[Pomp-commits] r794 - in pkg/pomp: . R tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 8 11:57:25 CET 2013
Author: kingaa
Date: 2013-01-08 11:57:25 +0100 (Tue, 08 Jan 2013)
New Revision: 794
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/mif.R
pkg/pomp/tests/bbs.Rout.save
pkg/pomp/tests/gompertz.Rout.save
pkg/pomp/tests/ou2-bsmc.Rout.save
pkg/pomp/tests/ou2-mif.Rout.save
Log:
- update tests
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2013-01-08 03:21:32 UTC (rev 793)
+++ pkg/pomp/DESCRIPTION 2013-01-08 10:57:25 UTC (rev 794)
@@ -2,7 +2,7 @@
Type: Package
Title: Statistical inference for partially observed Markov processes
Version: 0.43-6
-Date: 2013-01-07
+Date: 2013-01-08
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/pomp/R/mif.R
===================================================================
--- pkg/pomp/R/mif.R 2013-01-08 03:21:32 UTC (rev 793)
+++ pkg/pomp/R/mif.R 2013-01-08 10:57:25 UTC (rev 794)
@@ -38,7 +38,8 @@
particles,
rw.sd,
Np, cooling.factor, var.factor, ic.lag,
- method, tol, max.fail,
+ method,
+ tol, max.fail,
verbose, transform, .ndone) {
transform <- as.logical(transform)
@@ -194,8 +195,7 @@
if (!all(is.finite(theta[c(pars,ivps)]))) {
stop(
- sQuote("mif"),
- " error: mif cannot estimate non-finite parameters.\n",
+ sQuote("mif")," cannot estimate non-finite parameters.\n",
"The following ",if (transform) "transformed ", "parameters are non-finite: ",
paste(
c(pars,ivps)[!is.finite(theta[c(pars,ivps)])],
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2013-01-08 03:21:32 UTC (rev 793)
+++ pkg/pomp/tests/bbs.Rout.save 2013-01-08 10:57:25 UTC (rev 794)
@@ -1,5 +1,5 @@
-R version 2.15.0 (2012-03-30)
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -45,7 +45,7 @@
Walker's alias method used: results are different from R < 2.2.0
> signif(coef(fit1),3)
gamma mu iota beta beta.sd pop rho sigma
- 0.333 0.000 0.000 3.460 0.000 1400.000 0.900 2.050
+ 0.333 0.000 0.000 3.220 0.000 1400.000 0.900 2.240
S.0 I.0 R.0
0.999 0.001 0.000
>
@@ -58,4 +58,4 @@
>
> proc.time()
user system elapsed
- 2.816 0.028 2.867
+ 2.656 0.056 2.736
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2013-01-08 03:21:32 UTC (rev 793)
+++ pkg/pomp/tests/gompertz.Rout.save 2013-01-08 10:57:25 UTC (rev 794)
@@ -1,5 +1,5 @@
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -57,7 +57,7 @@
+ rw.sd=c(r=0.02,K=0.02)
+ )
+ )
-Error : 'mif' error: mif cannot estimate non-finite parameters.
+Error : 'mif' cannot estimate non-finite parameters.
The following transformed parameters are non-finite: r
>
> set.seed(93848585L)
@@ -131,4 +131,4 @@
>
> proc.time()
user system elapsed
- 1.496 0.056 1.567
+ 1.496 0.032 1.546
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2013-01-08 03:21:32 UTC (rev 793)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2013-01-08 10:57:25 UTC (rev 794)
@@ -1,5 +1,5 @@
-R version 2.15.0 (2012-03-30)
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -62,7 +62,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 3.02021 secs
+Time difference of 2.9886 secs
>
> print(
+ cbind(
@@ -74,8 +74,8 @@
+ )
prior.mean posterior.mean truth 2.5% 50% 97.5%
alpha.1 0.8000000 0.8000000 0.8 0.8000000 0.8000000 0.8000000
-alpha.2 -0.4999287 -0.4853833 -0.5 -0.5353593 -0.4881214 -0.4521997
-alpha.3 0.2996065 0.3186368 0.3 0.2933113 0.3120256 0.3476582
+alpha.2 -0.4999287 -0.5105023 -0.5 -0.5402483 -0.4993459 -0.4536930
+alpha.3 0.2996065 0.3148637 0.3 0.2823821 0.3260754 0.3388949
alpha.4 0.9000000 0.9000000 0.9 0.9000000 0.9000000 0.9000000
sigma.1 3.0000000 3.0000000 3.0 3.0000000 3.0000000 3.0000000
sigma.2 -0.5000000 -0.5000000 -0.5 -0.5000000 -0.5000000 -0.5000000
@@ -85,9 +85,9 @@
x2.0 4.0000000 4.0000000 4.0 4.0000000 4.0000000 4.0000000
>
> print(min(smc$eff.sample.size))
-[1] 40.66176
+[1] 22.94863
> print(smc$log.evidence)
-[1] 44.55899
+[1] 45.47584
>
> smc <- bsmc(ou2,ntries=5,Np=5000,smooth=0.1,est=estnames,seed=648651945L)
> print(smc$eff.sample.size)
@@ -98,4 +98,4 @@
>
> proc.time()
user system elapsed
- 4.848 0.040 4.912
+ 4.804 0.080 4.912
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2013-01-08 03:21:32 UTC (rev 793)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2013-01-08 10:57:25 UTC (rev 794)
@@ -1,5 +1,5 @@
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -167,7 +167,7 @@
+ Np=11,cooling.factor=0.95,ic.lag=10,var.factor=1
+ )
+ )
-Error : 'mif' error: mif cannot estimate non-finite parameters.
+Error : 'mif' cannot estimate non-finite parameters.
The following parameters are non-finite: alpha.4
>
> try(
@@ -180,7 +180,7 @@
+ Np=11,cooling.factor=0.95,ic.lag=10,var.factor=1
+ )
+ )
-Error : 'mif' error: mif cannot estimate non-finite parameters.
+Error : 'mif' cannot estimate non-finite parameters.
The following parameters are non-finite: x2.0
>
> fit <- mif(
@@ -267,4 +267,4 @@
>
> proc.time()
user system elapsed
- 13.728 0.036 13.921
+ 13.280 0.056 13.499
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