[Pomp-commits] r1039 - in pkg/pomp: . R tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jan 1 22:20:29 CET 2015
Author: kingaa
Date: 2015-01-01 22:20:29 +0100 (Thu, 01 Jan 2015)
New Revision: 1039
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/example.R
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-bsmc2.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:
- minor cosmetic tweak
- update all .Rout.save files
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/DESCRIPTION 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.56-1
-Date: 2014-12-16
+Version: 0.56-2
+Date: 2015-01-01
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/R/example.R
===================================================================
--- pkg/pomp/R/example.R 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/R/example.R 2015-01-01 21:20:29 UTC (rev 1039)
@@ -28,7 +28,7 @@
get(objs$value[i],envir=evalEnv),
envir=envir)
}
- cat("newly created pomp object(s):\n",objs$value,"\n")
+ cat("newly created object(s):\n",objs$value,"\n")
obj <- NULL
} else {
stop(sQuote("envir")," must be an environment or NULL")
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
bbs
>
> guess <- c(
@@ -72,8 +68,8 @@
> options(warn=2)
> ofun <- traj.match.objfun(window(bbs,end=3),est=c("beta","gamma"),transform=TRUE,maxsteps=10,rtol=1e-6)
> try(optim(fn=ofun,par=c(0,-1),method="Nelder-Mead",control=list(reltol=1e-10)))
-DLSODA- At current T (=R1), MXSTEP (=I1) steps
- taken on this call before reaching TOUT
+DLSODA- At current T (=R1), MXSTEP (=I1) steps
+ taken on this call before reaching TOUT
In above message, I1 = 10
In above message, R1 = 0.609738
@@ -84,4 +80,4 @@
>
> proc.time()
user system elapsed
- 2.795 0.053 2.839
+ 2.725 0.017 2.733
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/bbs.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,7 +20,7 @@
Loading required package: nloptr
>
> pompExample(bbs)
-newly created pomp object(s):
+newly created object(s):
bbs
>
> set.seed(48857734L)
@@ -69,4 +69,4 @@
>
> proc.time()
user system elapsed
- 6.716 0.076 6.831
+ 7.769 0.051 7.832
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/blowflies.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
blowflies1 blowflies2
>
> init.state(blowflies1)
@@ -74,4 +70,4 @@
>
> proc.time()
user system elapsed
- 1.430 0.051 1.473
+ 1.493 0.039 1.519
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/dacca.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,17 +16,13 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
Loading required package: subplex
Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
>
> set.seed(1420306530L)
>
> pompExample(dacca)
-newly created pomp object(s):
+newly created object(s):
dacca
>
> x <- as.data.frame(dacca)
@@ -111,4 +107,4 @@
>
> proc.time()
user system elapsed
- 13.216 0.040 13.260
+ 14.817 0.035 14.853
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/dimchecks.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,17 +16,13 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
Loading required package: subplex
Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
>
> set.seed(1420306530L)
>
> pompExample(ricker)
-newly created pomp object(s):
+newly created object(s):
ricker
> po <- ricker
>
@@ -156,7 +152,7 @@
> stopifnot(identical(g1,g3[,4:6,]))
>
> pompExample(gompertz)
-newly created pomp object(s):
+newly created object(s):
gompertz
> p <- parmat(coef(gompertz),5)
> f1 <- partrans(gompertz,p,"inv")
@@ -166,4 +162,4 @@
>
> proc.time()
user system elapsed
- 0.532 0.037 0.555
+ 0.489 0.041 0.517
Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/fhn.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,12 +16,8 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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")
@@ -95,4 +91,4 @@
>
> proc.time()
user system elapsed
- 0.99 0.04 1.02
+ 0.927 0.060 0.950
Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/filtfail.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,12 +16,8 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
Loading required package: subplex
Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
>
> set.seed(834454394L)
>
@@ -120,4 +116,4 @@
>
> proc.time()
user system elapsed
- 0.572 0.031 0.581
+ 0.489 0.053 0.529
Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/gillespie.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,12 +16,8 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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,
@@ -121,7 +117,7 @@
105 0.1666667
>
> pompExample(gillespie.sir)
-newly created pomp object(s):
+newly created object(s):
