[Pomp-commits] r1063 - in pkg/pompExamples: . src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 28 15:30:56 CET 2015
Author: kingaa
Date: 2015-01-28 15:30:56 +0100 (Wed, 28 Jan 2015)
New Revision: 1063
Removed:
pkg/pompExamples/src/Makevars
Modified:
pkg/pompExamples/DESCRIPTION
pkg/pompExamples/src/budmoth.c
pkg/pompExamples/src/cholmodel.c
pkg/pompExamples/tests/bbp.Rout.save
pkg/pompExamples/tests/budmoth.Rout.save
pkg/pompExamples/tests/ebola.Rout.save
pkg/pompExamples/tests/parus.Rout.save
pkg/pompExamples/tests/pertussis.Rout.save
Log:
- remove unneeded Makevars (use LinkingTo field instead)
Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/DESCRIPTION 2015-01-28 14:30:56 UTC (rev 1063)
@@ -18,6 +18,7 @@
Description: More 'pomp' examples.
Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.58-6)
Suggests: plyr, reshape2, ggplot2, knitr, markdown
+LinkingTo: pomp
License: GPL (>= 2)
LazyData: false
BuildVignettes: true
Deleted: pkg/pompExamples/src/Makevars
===================================================================
--- pkg/pompExamples/src/Makevars 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/src/Makevars 2015-01-28 14:30:56 UTC (rev 1063)
@@ -1,2 +0,0 @@
-POMP_INC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'library(pomp); cat(system.file("include",package="pomp"))')
-PKG_CFLAGS = -I $(POMP_INC)
Modified: pkg/pompExamples/src/budmoth.c
===================================================================
--- pkg/pompExamples/src/budmoth.c 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/src/budmoth.c 2015-01-28 14:30:56 UTC (rev 1063)
@@ -65,7 +65,6 @@
int *stateindex, int *parindex, int *covindex,
int ncovars, double *covars, double t)
{
- double Q, N, S;
double tol = 1e-6;
f[stateindex[0]] = ALPHA; // ALPHA equation
@@ -142,10 +141,7 @@
const int *stateindex, const int *parindex, const int *covindex,
int covdim, const double *covar)
{
- double noise;
double sig2lambda;
- double Q, N, S;
- double tol = 1e-6;
double f1, f2, f3;
// check the discrete-time assumption
Modified: pkg/pompExamples/src/cholmodel.c
===================================================================
--- pkg/pompExamples/src/cholmodel.c 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/src/cholmodel.c 2015-01-28 14:30:56 UTC (rev 1063)
@@ -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/pompExamples/tests/bbp.Rout.save
===================================================================
--- pkg/pompExamples/tests/bbp.Rout.save 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/bbp.Rout.save 2015-01-28 14:30:56 UTC (rev 1063)
@@ -30,4 +30,4 @@
>
> proc.time()
user system elapsed
- 0.728 0.028 0.786
+ 0.575 0.045 0.608
Modified: pkg/pompExamples/tests/budmoth.Rout.save
===================================================================
--- pkg/pompExamples/tests/budmoth.Rout.save 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/budmoth.Rout.save 2015-01-28 14:30:56 UTC (rev 1063)
@@ -127,4 +127,4 @@
>
> proc.time()
user system elapsed
- 0.732 0.060 0.818
+ 0.626 0.053 0.668
Modified: pkg/pompExamples/tests/ebola.Rout.save
===================================================================
--- pkg/pompExamples/tests/ebola.Rout.save 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/ebola.Rout.save 2015-01-28 14:30:56 UTC (rev 1063)
@@ -28,40 +28,16 @@
newly created object(s):
ebolaModel
> ebolaModel(country="Guinea") -> po
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic -g -O2 -c /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.c -o /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.o
-gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.so /tmp/RtmpU0NeMt/pomp2583FF7C2A2A.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-model codes written to '/tmp/RtmpU0NeMt/pomp2583FF7C2A2A.c'
-link to shared-object library '/tmp/RtmpU0NeMt/pomp2583FF7C2A2A.so'
> pf <- pfilter(simulate(po),Np=100)
> tj <- trajectory(po)
>
> ebolaModel(country="SierraLeone",na.rm=TRUE,type='cum') -> po
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic -g -O2 -c /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.c -o /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.o
-gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.so /tmp/RtmpU0NeMt/pompDA1B7D4C88B1.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-model codes written to '/tmp/RtmpU0NeMt/pompDA1B7D4C88B1.c'
-link to shared-object library '/tmp/RtmpU0NeMt/pompDA1B7D4C88B1.so'
> pf <- pfilter(simulate(po),Np=100)
> tj <- trajectory(po)
> dd <- simulate(po,as.data.frame=TRUE,obs=TRUE)
> dd$week <- dd$time
> po <- ebolaModel(data=subset(dd,select=c(week,cases,deaths)))
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-gcc -std=gnu99 -I/usr/local/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/apps/R/R-3.1.2/lib64/R/library/pomp/include -fpic -g -O2 -c /tmp/RtmpU0NeMt/pompBF9800D29D72.c -o /tmp/RtmpU0NeMt/pompBF9800D29D72.o
-gcc -std=gnu99 -shared -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -L/usr/local/lib64 -o /tmp/RtmpU0NeMt/pompBF9800D29D72.so /tmp/RtmpU0NeMt/pompBF9800D29D72.o -L/usr/local/apps/R/R-3.1.2/lib64/R/lib -lR
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Entering directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-make[1]: Leaving directory `/userdata/kingaa/projects/pomp/pkg/pompExamples.Rcheck/tests'
-model codes written to '/tmp/RtmpU0NeMt/pompBF9800D29D72.c'
-link to shared-object library '/tmp/RtmpU0NeMt/pompBF9800D29D72.so'
>
> proc.time()
user system elapsed
- 2.032 0.228 3.798
+ 1.837 0.246 2.034
Modified: pkg/pompExamples/tests/parus.Rout.save
===================================================================
--- pkg/pompExamples/tests/parus.Rout.save 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/parus.Rout.save 2015-01-28 14:30:56 UTC (rev 1063)
@@ -41,4 +41,4 @@
>
> proc.time()
user system elapsed
- 0.716 0.060 0.806
+ 0.638 0.025 0.650
Modified: pkg/pompExamples/tests/pertussis.Rout.save
===================================================================
--- pkg/pompExamples/tests/pertussis.Rout.save 2015-01-28 14:30:53 UTC (rev 1062)
+++ pkg/pompExamples/tests/pertussis.Rout.save 2015-01-28 14:30:56 UTC (rev 1063)
@@ -168,4 +168,4 @@
>
> proc.time()
user system elapsed
- 18.417 0.068 18.567
+ 23.862 0.074 23.943
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