[Pomp-commits] r880 - www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 10 23:43:03 CET 2014
Author: kingaa
Date: 2014-01-10 23:43:03 +0100 (Fri, 10 Jan 2014)
New Revision: 880
Modified:
www/vignettes/Makefile
www/vignettes/advanced_topics_in_pomp.R
www/vignettes/advanced_topics_in_pomp.pdf
www/vignettes/bsmc-ricker-flat-prior.rda
www/vignettes/bsmc-ricker-normal-prior.rda
www/vignettes/complex-sir-def.rda
www/vignettes/gompertz-multi-mif.rda
www/vignettes/gompertz-trajmatch.rda
www/vignettes/intro_to_pomp.R
www/vignettes/intro_to_pomp.Rnw
www/vignettes/intro_to_pomp.pdf
www/vignettes/nlf-fits.rda
www/vignettes/nlf-lag-tests.rda
www/vignettes/nlf-multi-short.rda
www/vignettes/plugin-C-code.rda
www/vignettes/plugin-R-code.rda
www/vignettes/ricker-first-probe.rda
www/vignettes/ricker-mif.rda
www/vignettes/ricker-probe-match.rda
www/vignettes/ricker-probe.rda
www/vignettes/sim-sim.rda
www/vignettes/sir-pomp-def.rda
www/vignettes/vectorized-C-code.rda
www/vignettes/vectorized-R-code.rda
Log:
- update the vignettes
Modified: www/vignettes/Makefile
===================================================================
--- www/vignettes/Makefile 2014-01-10 19:51:10 UTC (rev 879)
+++ www/vignettes/Makefile 2014-01-10 22:43:03 UTC (rev 880)
@@ -9,10 +9,10 @@
vignettes: advanced_topics_in_pomp.pdf advanced_topics_in_pomp.R intro_to_pomp.pdf intro_to_pomp.R
%.R: %.Rnw
- $(REXE) CMD Stangle $*
+ $(REXE) CMD Stangle $*.Rnw
%.tex: %.Rnw
- $(REXE) CMD Sweave $*
+ $(REXE) CMD Sweave $*.Rnw
%.pdf: %.tex
$(PDFLATEX) $*
Modified: www/vignettes/advanced_topics_in_pomp.R
===================================================================
--- www/vignettes/advanced_topics_in_pomp.R 2014-01-10 19:51:10 UTC (rev 879)
+++ www/vignettes/advanced_topics_in_pomp.R 2014-01-10 22:43:03 UTC (rev 880)
@@ -1,4 +1,4 @@
-### R code from vignette source 'advanced_topics_in_pomp'
+### R code from vignette source 'advanced_topics_in_pomp.Rnw'
### Encoding: UTF-8
###################################################
Modified: www/vignettes/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)
Modified: www/vignettes/bsmc-ricker-flat-prior.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/bsmc-ricker-normal-prior.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/complex-sir-def.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/gompertz-multi-mif.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/gompertz-trajmatch.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/intro_to_pomp.R
===================================================================
--- www/vignettes/intro_to_pomp.R 2014-01-10 19:51:10 UTC (rev 879)
+++ www/vignettes/intro_to_pomp.R 2014-01-10 22:43:03 UTC (rev 880)
@@ -1,4 +1,4 @@
-### R code from vignette source 'intro_to_pomp'
+### R code from vignette source 'intro_to_pomp.Rnw'
### Encoding: UTF-8
###################################################
@@ -401,11 +401,9 @@
## theta.true <- coef(gompertz)
## theta.mif <- apply(sapply(mf,coef),1,mean)
## loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-## loglik.mif.est <- logmeanexp(loglik.mif)
-## loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
+## loglik.mif.est <- logmeanexp(loglik.mif,se=TRUE)
## loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-## loglik.true.est <- logmeanexp(loglik.true)
-## loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
+## loglik.true.est <- logmeanexp(loglik.true,se=TRUE)
###################################################
@@ -446,41 +444,35 @@
theta.true <- coef(gompertz)
theta.mif <- apply(sapply(mf,coef),1,mean)
loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-loglik.mif.est <- logmeanexp(loglik.mif)
-loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
+loglik.mif.est <- logmeanexp(loglik.mif,se=TRUE)
loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-loglik.true.est <- logmeanexp(loglik.true)
-loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
+loglik.true.est <- logmeanexp(loglik.true,se=TRUE)
toc <- Sys.time()
etime <- toc-tic
save(
mf,estpars,
theta.mif,theta.true,
loglik.mif.est,loglik.true.est,
- loglik.mif.se,loglik.true.se,
etime,
file=binary.file,
compress="xz"
)
}
rbind(
-# guess=c(signif(theta.guess[estpars],3),loglik=round(loglik.guess,1)),
- mle=c(signif(theta.mif[estpars],3),loglik=round(loglik.mif.est,1),loglik.se=signif(loglik.mif.se,2)),
- truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true.est,1),loglik.se=signif(loglik.true.se,2))
+ mle=c(signif(theta.mif[estpars],3),loglik=round(loglik.mif.est[1],1),loglik.se=signif(loglik.mif.est[2],2)),
+ truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true.est[1],1),loglik.se=signif(loglik.true.est[2],2))
) -> results.table
###################################################
