[Pomp-commits] r590 - in pkg: . inst tests

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

Author: kingaa
Date: 2012-01-11 14:12:24 +0100 (Wed, 11 Jan 2012)
New Revision: 590

Added:
   pkg/tests/steps.R
   pkg/tests/steps.Rout.save
Modified:
   pkg/DESCRIPTION
   pkg/inst/ChangeLog
   pkg/inst/NEWS
Log:
- version 0.40-2


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-01-11 12:28:38 UTC (rev 589)
+++ pkg/DESCRIPTION	2012-01-11 13:12:24 UTC (rev 590)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.40-1
-Date: 2012-01-09
+Version: 0.40-2
+Date: 2012-01-11
 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	2012-01-11 12:28:38 UTC (rev 589)
+++ pkg/inst/ChangeLog	2012-01-11 13:12:24 UTC (rev 590)
@@ -1,5 +1,11 @@
+2012-01-11  kingaa
+
+	* [r589] src/euler.c: - bug fix: inappropriate choice of number of
+	  steps in some circumstances
+
 2012-01-10  kingaa
 
+	* [r588] inst/ChangeLog: - update ChangeLog for version 0.40-1
 	* [r587] .Rbuildignore: - don't ignore .rda files in inst/doc
 
 2012-01-09  kingaa

Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS	2012-01-11 12:28:38 UTC (rev 589)
+++ pkg/inst/NEWS	2012-01-11 13:12:24 UTC (rev 590)
@@ -1,4 +1,8 @@
 NEWS
+0.40-2
+     o  A bug to do with computation of the number of steps needed in discrete-time simulation and trajectory computations has been fixed.
+     	This bug was introduced in version 0.40-1.
+
 0.40-1
      o  It is now possible for discrete-time determistic skeletons to have a general step-size.
      	Before, the stepsize was always forced to be 1.

Added: pkg/tests/steps.R
===================================================================
--- pkg/tests/steps.R	                        (rev 0)
+++ pkg/tests/steps.R	2012-01-11 13:12:24 UTC (rev 590)
@@ -0,0 +1,18 @@
+library(pomp)
+
+set.seed(54588699L)
+
+data(ricker)
+coef(ricker,"log.sigma") <- -Inf
+tm <- sort(runif(n=20,max=3))
+x <- trajectory(ricker,times=tm)["N",,]
+y <- simulate(ricker,times=tm,states=TRUE)["N",,]
+stopifnot(identical(x,y))
+
+data(verhulst)
+coef(verhulst,c("n.0","sigma")) <- c(15,0)
+tm <- sort(runif(n=100,max=1))
+x <- trajectory(verhulst,times=tm)["n",,]
+y <- simulate(verhulst,times=tm,states=TRUE)["n",,]
+table(cut(x-y,breaks=10))
+

Added: pkg/tests/steps.Rout.save
===================================================================
--- pkg/tests/steps.Rout.save	                        (rev 0)
+++ pkg/tests/steps.Rout.save	2012-01-11 13:12:24 UTC (rev 590)
@@ -0,0 +1,47 @@
+
+R version 2.14.1 (2011-12-22)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(pomp)
+Loading required package: mvtnorm
+Loading required package: subplex
+Loading required package: deSolve
+> 
+> set.seed(54588699L)
+> 
+> data(ricker)
+> coef(ricker,"log.sigma") <- -Inf
+> tm <- sort(runif(n=20,max=3))
+> x <- trajectory(ricker,times=tm)["N",,]
+> y <- simulate(ricker,times=tm,states=TRUE)["N",,]
+> stopifnot(identical(x,y))
+> 
+> data(verhulst)
+> coef(verhulst,c("n.0","sigma")) <- c(15,0)
+> tm <- sort(runif(n=100,max=1))
+> x <- trajectory(verhulst,times=tm)["n",,]
+> y <- simulate(verhulst,times=tm,states=TRUE)["n",,]
+> table(cut(x-y,breaks=10))
+
+(0.000885,0.0115]   (0.0115,0.0222]   (0.0222,0.0328]   (0.0328,0.0434] 
+               13                14                16                 8 
+  (0.0434,0.0541]   (0.0541,0.0647]   (0.0647,0.0753]    (0.0753,0.086] 
+                9                11                 7                 4 
+   (0.086,0.0966]    (0.0966,0.107] 
+               10                 8 
+> 
+>