[Pomp-commits] r1249 - pkg/pomp pkg/pomp/inst www/vignettes

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

Author: kingaa
Date: 2015-07-06 12:49:42 +0200 (Mon, 06 Jul 2015)
New Revision: 1249

Added:
   pkg/pomp/inst/TODO.md
Removed:
   pkg/pomp/inst/TODO
Modified:
   pkg/pomp/DESCRIPTION
   www/vignettes/pompjss.Rnw
Log:
- change TODO to markdown format
- put VignetteEngine line in pompjss.Rnw

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-07-02 18:02:54 UTC (rev 1248)
+++ pkg/pomp/DESCRIPTION	2015-07-06 10:49:42 UTC (rev 1249)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.69-4
-Date: 2015-07-02
+Version: 0.69-5
+Date: 2015-07-06
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Deleted: pkg/pomp/inst/TODO
===================================================================
--- pkg/pomp/inst/TODO	2015-07-02 18:02:54 UTC (rev 1248)
+++ pkg/pomp/inst/TODO	2015-07-06 10:49:42 UTC (rev 1249)
@@ -1,31 +0,0 @@
-TO-DO LIST
-
-* write pompCBuilder support for 'onestep.dens' and 'gillespie.sim' plugins.
-
-* effects of replacing 'sample.int' with systematic resampling inside 'bsmc'
-
-* parameter transformations: put 'transform' option into each estimation routine
-  (spect.match)
-
-* unit tests for 'sannbox'
-
-* Improve 'pmcmc' to take advantage of all particles.
-
-* Partial rejection control for 'pfilter'?
-
-* Adaptive particle numbers in pfilter.
-
-* Write 'plot' and 'print' methods for 'pfilterd.pomp' objects.  
-  Would this display effective sample size, conditional log likelihood, filter means, prediction variances, prediction means?
-
-* Add plugin for adaptive tau leaping algorithm.
-
-* Parallel 'pfilter' algorithm.
-
-* Add LPA model examples.
-
-* SDE examples.
-
-* Extended Kalman filter.
-
-* Plugin for compartmental models.

Added: pkg/pomp/inst/TODO.md
===================================================================
--- pkg/pomp/inst/TODO.md	                        (rev 0)
+++ pkg/pomp/inst/TODO.md	2015-07-06 10:49:42 UTC (rev 1249)
@@ -0,0 +1,24 @@
+### pomp to-do list
+
+- improve 'pmcmc' to take advantage of all particles
+- documentation on 'mifList', 'pmcmcList', etc.
+- 'transform' argument for pmcmc?
+- 'initializer' -> 'rinit' and perhaps 'dinit'
+- documentation: "regular parameters" instead of "non-IVP"
+- add 'coef' method for 'mifList' objects
+- objective function for spectrum matching
+- one-point SCQL function for possible use in fitting initial conditions
+- save particle filtering variance?  Prediction means are optional.  Only interesting for end-user if one wants to look at residuals.
+- write pompCBuilder support for 'onestep.dens' and 'gillespie.sim' plugins.
+- parameter transformations: put 'transform' option into each estimation routine (spect.match)
+- unit tests for 'sannbox'
+- partial rejection control for 'pfilter'?
+- adaptive particle numbers in pfilter.
+- improve 'plot' and 'print' methods for 'pfilterd.pomp' objects.  
+    - Would this display effective sample size, conditional log likelihood, filter means, prediction variances, prediction means?
+- Add plugin for adaptive tau leaping algorithm.
+- Parallel 'pfilter' algorithm.
+- Add LPA model examples.
+- SDE examples.
+- Extended Kalman filter.
+- Plugin for compartmental models.

Modified: www/vignettes/pompjss.Rnw
===================================================================
--- www/vignettes/pompjss.Rnw	2015-07-02 18:02:54 UTC (rev 1248)
+++ www/vignettes/pompjss.Rnw	2015-07-06 10:49:42 UTC (rev 1249)
@@ -1,5 +1,5 @@
 \documentclass[article,pdftex,shortnames,nojss]{jss}
-
+%\VignetteEngine{knitr::knitr}
 \usepackage[ruled,noline,linesnumbered]{algorithm2e}
 \SetKwFor{For}{for}{do}{end}
 \SetKwFor{While}{while}{do}{end}