gillespie.sir
>
> tail(as.data.frame(simulate(gillespie.sir,times=time(gsir),t0=timezero(gsir),seed=1165270654L)))
@@ -135,4 +131,4 @@
>
> proc.time()
user system elapsed
- 2.637 0.064 2.693
+ 2.565 0.041 2.592
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/gompertz.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,16 +16,12 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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)
-newly created pomp object(s):
+newly created object(s):
gompertz
>
> po <- gompertz
@@ -137,4 +133,4 @@
>
> proc.time()
user system elapsed
- 1.762 0.063 1.806
+ 1.797 0.038 1.822
Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/logistic.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,12 +16,8 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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)),
@@ -126,4 +122,4 @@
>
> proc.time()
user system elapsed
- 0.911 0.033 0.933
+ 0.874 0.030 0.887
Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-abc.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -18,14 +18,10 @@
> ### OU2 test of abc for pomp
>
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
>
> pdf(file='ou2-abc.pdf')
@@ -135,4 +131,4 @@
>
> proc.time()
user system elapsed
- 11.588 0.056 11.647
+ 11.085 0.055 11.138
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,16 +16,12 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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)
-newly created pomp object(s):
+newly created object(s):
ou2
>
> time(ou2) <- 1:10
@@ -63,7 +59,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 3.021244 secs
+Time difference of 3.430529 secs
>
> print(
+ cbind(
@@ -105,4 +101,4 @@
>
> proc.time()
user system elapsed
- 4.967 0.053 5.012
+ 5.498 0.064 5.527
Modified: pkg/pomp/tests/ou2-bsmc2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc2.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-bsmc2.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -21,7 +21,7 @@
>
> set.seed(398585L)
> pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
ou2
>
> time(ou2) <- 1:10
@@ -56,7 +56,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 2.042303 secs
+Time difference of 2.234756 secs
>
> print(
+ cbind(
@@ -98,4 +98,4 @@
>
> proc.time()
user system elapsed
- 3.576 0.104 3.707
+ 3.846 0.045 3.881
Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-forecast.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,17 +16,13 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
Loading required package: subplex
Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
>
> set.seed(921625222L)
>
> pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
ou2
> tm <- time(ou2)
> y <- obs(ou2)
@@ -65,4 +61,4 @@
>
> proc.time()
user system elapsed
- 1.456 0.016 1.463
+ 1.376 0.042 1.402
Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-kalman.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,12 +16,8 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
Loading required package: subplex
Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
>
> set.seed(577639485L)
>
@@ -72,7 +68,7 @@
+ }
>
> pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
ou2
>
> # true coefficients
@@ -168,7 +164,7 @@
117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 3.49406 secs
+Time difference of 3.235065 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
@@ -192,4 +188,4 @@
>
> proc.time()
user system elapsed
- 4.096 0.029 4.104
+ 3.769 0.026 3.787
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
>
> set.seed(64857673L)
@@ -74,4 +70,4 @@
>
> proc.time()
user system elapsed
- 23.726 0.048 23.790
+ 24.537 0.066 24.614
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
>
> set.seed(64857673L)
@@ -285,4 +281,4 @@
>
> proc.time()
user system elapsed
- 14.330 0.061 14.397
+ 13.791 0.053 13.848
Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-mif2.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
>
> pdf(file="ou2-mif2.pdf")
@@ -139,4 +135,4 @@
>
> proc.time()
user system elapsed
- 63.315 0.042 63.432
+ 62.157 0.075 62.274
Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-nlf.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,17 +16,13 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
Loading required package: subplex
Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
>
> set.seed(583615606L)
>
> pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
ou2
> estnames=c("alpha.2","alpha.3","tau")
> theta.truth <- coef(ou2)
@@ -89,4 +85,4 @@
>
> proc.time()
user system elapsed
- 5.413 0.023 5.433
+ 5.003 0.037 5.037
Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
>
