[Pomp-commits] r996 - in pkg/pomp: . tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jul 10 12:39:45 CEST 2014
Author: kingaa
Date: 2014-07-10 12:39:45 +0200 (Thu, 10 Jul 2014)
New Revision: 996
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/tests/bbs-trajmatch.Rout.save
pkg/pomp/tests/bbs.Rout.save
pkg/pomp/tests/blowflies.Rout.save
pkg/pomp/tests/dacca.Rout.save
pkg/pomp/tests/dimchecks.Rout.save
pkg/pomp/tests/fhn.Rout.save
pkg/pomp/tests/filtfail.Rout.save
pkg/pomp/tests/gillespie.Rout.save
pkg/pomp/tests/gompertz.Rout.save
pkg/pomp/tests/logistic.Rout.save
pkg/pomp/tests/ou2-abc.Rout.save
pkg/pomp/tests/ou2-bsmc.Rout.save
pkg/pomp/tests/ou2-forecast.Rout.save
pkg/pomp/tests/ou2-kalman.Rout.save
pkg/pomp/tests/ou2-mif-fp.Rout.save
pkg/pomp/tests/ou2-mif.Rout.save
pkg/pomp/tests/ou2-mif2.Rout.save
pkg/pomp/tests/ou2-nlf.Rout.save
pkg/pomp/tests/ou2-pmcmc.Rout.save
pkg/pomp/tests/ou2-probe.Rout.save
pkg/pomp/tests/ou2-procmeas.Rout.save
pkg/pomp/tests/ou2-simulate.Rout.save
pkg/pomp/tests/ou2-trajmatch.Rout.save
pkg/pomp/tests/partrans.Rout.save
pkg/pomp/tests/pfilter.Rout.save
pkg/pomp/tests/pomppomp.Rout.save
pkg/pomp/tests/prior.Rout.save
pkg/pomp/tests/ricker-bsmc.Rout.save
pkg/pomp/tests/ricker-probe.Rout.save
pkg/pomp/tests/ricker-spect.Rout.save
pkg/pomp/tests/ricker.Rout.save
pkg/pomp/tests/rw2.Rout.save
pkg/pomp/tests/sir.Rout.save
pkg/pomp/tests/skeleton.Rout.save
pkg/pomp/tests/steps.Rout.save
pkg/pomp/tests/synlik.Rout.save
pkg/pomp/tests/verhulst.Rout.save
Log:
- update test .Rout.save files for R-3.1.1
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/DESCRIPTION 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.53-2
-Date: 2014-07-02
+Version: 0.53-3
+Date: 2014-07-10
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")),
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(bbs)
newly created pomp object(s):
@@ -82,4 +84,4 @@
>
> proc.time()
user system elapsed
- 2.396 0.048 2.469
+ 2.795 0.053 2.839
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/bbs.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(bbs)
newly created pomp object(s):
@@ -47,9 +49,6 @@
+ )
>
> fit1 <- bsmc(bbs,params=coef(bbs),Np=1000,transform=TRUE,est=c("beta","sigma"),smooth=0.2)
-Warning message:
-In sample.int(n = Np, size = Np, replace = TRUE, prob = g) :
- 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 4.300 0.000 1400.000 0.900 2.050
@@ -65,4 +64,4 @@
>
> proc.time()
user system elapsed
- 2.888 0.064 3.011
+ 2.957 0.036 2.983
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/blowflies.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(blowflies)
newly created pomp object(s):
@@ -72,4 +74,4 @@
>
> proc.time()
user system elapsed
- 1.216 0.036 1.283
+ 1.430 0.051 1.473
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/dacca.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> set.seed(1420306530L)
>
@@ -109,4 +111,4 @@
>
> proc.time()
user system elapsed
- 11.056 0.036 11.143
+ 13.216 0.040 13.260
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/dimchecks.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> set.seed(1420306530L)
>
@@ -164,4 +166,4 @@
>
> proc.time()
user system elapsed
- 0.504 0.064 0.591
+ 0.532 0.037 0.555
Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/fhn.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pdf.options(useDingbats=FALSE)
> pdf(file="fhn.pdf")
@@ -93,4 +95,4 @@
>
> proc.time()
user system elapsed
- 1.024 0.064 1.220
+ 0.99 0.04 1.02
Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/filtfail.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> set.seed(834454394L)
>
@@ -118,4 +120,4 @@
>
> proc.time()
user system elapsed
- 0.552 0.036 0.605
+ 0.572 0.031 0.581
Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/gillespie.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> params <- c(
+ nu=1/70,
@@ -133,4 +135,4 @@
>
> proc.time()
user system elapsed
- 2.664 0.068 2.758
+ 2.637 0.064 2.693
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/gompertz.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
> options(digits=4)
>
> pompExample(gompertz)
@@ -135,4 +137,4 @@
>
> proc.time()
user system elapsed
- 1.552 0.048 1.622
+ 1.762 0.063 1.806
Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/logistic.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> po <- pomp(
+ data=rbind(obs=rep(0,1000)),
@@ -124,4 +126,4 @@
>
> proc.time()
user system elapsed
- 0.916 0.044 1.078
+ 0.911 0.033 0.933
Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-abc.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -135,4 +135,4 @@
>
> proc.time()
user system elapsed
- 9.604 0.052 9.963
+ 11.588 0.056 11.647
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> set.seed(398585L)
> pompExample(ou2)
@@ -55,16 +57,13 @@
+ lower=prior.bounds[estnames,"lower"],
+ upper=prior.bounds[estnames,"upper"]
+ )
-Warning message:
-In sample.int(n = Np, size = Np, replace = TRUE, prob = g) :
- Walker's alias method used: results are different from R < 2.2.0
> toc <- Sys.time()
>
> prior <- smc$prior
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 2.999716 secs
+Time difference of 3.021244 secs
>
> print(
+ cbind(
@@ -106,4 +105,4 @@
>
> proc.time()
user system elapsed
- 4.896 0.068 4.995
+ 4.967 0.053 5.012
Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-forecast.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> set.seed(921625222L)
