[Pomp-commits] r631 - pkg/inst/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 27 16:20:08 CEST 2012
Author: kingaa
Date: 2012-03-27 16:20:08 +0200 (Tue, 27 Mar 2012)
New Revision: 631
Modified:
pkg/inst/doc/intro_to_pomp.Rnw
pkg/inst/doc/intro_to_pomp.pdf
pkg/inst/doc/manual.pdf
Log:
- compress the manual and fix some typos in the intro vignette
Modified: pkg/inst/doc/intro_to_pomp.Rnw
===================================================================
--- pkg/inst/doc/intro_to_pomp.Rnw 2012-03-27 12:03:57 UTC (rev 630)
+++ pkg/inst/doc/intro_to_pomp.Rnw 2012-03-27 14:20:08 UTC (rev 631)
@@ -520,7 +520,8 @@
gompertz <- pomp(
gompertz,
parameter.transform=function(params,...){
- params <- exp(params[c("log.r","log.K","log.tau","log.sigma","log.X.0")])
+ params <- exp(params[c("log.r","log.K","log.tau",
+ "log.sigma","log.X.0")])
names(params) <- c("r","K","tau","sigma","X.0")
params
},
@@ -548,7 +549,7 @@
On the other hand, given parameter values on the estimation scale, one can set the parameters by
<<eval=T>>=
coef(gompertz,transform=TRUE) <- c(log.r=log(0.1),log.K=0,
- log.tau=log(0.1),log.sigma=log(0.1),X.0=0)
+ log.tau=log(0.1),log.sigma=log(0.1),log.X.0=0)
@
and get them by
<<eval=T>>=
@@ -635,7 +636,6 @@
)
}
)
-##mf <- lapply(mf,continue,Nmif=50)
@
Note that we've set \code{transform=TRUE} in the above.
@@ -1057,7 +1057,8 @@
starts <- replicate(n=5,
{
p <- coef(gompertz)
- p[c("K","r")] <- rlnorm(n=2,meanlog=log(p[c("K","r")]),sdlog=0.1)
+ p[c("K","r")] <- rlnorm(n=2,meanlog=log(p[c("K","r")]),
+ sdlog=0.1)
p
},
simplify=FALSE
@@ -1066,7 +1067,9 @@
Then to make the results from different starts comparable, use the \code{seed} argument to initialize the random number generator the same way for each fit:
<<nlf-gompertz-fits,eval=F>>=
out <- list()
-for (j in 1:5) { # Do fits. method, trace, and nasymp are explained below
+## Do the fitting.
+## method, trace, and nasymp are explained below
+for (j in 1:5) {
out[[j]] <- nlf(
gompertz,
start=starts[[j]],
Modified: pkg/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/manual.pdf
===================================================================
--- pkg/inst/doc/manual.pdf 2012-03-27 12:03:57 UTC (rev 630)
+++ pkg/inst/doc/manual.pdf 2012-03-27 14:20:08 UTC (rev 631)
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[TRUNCATED]
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svnlook diff /svnroot/pomp -r 631
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