[Pomp-commits] r662 - in pkg: . inst/doc

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

Author: kingaa
Date: 2012-04-16 16:00:20 +0200 (Mon, 16 Apr 2012)
New Revision: 662

Modified:
   pkg/DESCRIPTION
   pkg/inst/doc/intro_to_pomp.Rnw
   pkg/inst/doc/intro_to_pomp.pdf
   pkg/inst/doc/pomp.bib
Log:
- small changes to vignettes
- require R version >= 2.15.0


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-04-15 16:07:02 UTC (rev 661)
+++ pkg/DESCRIPTION	2012-04-16 14:00:20 UTC (rev 662)
@@ -2,13 +2,13 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.41-6
-Date: 2012-04-15
+Date: 2012-04-16
 Revision: $Rev$
 Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
 Maintainer: Aaron A. King <kingaa at umich.edu>
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially-observed Markov processes
-Depends: R(>= 2.13.1), stats, methods, graphics, mvtnorm, subplex, deSolve
+Depends: R(>= 2.15.0), stats, methods, graphics, mvtnorm, subplex, deSolve
 License: GPL(>= 2)
 LazyLoad: true
 LazyData: false

Modified: pkg/inst/doc/intro_to_pomp.Rnw
===================================================================
--- pkg/inst/doc/intro_to_pomp.Rnw	2012-04-15 16:07:02 UTC (rev 661)
+++ pkg/inst/doc/intro_to_pomp.Rnw	2012-04-16 14:00:20 UTC (rev 662)
@@ -353,7 +353,6 @@
                  gompertz,
                  dmeasure=gompertz.meas.dens
                  )
-coef(gompertz) <- theta
 @ 
 The result of the above is a new \code{pomp} object \code{gompertz} in every way identical to the one we had before, but with the measurement-model density function \code{dmeasure} now specified.
 
@@ -611,32 +610,30 @@
 @ 
 <<gompertz-multi-mif-calc,eval=F,echo=T>>=
 estpars <- c("r","sigma","tau")
-mf <- replicate(
-                n=10,
-                {
-                  theta.guess <- theta.true
-                  theta.guess[estpars] <- rlnorm(
-                                                 n=length(estpars),
-                                                 meanlog=log(theta.guess[estpars]),
-                                                 sdlog=1
-                                                 )
-                  mif(
-                      gompertz,
-                      Nmif=100,
-                      start=theta.guess,
-                      transform=TRUE,
-                      pars=estpars,
-                      rw.sd=c(
-                        r=0.02,sigma=0.02,tau=0.05
-                        ),
-                      Np=2000,
-                      var.factor=4,
-                      ic.lag=10,
-                      cooling.factor=0.999,
-                      max.fail=10
-                      )
-                }
+replicate(
+          n=10,
+          {
+            theta.guess <- theta.true
+            theta.guess[estpars] <- rlnorm(
+                                           n=length(estpars),
+                                           meanlog=log(theta.guess[estpars]),
+                                           sdlog=1
+                                           )
+            mif(
+                gompertz,
+                Nmif=100,
+                start=theta.guess,
+                transform=TRUE,
+                pars=estpars,
+                rw.sd=c(r=0.02,sigma=0.02,tau=0.05),
+                Np=2000,
+                var.factor=4,
+                ic.lag=10,
+                cooling.factor=0.999,
+                max.fail=10
                 )
+          }
+          ) -> mf
 @ 
 
 Note that we've set \code{transform=TRUE} in the above.

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

Modified: pkg/inst/doc/pomp.bib
===================================================================
--- pkg/inst/doc/pomp.bib	2012-04-15 16:07:02 UTC (rev 661)
+++ pkg/inst/doc/pomp.bib	2012-04-16 14:00:20 UTC (rev 662)
@@ -1,5 +1,5 @@
-% This file was created with JabRef 2.6.
-% Encoding: ISO8859_1
+% This file was created with JabRef 2.7b.
+% Encoding: UTF8
 
 @ARTICLE{Andrieu2010,
   author = {Andrieu, Christophe and Doucet, Arnaud and Holenstein, Roman},
@@ -91,14 +91,19 @@
 
 @ARTICLE{Breto2011,
   author = {Bret{\'o}, Carles and Ionides, Edward L.},
-  title = {Compound {M}arkov counting processes and their applications to modeling
+  title = {Compound Markov counting processes and their applications to modeling
 	infinitesimally over-dispersed systems},
   journal = {Stochastic Processes and their Applications},
-  year = {in press},
+  year = {2011},
+  volume = {121},
+  pages = {2571--2591},
+  number = {11},
+  month = nov,
+  __markedentry = {[kingaa:]},
   abstract = {We propose an infinitesimal dispersion index for Markov counting processes.
 	We show that, under standard moment existence conditions, a process
 	is infinitesimally (over-)equi-dispersed if, and only if, it is simple
-	(compound), i.e., it increases in jumps of one (or more) unit(s),
+	(compound), i.e. it increases in jumps of one (or more) unit(s),
 	even though infinitesimally equi-dispersed processes might be under-,
 	equi- or over-dispersed using previously studied indices. Compound
 	processes arise, for example, when introducing continuous-time white
@@ -107,11 +112,12 @@
 	models and queuing networks, suitable for applications where moment
 	constraints inherent to simple processes do not hold.},
   doi = {10.1016/j.spa.2011.07.005},
+  file = {Breto2011.pdf:Breto2011.pdf:PDF},
   issn = {0304-4149},
-  keywords = {Continuous time, Counting Markov process, Birth-death process, Environmental
+  keywords = {Continuous time, Counting Markov process, Birth–death process, Environmental
 	stochasticity, Infinitesimal over-dispersion, Simultaneous events},
   owner = {kingaa},
-  timestamp = {2011.08.17}
+  timestamp = {2012.01.17}
 }
 
 @BOOK{Davison1997,