[Pomp-commits] r590 - in pkg: . inst tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 11 14:12:29 CET 2012
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
+>
+>
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