dm[2L]
- ntimes <- dm[3L]
nm <- rownames(retval)
dim(retval) <- c(dm[1L],prod(dm[-1L]))
rownames(retval) <- nm
Modified: pkg/pomp/src/cholmodel.c
===================================================================
--- pkg/pomp/src/cholmodel.c 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/src/cholmodel.c 2015-06-17 12:56:36 UTC (rev 1207)
@@ -40,7 +40,7 @@
void _cholmodel_untrans (double *pt, double *p, int *parindex)
{
- int k, nrstage = (int) NRSTAGE;
+ int nrstage = (int) NRSTAGE;
pt[parindex[0]] = log(TAU);
pt[parindex[1]] = log(GAMMA);
pt[parindex[2]] = log(EPS);
@@ -56,7 +56,7 @@
void _cholmodel_trans (double *pt, double *p, int *parindex)
{
- int k, nrstage = (int) NRSTAGE;
+ int nrstage = (int) NRSTAGE;
pt[parindex[0]] = exp(TAU);
pt[parindex[1]] = exp(GAMMA);
pt[parindex[2]] = exp(EPS);
Modified: pkg/pomp/src/dprior.c
===================================================================
--- pkg/pomp/src/dprior.c 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/src/dprior.c 2015-06-17 12:56:36 UTC (rev 1207)
@@ -42,8 +42,7 @@
case Rfun: // use R function
{
- SEXP pvec, rho, ans;
- int use_names = 0;
+ SEXP pvec, rho;
double *pp, *ps, *pt;
int j;
Modified: pkg/pomp/src/initstate.c
===================================================================
--- pkg/pomp/src/initstate.c 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/src/initstate.c 2015-06-17 12:56:36 UTC (rev 1207)
@@ -103,7 +103,7 @@
case Rfun: // use R function
{
- SEXP par, rho, x1, x2, mindex;
+ SEXP par, rho, x1, x2;
double *p, *pp, *xp, *xt;
int j, *midx;
Modified: pkg/pomp/src/pomp_fun.c
===================================================================
--- pkg/pomp/src/pomp_fun.c 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/src/pomp_fun.c 2015-06-17 12:56:36 UTC (rev 1207)
@@ -68,7 +68,7 @@
break;
- default:
+ case undef: default:
error("operation cannot be completed: some needed function has not been specified");
break;
}
Modified: pkg/pomp/src/rprior.c
===================================================================
--- pkg/pomp/src/rprior.c 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/src/rprior.c 2015-06-17 12:56:36 UTC (rev 1207)
@@ -109,7 +109,7 @@
case native: // use native routine
{
- double *pp, *ps;
+ double *ps;
int *pidx = 0;
pomp_rprior *ff = NULL;
int j;
Modified: pkg/pomp/src/simulate.c
===================================================================
--- pkg/pomp/src/simulate.c 2015-06-15 19:31:53 UTC (rev 1206)
+++ pkg/pomp/src/simulate.c 2015-06-17 12:56:36 UTC (rev 1207)
@@ -14,7 +14,6 @@
SEXP ans, ans_names;
SEXP po, popo;
SEXP statenames, paramnames, obsnames, statedim, obsdim;
- SEXP rmeas;
int nsims, nparsets, nreps, npars, nvars, ntimes, nobs;
int qobs, qstates;
int *dim, dims[3];
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