[Pomp-commits] r25 - in pkg: . inst inst/doc src

[noreply at r-forge.r-project.org]

Author: kingaa
Date: 2008-07-26 16:38:07 +0200 (Sat, 26 Jul 2008)
New Revision: 25

Modified:
   pkg/DESCRIPTION
   pkg/inst/ChangeLog
   pkg/inst/NEWS
   pkg/inst/doc/compiled_code_in_pomp.pdf
   pkg/inst/doc/intro_to_pomp.Rnw
   pkg/inst/doc/intro_to_pomp.pdf
   pkg/src/ou2.c
Log:
bug fix in "intro_to_pomp.Rnw"

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-07-25 21:27:38 UTC (rev 24)
+++ pkg/DESCRIPTION	2008-07-26 14:38:07 UTC (rev 25)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Partially-observed Markov processes
-Version: 0.20-5
-Date: 2008-07-25
+Version: 0.20-6
+Date: 2008-07-26
 Author: Aaron A. King, Edward L. Ionides, Carles Martinez Breto
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Description: Inference methods for partially-observed Markov processes

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-07-25 21:27:38 UTC (rev 24)
+++ pkg/inst/ChangeLog	2008-07-26 14:38:07 UTC (rev 25)
@@ -1,5 +1,10 @@
 2008-07-25  kingaa
 
+	* R/pfilter-mif.R:
+	* inst/NEWS:
+	* inst/NEWS:
+	* data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf,
+	  inst/doc/intro_to_pomp.pdf:
 	* tests/ou2-mif.Rout.save: no need to set rw.sd for parameters that
 	  aren't estimated
 	* inst/examples/logistic.R, inst/examples/rw2.R,
@@ -67,5 +72,5 @@
 
 2007-06-25  stefan7th
 
-	* README, ., R, man, www, www/index.php: Email in Readme changed
+	* ., R, man: Email in Readme changed
 

Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS	2008-07-25 21:27:38 UTC (rev 24)
+++ pkg/inst/NEWS	2008-07-26 14:38:07 UTC (rev 25)
@@ -1,8 +1,12 @@
+NEW IN VERSION 0.20-6:
+
+    o   bug fix in "intro_to_pomp" vignette
+    
 NEW IN VERSION 0.20-5:
 
-	o   better error handling and improved documentation for 'mif'
+    o   better error handling and improved documentation for 'mif'
 
-	o   testing of examples in the 'examples' directory, including compilation, linking, and running of dynamically-loadable library on unix machines
+    o   testing of examples in the 'examples' directory, including compilation, linking, and running of dynamically-loadable library on unix machines
 
 NEW IN VERSION 0.20-4:
 

Modified: pkg/inst/doc/compiled_code_in_pomp.pdf
===================================================================
(Binary files differ)

Modified: pkg/inst/doc/intro_to_pomp.Rnw
===================================================================
--- pkg/inst/doc/intro_to_pomp.Rnw	2008-07-25 21:27:38 UTC (rev 24)
+++ pkg/inst/doc/intro_to_pomp.Rnw	2008-07-26 14:38:07 UTC (rev 25)
@@ -110,7 +110,7 @@
       for (j in 1:nreps) {
         eps[1] <- (x['x1',j,k]-params['alpha.1',j]*x['x1',j,k-1]-params['alpha.3',j]*x['x2',j,k-1])/params['sigma.1',j]
         eps[2] <- (x['x2',j,k]-params['alpha.2',j]*x['x1',j,k-1]-params['alpha.4',j]*x['x2',j,k-1]-params['sigma.2',j]*eps[1])/params['sigma.3',j]
-        d[j,k-1] <- sum(dnorm(eps,mean=0,sd=1,log=TRUE),na.rm=T)
+        d[j,k-1] <- sum(dnorm(eps,mean=0,sd=1,log=TRUE),na.rm=T)-sum(log(params[c('sigma.1','sigma.3'),j]))
       }
     }
     if (log) d else exp(d)

Modified: pkg/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)

Modified: pkg/src/ou2.c
===================================================================
--- pkg/src/ou2.c	2008-07-25 21:27:38 UTC (rev 24)
+++ pkg/src/ou2.c	2008-07-26 14:38:07 UTC (rev 25)
@@ -174,7 +174,7 @@
   eps[1] -= sigma2*eps[0];
   eps[1] /= sigma3;
 
-  val = dnorm(eps[0],0.0,1.0,1)+dnorm(eps[1],0.0,1.0,1);
+  val = dnorm(eps[0],0.0,1.0,1)+dnorm(eps[1],0.0,1.0,1)-log(sigma1)-log(sigma3);
   return ((give_log) ? val : exp(val));
 }