[Pomp-commits] r756 - in pkg/pomp: . inst tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 3 17:07:45 CEST 2012
Author: kingaa
Date: 2012-08-03 17:07:45 +0200 (Fri, 03 Aug 2012)
New Revision: 756
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/inst/NEWS
pkg/pomp/tests/ou2-probe.R
pkg/pomp/tests/ou2-probe.Rout.save
pkg/pomp/tests/ricker-bsmc.R
pkg/pomp/tests/ricker-bsmc.Rout.save
pkg/pomp/tests/ricker-probe.R
pkg/pomp/tests/ricker-probe.Rout.save
Log:
- clean up tests
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2012-07-31 20:54:21 UTC (rev 755)
+++ pkg/pomp/DESCRIPTION 2012-08-03 15:07:45 UTC (rev 756)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.43-3
-Date: 2012-07-31
+Version: 0.43-4
+Date: 2012-08-03
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/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2012-07-31 20:54:21 UTC (rev 755)
+++ pkg/pomp/inst/NEWS 2012-08-03 15:07:45 UTC (rev 756)
@@ -1,4 +1,7 @@
NEWS
+0.43-4
+ o Clean up tests.
+
0.43-3
o Fix bug in 'pompBuilder' on mac.
Modified: pkg/pomp/tests/ou2-probe.R
===================================================================
--- pkg/pomp/tests/ou2-probe.R 2012-07-31 20:54:21 UTC (rev 755)
+++ pkg/pomp/tests/ou2-probe.R 2012-08-03 15:07:45 UTC (rev 756)
@@ -82,7 +82,8 @@
z1 <- tail(x$y1,-1)
y2 <- head(x$y2,-1)
z2 <- tail(x$y2,-1)
-max(abs(pb at datvals-c(mean(y1*z1)/mean(x$y1^2),mean(y2*z2)/mean(x$y2^2),mean(y1*z1)/mean(y1*y1),mean(y2*z2)/mean(y2*y2))))
+small.diff <- pb at datvals-c(mean(y1*z1)/mean(x$y1^2),mean(y2*z2)/mean(x$y2^2),mean(y1*z1)/mean(y1*y1),mean(y2*z2)/mean(y2*y2))
+stopifnot(max(abs(small.diff))<.Machine$double.eps*100)
po <- simulate(ou2)
pb <- probe(
Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save 2012-07-31 20:54:21 UTC (rev 755)
+++ pkg/pomp/tests/ou2-probe.Rout.save 2012-08-03 15:07:45 UTC (rev 756)
@@ -1,5 +1,5 @@
-R version 2.15.0 (2012-03-30)
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -193,8 +193,8 @@
> z1 <- tail(x$y1,-1)
> y2 <- head(x$y2,-1)
> z2 <- tail(x$y2,-1)
-> max(abs(pb at datvals-c(mean(y1*z1)/mean(x$y1^2),mean(y2*z2)/mean(x$y2^2),mean(y1*z1)/mean(y1*y1),mean(y2*z2)/mean(y2*y2))))
-[1] 1.110223e-16
+> small.diff <- pb at datvals-c(mean(y1*z1)/mean(x$y1^2),mean(y2*z2)/mean(x$y2^2),mean(y1*z1)/mean(y1*y1),mean(y2*z2)/mean(y2*y2))
+> stopifnot(max(abs(small.diff))<.Machine$double.eps*100)
>
> po <- simulate(ou2)
> pb <- probe(
@@ -294,4 +294,4 @@
>
> proc.time()
user system elapsed
- 1.292 0.028 1.377
+ 1.320 0.040 1.484
Modified: pkg/pomp/tests/ricker-bsmc.R
===================================================================
--- pkg/pomp/tests/ricker-bsmc.R 2012-07-31 20:54:21 UTC (rev 755)
+++ pkg/pomp/tests/ricker-bsmc.R 2012-08-03 15:07:45 UTC (rev 756)
@@ -15,11 +15,11 @@
fit <- bsmc(ricker,params=params,est=c("r","sigma"),transform=TRUE,smooth=0.2)
-print(apply(fit$prior[c("r","sigma"),],1,mean))
+invisible(apply(fit$prior[c("r","sigma"),],1,mean))
-print(apply(fit$post[c("r","sigma"),],1,mean))