> dprior.ou2 <- function (params, log, ...) {
@@ -118,4 +114,4 @@
>
> proc.time()
user system elapsed
- 27.262 0.036 27.325
+ 26.822 0.042 26.880
Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-probe.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,18 +16,14 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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")
>
> pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
ou2
>
> pm.ou2 <- probe(
@@ -297,7 +293,7 @@
sim.5 0.5542739 0.6216561 -0.4089672 -0.7236761 0.06850115
>
> pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
ou2
>
> good <- probe(
@@ -344,4 +340,4 @@
>
> proc.time()
user system elapsed
- 8.873 0.076 8.949
+ 8.501 0.048 8.545
Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
>
> po <- window(ou2,end=10)
@@ -58,4 +54,4 @@
>
> proc.time()
user system elapsed
- 0.526 0.044 0.560
+ 0.493 0.037 0.495
Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-simulate.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
>
> ## fix some parameters
@@ -39,7 +35,7 @@
> ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.006201267 secs
+Time difference of 0.007747889 secs
>
> coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
>
@@ -50,4 +46,4 @@
>
> proc.time()
user system elapsed
- 0.523 0.016 0.530
+ 0.501 0.022 0.507
Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,17 +16,13 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
Loading required package: subplex
Loading required package: nloptr
-Loading required package: deSolve
-Loading required package: coda
-Loading required package: lattice
>
> set.seed(93885485L)
>
> pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
ou2
> true.p <- coef(ou2)
> simdata <- simulate(ou2,nsim=5,params=true.p,seed=394885)
@@ -159,7 +155,7 @@
> stopifnot(fit$convergence==0)
>
> pompExample(ou2)
-newly created pomp object(s):
+newly created object(s):
ou2
> p <- coef(ou2)
> ou2 at params <- numeric(0)
@@ -179,4 +175,4 @@
>
> proc.time()
user system elapsed
- 1.771 0.065 1.824
+ 1.740 0.048 1.765
Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/partrans.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
gompertz
>
> pars <- coef(gompertz)
@@ -56,4 +52,4 @@
>
> proc.time()
user system elapsed
- 0.500 0.053 0.522
+ 0.492 0.020 0.494
Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/pfilter.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
>
> set.seed(9994847L)
@@ -49,7 +45,7 @@
-479.61 0.46
>
> pompExample(euler.sir)
-newly created pomp object(s):
+newly created object(s):
euler.sir
> pf <- pfilter(euler.sir,Np=100,seed=394343L)
> print(coef(pf))
@@ -81,4 +77,4 @@
>
> proc.time()
user system elapsed
- 10.454 0.035 10.489
+ 9.887 0.037 9.924
Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/pomppomp.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ricker
> y1 <- obs(simulate(ricker,seed=1066L))
> r2 <- pomp(ricker,measurement.model=y~pois(lambda=N*phi))
@@ -59,4 +55,4 @@
>
> proc.time()
user system elapsed
- 0.562 0.032 0.582
+ 0.489 0.030 0.504
Modified: pkg/pomp/tests/prior.Rout.save
===================================================================
--- pkg/pomp/tests/prior.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/prior.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ou2
> coef(ou2,"alpha.sd") <- 5
Warning message:
@@ -76,4 +72,4 @@
>
> proc.time()
user system elapsed
- 0.697 0.016 0.703
+ 0.683 0.025 0.694
Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ricker
>
> pdf(file="ricker-bsmc.pdf")
@@ -58,4 +54,4 @@
>
> proc.time()
user system elapsed
- 3.035 0.057 3.068
+ 2.571 0.057 2.614
Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ricker-probe.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,15 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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):
+newly created object(s):
ricker
>
> pdf(file="ricker-probe.pdf")
@@ -301,4 +297,4 @@
>
> proc.time()
user system elapsed
- 14.323 0.079 14.418
+ 13.643 0.070 13.713
Modified: pkg/pomp/tests/ricker-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-spect.Rout.save 2015-01-01 21:20:25 UTC (rev 1038)
+++ pkg/pomp/tests/ricker-spect.Rout.save 2015-01-01 21:20:29 UTC (rev 1039)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -16,17 +16,13 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: mvtnorm
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")
>
> pompExample(ricker)
-newly created pomp object(s):
+newly created object(s):
ricker
>
> set.seed(6457673L)
@@ -74,4 +70,4 @@
>
> proc.time()
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1039
More information about the pomp-commits
mailing list