[Pomp-commits] r533 - in pkg: . inst

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

Author: kingaa
Date: 2011-08-08 18:41:41 +0200 (Mon, 08 Aug 2011)
New Revision: 533

Added:
   pkg/inst/TODO
Modified:
   pkg/DESCRIPTION
   pkg/inst/ChangeLog
Log:


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2011-08-08 16:27:24 UTC (rev 532)
+++ pkg/DESCRIPTION	2011-08-08 16:41:41 UTC (rev 533)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.39-1
-Date: 2011-08-03
+Date: 2011-08-09
 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

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2011-08-08 16:27:24 UTC (rev 532)
+++ pkg/inst/ChangeLog	2011-08-08 16:41:41 UTC (rev 533)
@@ -1,5 +1,29 @@
+2011-08-08  kingaa
+
+	* [r532] data/gillespie.sir.rda, inst/data-R/gillespie.sir.R,
+	  inst/examples/gompertz.R, inst/examples/sir.R,
+	  inst/examples/sir.c, man/gompertz.Rd: - include parameter
+	  transformations in 'gillespie.sir'
+	  - bring examples into line with codes in vignettes
+	* [r531] data/verhulst.rda, inst/data-R/verhulst.R,
+	  tests/verhulst.R, tests/verhulst.Rout.save: - re-code verhulst
+	  example with more exemplary style.
+	  - include a new unit-test in tests/verhulst.R
+
+2011-08-02  kingaa
+
+	* [r530] DESCRIPTION, R/mif-methods.R, R/pomp-methods.R,
+	  inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
+	  man/mif-methods.Rd, tests/gompertz.R, tests/gompertz.Rout.save: -
+	  add 'transform' argument to 'conv.rec' method for 'mif' objects
+	  - add new unit test 'tests/gompertz.R' which tests the
+	  transformation facilities in 'coef', 'coef<-', and 'conv.rec'
+	  - small changes to 'intro_to_pomp' vignette
+	  - bug fix in 'pomp:::pomp.transform'
+
 2011-07-28  kingaa
 
+	* [r529] inst/ChangeLog:
 	* [r528] DESCRIPTION, R/pomp-methods.R, R/pomp.R,
 	  data/blowflies.rda, data/dacca.rda, data/euler.sir.rda,
 	  data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda,

Added: pkg/inst/TODO
===================================================================
--- pkg/inst/TODO	                        (rev 0)
+++ pkg/inst/TODO	2011-08-08 16:41:41 UTC (rev 533)
@@ -0,0 +1,18 @@
+* Create objective functions for 'probe.match', 'traj.match', and
+   'spect.match' so that  users can roll their own optimization
+   routines.  Use 'nloptr' as the target optimizer package?
+
+* Improve 'pmcmc' to take advantage of all particles.
+
+* Partial rejection control for 'pfilter'?
+
+* Better documentation/rationalization for 'zeronames'.
+
+* It might be possible to make the writing of basic model functions
+   using R expressions rather than functions.
+
+* Write 'plot' method for 'pfilterd.pomp' objects.  This would display
+  effective sample size, conditional log likelihood, filter means,
+  prediction variances, prediction means?
+
+* Add plugin for adaptive tau leaping algorithm.