+invisible(apply(fit$post[c("r","sigma"),],1,mean))
-print(coef(fit))
+invisible(coef(fit))
plot(fit,thin=300)
Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save 2012-07-31 20:54:21 UTC (rev 755)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save 2012-08-03 15:07:45 UTC (rev 756)
@@ -1,5 +1,5 @@
-R version 2.15.0 (2012-03-30)
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -39,17 +39,11 @@
In sample.int(n = Np, size = Np, replace = TRUE, prob = g) :
Walker's alias method used: results are different from R < 2.2.0
>
-> print(apply(fit$prior[c("r","sigma"),],1,mean))
- r sigma
- 3.4894675 -0.7495206
+> invisible(apply(fit$prior[c("r","sigma"),],1,mean))
>
-> print(apply(fit$post[c("r","sigma"),],1,mean))
- r sigma
- 3.890965 -1.766350
+> invisible(apply(fit$post[c("r","sigma"),],1,mean))
>
-> print(coef(fit))
- r sigma phi N.0 e.0
-50.0502049 0.1702842 10.0000000 7.0000000 0.0000000
+> invisible(coef(fit))
>
> plot(fit,thin=300)
>
@@ -59,4 +53,4 @@
>
> proc.time()
user system elapsed
- 21.989 0.068 22.270
+ 23.861 0.076 24.137
Modified: pkg/pomp/tests/ricker-probe.R
===================================================================
--- pkg/pomp/tests/ricker-probe.R 2012-07-31 20:54:21 UTC (rev 755)
+++ pkg/pomp/tests/ricker-probe.R 2012-08-03 15:07:45 UTC (rev 756)
@@ -16,7 +16,7 @@
seed=838775L
)
plot(pb)
-summary(pb)
+invisible(summary(pb))
pb <- probe(
po,
@@ -25,7 +25,7 @@
seed=838775L
)
plot(pb)
-summary(pb)
+invisible(summary(pb))
pb <- probe(
po,
@@ -34,7 +34,7 @@
seed=838775L
)
plot(pb)
-summary(pb)
+invisible(summary(pb))
pb <- probe(
po,
@@ -43,7 +43,7 @@
seed=838775L
)
plot(pb)
-summary(pb)
+invisible(summary(pb))
pb <- probe(
po,
@@ -57,8 +57,8 @@
nsim=1000,
seed=838775L
)
-pb at datvals
-summary(pb)
+invisible(pb at datvals)
+invisible(summary(pb))
plot(pb)
pb <- probe(
@@ -80,13 +80,13 @@
nsim=1000,
seed=838775L
)
-pb at datvals
-summary(pb)
+invisible(pb at datvals)
+invisible(summary(pb))
plot(pb)
pbm <- probe.match(pb,eval.only=TRUE)
plot(pbm)
-summary(pbm)
+invisible(summary(pb))
coef(po) <- c(r=10,sigma=0.3,phi=20,N.0=5,e.0=0)
@@ -102,8 +102,8 @@
nsim=1000,
seed=838775L
)
-pb at datvals
-summary(pb)
+invisible(pb at datvals)
+invisible(summary(pb))
plot(pb)
pm <- probe.match(
@@ -119,7 +119,7 @@
)
plot(pm)
-cbind(truth=coef(ricker),est=coef(pm),guess=coef(po))
+invisible(cbind(truth=coef(ricker),est=coef(pm),guess=coef(po)))
pb <- probe(
po,
@@ -132,8 +132,8 @@
nsim=1000,
seed=838775L
)
-pb at datvals
-summary(pb)
+invisible(pb at datvals)
+invisible(summary(pb))
plot(pb)
pm <- probe.match(
@@ -151,7 +151,7 @@
plot(as(pm,"pomp"),variables="y")
plot(simulate(pm),variables="y")
-cbind(truth=coef(ricker),est=coef(pm),guess=coef(po))
+invisible(cbind(truth=coef(ricker),est=coef(pm),guess=coef(po)))
pb <- probe(
po,
@@ -165,8 +165,8 @@
nsim=1000,
seed=838775L
)
-pb at datvals
-summary(pb)
+invisible(pb at datvals)
+invisible(summary(pb))
plot(pb)
pb <- probe(
@@ -180,8 +180,8 @@
nsim=1000,
seed=838775L