-### code chunk number 41: intro_to_pomp.Rnw:689-690 (eval = FALSE)
+### code chunk number 41: intro_to_pomp.Rnw:685-686 (eval = FALSE)
###################################################
## theta.true <- coef(gompertz)
## theta.mif <- apply(sapply(mf,coef),1,mean)
## loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-## loglik.mif.est <- logmeanexp(loglik.mif)
-## loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
+## loglik.mif.est <- logmeanexp(loglik.mif,se=TRUE)
## loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-## loglik.true.est <- logmeanexp(loglik.true)
-## loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
+## loglik.true.est <- logmeanexp(loglik.true,se=TRUE)
###################################################
@@ -932,7 +924,7 @@
###################################################
-### code chunk number 69: intro_to_pomp.Rnw:1124-1125
+### code chunk number 69: intro_to_pomp.Rnw:1120-1121
###################################################
fits
@@ -1117,7 +1109,7 @@
###################################################
-### code chunk number 77: intro_to_pomp.Rnw:1270-1271
+### code chunk number 77: intro_to_pomp.Rnw:1266-1267
###################################################
apply(fvals,2,function(x)sd(x)/mean(x))
@@ -1130,7 +1122,7 @@
## transform.params=TRUE,
## est=c("K","r"),
## lags=2,
-## seed=7639873L,
+## seed=7639873,
## method="Nelder-Mead",
## trace=4,
## nasymp=5000
@@ -1149,7 +1141,7 @@
transform.params=TRUE,
est=c("K","r"),
lags=2,
- seed=7639873L,
+ seed=7639873,
method="Nelder-Mead",
trace=4,
nasymp=5000
@@ -1159,7 +1151,7 @@
###################################################
-### code chunk number 80: intro_to_pomp.Rnw:1309-1310
+### code chunk number 80: intro_to_pomp.Rnw:1305-1306
###################################################
set.seed(32329L)
@@ -1229,7 +1221,7 @@
###################################################
-### code chunk number 83: intro_to_pomp.Rnw:1347-1348
+### code chunk number 83: intro_to_pomp.Rnw:1343-1344
###################################################
apply(pars,2,sd)
Modified: www/vignettes/intro_to_pomp.Rnw
===================================================================
--- www/vignettes/intro_to_pomp.Rnw 2014-01-10 19:51:10 UTC (rev 879)
+++ www/vignettes/intro_to_pomp.Rnw 2014-01-10 22:43:03 UTC (rev 880)
@@ -646,11 +646,9 @@
theta.true <- coef(gompertz)
theta.mif <- apply(sapply(mf,coef),1,mean)
loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-loglik.mif.est <- logmeanexp(loglik.mif)
-loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
+loglik.mif.est <- logmeanexp(loglik.mif,se=TRUE)
loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-loglik.true.est <- logmeanexp(loglik.true)
-loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
+loglik.true.est <- logmeanexp(loglik.true,se=TRUE)
@
<<gompertz-multi-mif-eval,echo=F,results=hide>>=
@@ -668,16 +666,14 @@
mf,estpars,
theta.mif,theta.true,
loglik.mif.est,loglik.true.est,
- loglik.mif.se,loglik.true.se,
etime,
file=binary.file,
compress="xz"
)
}
rbind(
-# guess=c(signif(theta.guess[estpars],3),loglik=round(loglik.guess,1)),
- mle=c(signif(theta.mif[estpars],3),loglik=round(loglik.mif.est,1),loglik.se=signif(loglik.mif.se,2)),
- truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true.est,1),loglik.se=signif(loglik.true.se,2))
+ mle=c(signif(theta.mif[estpars],3),loglik=round(loglik.mif.est[1],1),loglik.se=signif(loglik.mif.est[2],2)),
+ truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true.est[1],1),loglik.se=signif(loglik.true.est[2],2))
) -> results.table
@
@@ -1277,7 +1273,7 @@
transform.params=TRUE,
est=c("K","r"),
lags=2,
- seed=7639873L,
+ seed=7639873,
method="Nelder-Mead",
trace=4,
nasymp=5000
Modified: www/vignettes/intro_to_pomp.pdf
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-fits.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-lag-tests.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-multi-short.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/plugin-C-code.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/plugin-R-code.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-first-probe.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-mif.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-probe-match.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-probe.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/sim-sim.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/sir-pomp-def.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/vectorized-C-code.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/vectorized-R-code.rda
===================================================================
(Binary files differ)
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