[Pomp-commits] r719 - in pkg/pompExamples: . data tests

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

Author: kingaa
Date: 2012-05-14 09:51:13 +0200 (Mon, 14 May 2012)
New Revision: 719

Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/data/pertussis.sim.rda
   pkg/pompExamples/tests/pertussis.R
   pkg/pompExamples/tests/pertussis.Rout.save
Log:
- update 'pertussis.sim'


Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2012-05-12 15:47:23 UTC (rev 718)
+++ pkg/pompExamples/DESCRIPTION	2012-05-14 07:51:13 UTC (rev 719)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.20-5
-Date: 2012-05-12
+Date: 2012-05-14
 Author: NCEAS Working Group on Inference for Mechanistic Models: Aaron King, Steve Ellner, Bruce Kendall, Daniel C. Reuman, Matt Ferrari, Ed Ionides, Helen Wearing
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Description: Inference methods for partially-observed Markov processes

Modified: pkg/pompExamples/data/pertussis.sim.rda
===================================================================
(Binary files differ)

Modified: pkg/pompExamples/tests/pertussis.R
===================================================================
--- pkg/pompExamples/tests/pertussis.R	2012-05-12 15:47:23 UTC (rev 718)
+++ pkg/pompExamples/tests/pertussis.R	2012-05-14 07:51:13 UTC (rev 719)
@@ -15,3 +15,22 @@
 
 system.time(pf <- pfilter(pertussis.sim$full.small,seed=3445886L,Np=1000))
 logLik(pf)
+
+pttest <- function (po, digits = 15) {
+  identical(
+            signif(coef(po),digits=digits),
+            signif(partrans(po,partrans(po,coef(po),dir='inv'),dir='for'),digits=digits)
+            )
+}
+
+stopifnot(all(sapply(pertussis.sim,pttest)))
+
+pttest <- function (po, digits = 15) {
+  identical(
+            signif(coef(po,trans=T),digits=digits),
+            signif(partrans(po,partrans(po,coef(po,trans=T),dir='f'),dir='inv'),digits=digits)
+            )
+}
+
+stopifnot(all(sapply(pertussis.sim,pttest)))
+

Modified: pkg/pompExamples/tests/pertussis.Rout.save
===================================================================
--- pkg/pompExamples/tests/pertussis.Rout.save	2012-05-12 15:47:23 UTC (rev 718)
+++ pkg/pompExamples/tests/pertussis.Rout.save	2012-05-14 07:51:13 UTC (rev 719)
@@ -1,5 +1,5 @@
 
-R Under development (unstable) (2012-05-07 r59324) -- "Unsuffered Consequences"
+R version 2.15.0 (2012-03-30)
 Copyright (C) 2012 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
 Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -147,10 +147,29 @@
 > 
 > system.time(pf <- pfilter(pertussis.sim$full.small,seed=3445886L,Np=1000))
    user  system elapsed 
- 22.373   0.004  22.451 
+ 22.637   0.004  22.720 
 > logLik(pf)
 [1] -3829.33
 > 
+> pttest <- function (po, digits = 15) {
++   identical(
++             signif(coef(po),digits=digits),
++             signif(partrans(po,partrans(po,coef(po),dir='inv'),dir='for'),digits=digits)
++             )
++ }
+> 
+> stopifnot(all(sapply(pertussis.sim,pttest)))
+> 
+> pttest <- function (po, digits = 15) {
++   identical(
++             signif(coef(po,trans=T),digits=digits),
++             signif(partrans(po,partrans(po,coef(po,trans=T),dir='f'),dir='inv'),digits=digits)
++             )
++ }
+> 
+> stopifnot(all(sapply(pertussis.sim,pttest)))
+> 
+> 
 > proc.time()
    user  system elapsed 
- 22.857   0.040  22.985 
+ 23.089   0.020  23.200