[Pomp-commits] r616 - in pkg: . data inst inst/data-R

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

Author: kingaa
Date: 2012-02-15 19:52:58 +0100 (Wed, 15 Feb 2012)
New Revision: 616

Modified:
   pkg/DESCRIPTION
   pkg/data/blowflies.rda
   pkg/data/dacca.rda
   pkg/data/euler.sir.rda
   pkg/data/gillespie.sir.rda
   pkg/data/gompertz.rda
   pkg/data/ou2.rda
   pkg/data/ricker.rda
   pkg/data/rw2.rda
   pkg/data/verhulst.rda
   pkg/inst/NEWS
   pkg/inst/data-R/gillespie.sir.R
Log:
- fix the Gillespie example


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-02-15 14:34:23 UTC (rev 615)
+++ pkg/DESCRIPTION	2012-02-15 18:52:58 UTC (rev 616)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.40-6
-Date: 2012-02-14
+Date: 2012-02-15
 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>

Modified: pkg/data/blowflies.rda
===================================================================
(Binary files differ)

Modified: pkg/data/dacca.rda
===================================================================
(Binary files differ)

Modified: pkg/data/euler.sir.rda
===================================================================
(Binary files differ)

Modified: pkg/data/gillespie.sir.rda
===================================================================
(Binary files differ)

Modified: pkg/data/gompertz.rda
===================================================================
(Binary files differ)

Modified: pkg/data/ou2.rda
===================================================================
(Binary files differ)

Modified: pkg/data/ricker.rda
===================================================================
(Binary files differ)

Modified: pkg/data/rw2.rda
===================================================================
(Binary files differ)

Modified: pkg/data/verhulst.rda
===================================================================
(Binary files differ)

Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS	2012-02-15 14:34:23 UTC (rev 615)
+++ pkg/inst/NEWS	2012-02-15 18:52:58 UTC (rev 616)
@@ -3,6 +3,9 @@
      o	When a pomp object is updated using 'pomp', the 'params' slot will now be copied over (appropriately transformed).
      	Before, it was simply dropped.
 
+     o	The 'gillespie.sir' example has been changed to make the reporting rate equal to 'rho'.
+     	Before, it was fixed at 10%.
+
 0.40-5
      o	More informative error messages when dimension of state space or data space disagree internally.
 

Modified: pkg/inst/data-R/gillespie.sir.R
===================================================================
--- pkg/inst/data-R/gillespie.sir.R	2012-02-15 14:34:23 UTC (rev 615)
+++ pkg/inst/data-R/gillespie.sir.R	2012-02-15 18:52:58 UTC (rev 616)
@@ -35,7 +35,7 @@
              "nbasis","degree","period"
              ),
            zeronames=c("cases"),
-           measurement.model=reports~binom(size=cases,prob=0.1),
+           measurement.model=reports~binom(size=cases,prob=exp(rho)),
            to.log.transform=c(
              "gamma","nu","mu","iota",
              "beta1","beta2","beta3",