>
@@ -63,4 +65,4 @@
>
> proc.time()
user system elapsed
- 1.580 0.068 1.753
+ 1.456 0.016 1.463
Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-kalman.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> set.seed(577639485L)
>
@@ -166,7 +168,7 @@
117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 3.437749 secs
+Time difference of 3.49406 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
@@ -190,4 +192,4 @@
>
> proc.time()
user system elapsed
- 4.004 0.056 4.089
+ 4.096 0.029 4.104
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -74,4 +74,4 @@
>
> proc.time()
user system elapsed
- 22.609 0.039 22.668
+ 23.726 0.048 23.790
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -285,4 +285,4 @@
>
> proc.time()
user system elapsed
- 14.306 0.041 14.344
+ 14.330 0.061 14.397
Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-mif2.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -139,4 +139,4 @@
>
> proc.time()
user system elapsed
- 59.213 0.057 59.317
+ 63.315 0.042 63.432
Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-nlf.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -89,4 +89,4 @@
>
> proc.time()
user system elapsed
- 4.684 0.064 4.808
+ 5.413 0.023 5.433
Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -118,4 +118,4 @@
>
> proc.time()
user system elapsed
- 24.093 0.136 24.494
+ 27.262 0.036 27.325
Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-probe.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
> set.seed(1066L)
>
> pdf(file="ou2-probe.pdf")
@@ -342,4 +344,4 @@
>
> proc.time()
user system elapsed
- 7.692 0.084 8.009
+ 8.873 0.076 8.949
Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ou2)
newly created pomp object(s):
@@ -56,4 +58,4 @@
>
> proc.time()
user system elapsed
- 0.520 0.040 0.579
+ 0.526 0.044 0.560
Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-simulate.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ou2)
newly created pomp object(s):
@@ -37,7 +39,7 @@
> ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.005120277 secs
+Time difference of 0.006201267 secs
>
> coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
>
@@ -48,4 +50,4 @@
>
> proc.time()
user system elapsed
- 0.504 0.064 0.585
+ 0.523 0.016 0.530
Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> set.seed(93885485L)
>
@@ -177,4 +179,4 @@
>
> proc.time()
user system elapsed
- 1.620 0.056 1.698
+ 1.771 0.065 1.824
Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/partrans.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(gompertz)
newly created pomp object(s):
@@ -54,4 +56,4 @@
>
> proc.time()
user system elapsed
- 0.496 0.044 0.557
+ 0.500 0.053 0.522
Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/pfilter.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ou2)
newly created pomp object(s):
@@ -79,4 +81,4 @@
>
> proc.time()
user system elapsed
- 8.652 0.076 8.902
+ 10.454 0.035 10.489
Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/pomppomp.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ricker)
newly created pomp object(s):
@@ -57,4 +59,4 @@
>
> proc.time()
user system elapsed
- 0.372 0.030 0.378
+ 0.562 0.032 0.582
Modified: pkg/pomp/tests/prior.Rout.save
===================================================================
--- pkg/pomp/tests/prior.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/prior.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ou2)
newly created pomp object(s):
@@ -74,4 +76,4 @@
>
> proc.time()
user system elapsed
- 0.700 0.044 0.764
+ 0.697 0.016 0.703
Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ricker)
newly created pomp object(s):
@@ -41,9 +43,6 @@
> Np <- 10000
>
> fit <- bsmc(po,Np=1000,est=c("r","sigma"),transform=TRUE,smooth=0.2)
-Warning message:
-In sample.int(n = Np, size = Np, replace = TRUE, prob = g) :
- Walker's alias method used: results are different from R < 2.2.0
>
> invisible(apply(fit$prior[c("r","sigma"),],1,mean))
>
@@ -59,4 +58,4 @@
>
> proc.time()
user system elapsed
- 2.972 0.068 3.210
+ 3.035 0.057 3.068
Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ricker-probe.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ricker)
newly created pomp object(s):
@@ -299,4 +301,4 @@
>
> proc.time()
user system elapsed
- 11.848 0.084 12.168
+ 14.323 0.079 14.418
Modified: pkg/pomp/tests/ricker-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-spect.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ricker-spect.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pdf(file="ricker-spect.pdf")
>
@@ -72,4 +74,4 @@
>
> proc.time()
user system elapsed
- 2.316 0.072 2.553
+ 2.650 0.029 2.670
Modified: pkg/pomp/tests/ricker.Rout.save
===================================================================
--- pkg/pomp/tests/ricker.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/ricker.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ricker)
newly created pomp object(s):
@@ -85,4 +87,4 @@
>
> proc.time()
user system elapsed
- 0.632 0.060 0.836
+ 0.611 0.023 0.626
Modified: pkg/pomp/tests/rw2.Rout.save
===================================================================
--- pkg/pomp/tests/rw2.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/rw2.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -168,7 +168,7 @@
}
y
}
-<environment: 0x310abf8>
+<environment: 0x2d8eeb0>
measurement model density, dmeasure =
function (y, x, t, params, log, covars, ...)