)
-pb at datvals
-summary(pb)
+invisible(pb at datvals)
+invisible(summary(pb))
plot(pb)
pb <- probe(
@@ -195,8 +195,8 @@
nsim=1000,
seed=838775L
)
-pb at datvals
-summary(pb)
+invisible(pb at datvals)
+invisible(summary(pb))
plot(pb)
pb <- probe(
@@ -219,8 +219,8 @@
nsim=1000,
seed=838775L
)
-pb at datvals
-summary(pb)
+invisible(pb at datvals)
+invisible(summary(pb))
plot(pb)
try(
Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save 2012-07-31 20:54:21 UTC (rev 755)
+++ pkg/pomp/tests/ricker-probe.Rout.save 2012-08-03 15:07:45 UTC (rev 756)
@@ -1,5 +1,5 @@
-R version 2.15.0 (2012-03-30)
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -37,23 +37,7 @@
+ seed=838775L
+ )
> plot(pb)
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
-[1] 0.782
-
-$pvals
-[1] 0.3496503
-
-$synth.loglik
-[1] -2.437844
-
+> invisible(summary(pb))
>
> pb <- probe(
+ po,
@@ -62,25 +46,7 @@
+ seed=838775L
+ )
> plot(pb)
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
-nlar.1^1 nlar.2^1 nlar.3^1
- 0.166 0.251 0.803
-
-$pvals
- nlar.1^1 nlar.2^1 nlar.3^1
-0.3336663 0.5034965 0.3956044
-
-$synth.loglik
-[1] 2.805501
-
+> invisible(summary(pb))
>
> pb <- probe(
+ po,
@@ -89,25 +55,7 @@
+ seed=838775L
+ )
> plot(pb)
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
-nlar.1^1 nlar.2^1 nlar.3^1
- 0.166 0.251 0.803
-
-$pvals
- nlar.1^1 nlar.2^1 nlar.3^1
-0.3336663 0.5034965 0.3956044
-
-$synth.loglik
-[1] 2.805501
-
+> invisible(summary(pb))
>
> pb <- probe(
+ po,
@@ -116,25 +64,7 @@
+ seed=838775L
+ )
> plot(pb)
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
-nlar.1^1 nlar.1^2 nlar.1^3
- 0.403 0.805 0.323
-
-$pvals
- nlar.1^1 nlar.1^2 nlar.1^3
-0.8071928 0.3916084 0.6473526
-
-$synth.loglik
-[1] 7.383561
-
+> invisible(summary(pb))
>
> pb <- probe(
+ po,
@@ -148,28 +78,8 @@
+ nsim=1000,
+ seed=838775L
+ )
-> pb at datvals
- marg.1 marg.2 marg.3
-1.000000e+00 2.308125e-18 9.896164e-19
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
-marg.1 marg.2 marg.3
- 0.855 0.284 0.275
-
-$pvals
- marg.1 marg.2 marg.3
-0.2917083 0.5694306 0.5514486
-
-$synth.loglik
-[1] 12.42156
-
+> invisible(pb at datvals)
+> invisible(summary(pb))
> plot(pb)
>
> pb <- probe(
@@ -191,72 +101,13 @@
+ nsim=1000,
+ seed=838775L
+ )
-> pb at datvals
- marg.1 marg.2 marg.3 acf.0.y acf.1.y
- 1.000000e+00 2.308125e-18 9.896164e-19 3.679493e+03 -1.275470e+03
- acf.3.y acf.5.y mean
- 4.212841e+02 2.954671e+02 4.430440e+00
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
- marg.1 marg.2 marg.3 acf.0.y acf.1.y acf.3.y acf.5.y mean
- 0.855 0.284 0.275 0.647 0.034 0.920 0.686 0.838
-
-$pvals
- marg.1 marg.2 marg.3 acf.0.y acf.1.y acf.3.y acf.5.y
-0.29170829 0.56943057 0.55144855 0.70729271 0.06993007 0.16183816 0.62937063
- mean
-0.32567433
-
-$synth.loglik
-[1] -14.89908
-
+> invisible(pb at datvals)
+> invisible(summary(pb))
> plot(pb)
>
> pbm <- probe.match(pb,eval.only=TRUE)
> plot(pbm)
-> summary(pbm)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
