[Pomp-commits] r956 - in www: . vignettes

Sat May 17 17:51:26 CEST 2014

Author: kingaa
Date: 2014-05-17 17:51:26 +0200 (Sat, 17 May 2014)
New Revision: 956

Modified:
   www/index.php
   www/vignettes/Makefile
   www/vignettes/advanced_topics_in_pomp.pdf
   www/vignettes/intro_to_pomp.R
   www/vignettes/intro_to_pomp.Rnw
   www/vignettes/intro_to_pomp.pdf
   www/vignettes/nlf-block-boot.rda
   www/vignettes/nlf-boot.rda
   www/vignettes/nlf-fit-from-truth.rda
   www/vignettes/nlf-fits.rda
   www/vignettes/nlf-lag-tests.rda
   www/vignettes/nlf-multi-short.rda
   www/vignettes/pomp.pdf
Log:
- fix bugs with NLF in intro vignette


Modified: www/index.php
===================================================================

--- www/index.php	2014-05-17 14:06:10 UTC (rev 955)
+++ www/index.php	2014-05-17 15:51:26 UTC (rev 956)
@@ -9,8 +9,8 @@
 preg_match("/<tr><td valign=top>Version:<\/td>\\n<td>(.+?)<\/td>/",$crancontents,$matches);
 $cranversion = $matches[1];
 $rforgepage = file_get_contents($rforgepkgs);
-preg_match("/Rev\.: <b>(.+?)<\/b>/",$rforgepage,$matches);
-$svnrevision = $matches[2];
+preg_match_all("/Rev\.: <b>(.+?)<\/b>/",$rforgepage,&$matches);
+$svnrevision = $matches[1][1];
 echo '<?xml version="1.0" encoding="UTF-8"?>';
 ?>
 <!DOCTYPE html

Modified: www/vignettes/Makefile
===================================================================
--- www/vignettes/Makefile	2014-05-17 14:06:10 UTC (rev 955)
+++ www/vignettes/Makefile	2014-05-17 15:51:26 UTC (rev 956)
@@ -3,6 +3,7 @@
 LATEX = latex
 BIBTEX = bibtex
 PDFLATEX = pdflatex
+RM = rm -f
 
 default: vignettes clean
 
@@ -10,11 +11,9 @@
 
 %.R: %.Rnw
 	$(RSCRIPT) -e 'library(knitr); purl("$*.Rnw")'
-#	$(REXE) CMD Stangle $*.Rnw
 
 %.tex: %.Rnw
 	$(RSCRIPT) -e 'library(knitr); knit("$*.Rnw")'
-#	$(REXE) CMD Sweave $*.Rnw
 
 %.pdf: %.tex
 	$(PDFLATEX) $*
@@ -26,4 +25,5 @@
 clean:
 	$(RM) *.tex *.log *.aux *.blg *.bbl *.out *.Rout *.toc *.lof *.lot *.brf
 	$(RM) *.c *.o *.so
-	$(RM) Rplots.pdf figure/*
+	$(RM) Rplots.pdf
+	$(RM) -r figure

Modified: www/vignettes/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/intro_to_pomp.R
===================================================================
--- www/vignettes/intro_to_pomp.R	2014-05-17 14:06:10 UTC (rev 955)
+++ www/vignettes/intro_to_pomp.R	2014-05-17 15:51:26 UTC (rev 956)
@@ -855,15 +855,15 @@
 print(res,digits=3)
 
 
-## ----first-nlf,eval=F----------------------------------------------------
-## pompExample(gompertz)
-## out <- nlf(
-##            gompertz,
-##            start=c(r=1,K=2,sigma=0.5,tau=0.5,X.0=1),
-##            partrans=TRUE,
-##            est=c("K","r"),
-##            lags=c(1,2)
-##            )
+## ----first-nlf,eval=T,results='hide'-------------------------------------
+pompExample(gompertz)
+out <- nlf(
+           gompertz,
+           start=c(r=1,K=2,sigma=0.5,tau=0.5,X.0=1),
+           transform.params=TRUE,
+           est=c("K","r"),
+           lags=c(1,2)
+           )
 
 
 ## ----nlf-gompertz-starts,eval=F------------------------------------------

Modified: www/vignettes/intro_to_pomp.Rnw
===================================================================
--- www/vignettes/intro_to_pomp.Rnw	2014-05-17 14:06:10 UTC (rev 955)
+++ www/vignettes/intro_to_pomp.Rnw	2014-05-17 15:51:26 UTC (rev 956)
@@ -1205,12 +1205,12 @@
 
 As a simple example we can use \code{nlf} to estimate the parameters \code{K} and \code{r} of the Gompertz model.  
 An example of a minimal call, accepting the defaults for all optional arguments, is 
-<<first-nlf,eval=F>>=
+<<first-nlf,eval=T,results='hide'>>=
 pompExample(gompertz)
 out <- nlf(
            gompertz,
            start=c(r=1,K=2,sigma=0.5,tau=0.5,X.0=1),
-           partrans=TRUE,
+           transform.params=TRUE,
            est=c("K","r"),
            lags=c(1,2)
            )

Modified: www/vignettes/intro_to_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-block-boot.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-boot.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-fit-from-truth.rda
===================================================================
(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/pomp.pdf
===================================================================
(Binary files differ)