{
@@ -181,7 +181,7 @@
f
else exp(f)
}
-<environment: 0x310abf8>
+<environment: 0x2d8eeb0>
prior simulator, rprior =
function not specified
prior density, dprior =
@@ -346,4 +346,4 @@
>
> proc.time()
user system elapsed
- 0.968 0.064 1.059
+ 0.928 0.056 0.968
Modified: pkg/pomp/tests/sir.Rout.save
===================================================================
--- pkg/pomp/tests/sir.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/sir.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -196,7 +196,7 @@
method = 0L, zeronames = zeronames, tcovar = tcovar,
covar = covar, args = pairlist(...), gnsi = .getnativesymbolinfo)
}
-<environment: 0x2fd9488>
+<environment: 0x2d72f88>
process model density, dprocess =
function (x, times, params, ..., tcovar, covar, log = FALSE,
.getnativesymbolinfo = TRUE)
@@ -205,7 +205,7 @@
params = params, tcovar = tcovar, covar = covar, log = log,
args = pairlist(...), gnsi = .getnativesymbolinfo)
}
-<environment: 0x30213e8>
+<environment: 0x2be3788>
measurement model simulator, rmeasure =
function (x, t, params, covars, ...)
{
@@ -278,7 +278,7 @@
> x <- simulate(po,nsim=3)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.8367867 secs
+Time difference of 0.9839017 secs
>
> pdf(file='sir.pdf')
>
@@ -295,7 +295,7 @@
> X3 <- trajectory(po,times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.528033 secs
+Time difference of 0.6020904 secs
> plot(t3,X3['I',1,],type='l')
>
> f1 <- dprocess(
@@ -347,7 +347,7 @@
> x <- simulate(po,nsim=100)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 2.492409 secs
+Time difference of 3.182583 secs
> plot(x[[1]],variables=c("S","I","R","cases","W"))
>
> t3 <- seq(0,20,by=1/52)
@@ -355,7 +355,7 @@
> X4 <- trajectory(po,times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.01736164 secs
+Time difference of 0.02289963 secs
> plot(t3,X4['I',1,],type='l')
>
> g2 <- dmeasure(
@@ -450,4 +450,4 @@
>
> proc.time()
user system elapsed
- 4.916 0.072 5.286
+ 5.871 0.068 5.916
Modified: pkg/pomp/tests/skeleton.Rout.save
===================================================================
--- pkg/pomp/tests/skeleton.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/skeleton.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ricker)
newly created pomp object(s):
@@ -96,4 +98,4 @@
>
> proc.time()
user system elapsed
- 0.652 0.060 0.828
+ 0.672 0.027 0.690
Modified: pkg/pomp/tests/steps.Rout.save
===================================================================
--- pkg/pomp/tests/steps.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/steps.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> set.seed(54588699L)
>
@@ -62,4 +64,4 @@
>
> proc.time()
user system elapsed
- 0.520 0.048 0.590
+ 0.531 0.023 0.544
Modified: pkg/pomp/tests/synlik.Rout.save
===================================================================
--- pkg/pomp/tests/synlik.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/synlik.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(ou2)
newly created pomp object(s):
@@ -118,4 +120,4 @@
>
> proc.time()
user system elapsed
- 7.312 0.032 7.443
+ 6.925 0.036 6.957
Modified: pkg/pomp/tests/verhulst.Rout.save
===================================================================
--- pkg/pomp/tests/verhulst.Rout.save 2014-07-08 11:57:52 UTC (rev 995)
+++ pkg/pomp/tests/verhulst.Rout.save 2014-07-10 10:39:45 UTC (rev 996)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> pompExample(verhulst)
newly created pomp object(s):
@@ -56,4 +58,4 @@
>
> proc.time()
user system elapsed
- 0.656 0.044 0.721
+ 0.614 0.053 0.655
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