- marg.1 marg.2 marg.3 acf.0.y acf.1.y acf.3.y acf.5.y mean
- 0.857 0.281 0.276 0.648 0.035 0.899 0.708 0.830
-
-$pvals
- marg.1 marg.2 marg.3 acf.0.y acf.1.y acf.3.y acf.5.y
-0.28771229 0.56343656 0.55344655 0.70529471 0.07192807 0.20379620 0.58541459
- mean
-0.34165834
-
-$synth.loglik
-[1] -14.7743
-
-$est
-character(0)
-
-$value
-[1] 15.31774
-
-$eval
-[1] 1 0
-
-$convergence
-[1] NA
-
-$msg
-[1] "no optimization performed"
-
+> invisible(summary(pb))
>
> coef(po) <- c(r=10,sigma=0.3,phi=20,N.0=5,e.0=0)
>
@@ -272,28 +123,8 @@
+ nsim=1000,
+ seed=838775L
+ )
-> pb at datvals
- marg.1 marg.2 marg.3
-1.000000e+00 2.308125e-18 9.896164e-19
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
- 10.0 0.3 20.0 5.0 0.0
-
-$nsim
-[1] 1000
-
-$quantiles
-marg.1 marg.2 marg.3
- 1.000 0.115 0.218
-
-$pvals
- marg.1 marg.2 marg.3
-0.001998002 0.231768232 0.437562438
-
-$synth.loglik
-[1] -19.71994
-
+> invisible(pb at datvals)
+> invisible(summary(pb))
> plot(pb)
>
> pm <- probe.match(
@@ -309,13 +140,7 @@
+ )
> plot(pm)
>
-> cbind(truth=coef(ricker),est=coef(pm),guess=coef(po))
- truth est guess
-r 44.70118 15.509632 10.0
-sigma 0.30000 0.300000 0.3
-phi 10.00000 32.376974 20.0
-N.0 7.00000 2.898467 5.0
-e.0 0.00000 0.000000 0.0
+> invisible(cbind(truth=coef(ricker),est=coef(pm),guess=coef(po)))
>
> pb <- probe(
+ po,
@@ -328,28 +153,8 @@
+ nsim=1000,
+ seed=838775L
+ )
-> pb at datvals
- nlar.1^1 nlar.1^2 nlar.1^3
--0.50800036 -0.12068721 0.01214788
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
- 10.0 0.3 20.0 5.0 0.0
-
-$nsim
-[1] 1000
-
-$quantiles
-nlar.1^1 nlar.1^2 nlar.1^3
- 0.999 0.078 0.065
-
-$pvals
- nlar.1^1 nlar.1^2 nlar.1^3
-0.003996004 0.157842158 0.131868132
-
-$synth.loglik
-[1] -5.862151
-
+> invisible(pb at datvals)
+> invisible(summary(pb))
> plot(pb)
>
> pm <- probe.match(
@@ -367,13 +172,7 @@
> plot(as(pm,"pomp"),variables="y")
> plot(simulate(pm),variables="y")
>
-> cbind(truth=coef(ricker),est=coef(pm),guess=coef(po))
- truth est guess
-r 44.70118 5.569172 10.0
-sigma 0.30000 0.300000 0.3
-phi 10.00000 32.412299 20.0
-N.0 7.00000 7.298905 5.0
-e.0 0.00000 0.000000 0.0
+> invisible(cbind(truth=coef(ricker),est=coef(pm),guess=coef(po)))
>
> pb <- probe(
+ po,
@@ -387,28 +186,8 @@
+ nsim=1000,
+ seed=838775L
+ )
-> pb at datvals
- marg.1 marg.2 marg.3
-24.879460 -5.950185 -2.211594
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
- 10.0 0.3 20.0 5.0 0.0
-
-$nsim
-[1] 1000
-
-$quantiles
-marg.1 marg.2 marg.3
- 1.00 0.00 0.32
-
-$pvals
- marg.1 marg.2 marg.3
-0.001998002 0.001998002 0.641358641
-
-$synth.loglik
-[1] -56.62876
-
+> invisible(pb at datvals)
+> invisible(summary(pb))
> plot(pb)
>
> pb <- probe(
@@ -422,28 +201,8 @@
+ nsim=1000,
+ seed=838775L
+ )
-> pb at datvals
- acf.0.y acf.1.y acf.2.y acf.3.y acf.4.y acf.5.y
-21.763354 -7.220449 -4.970518 3.099575 -2.823081 1.507337
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
-acf.0.y acf.1.y acf.2.y acf.3.y acf.4.y acf.5.y
- 0.592 0.067 0.315 0.907 0.144 0.658
-
-$pvals
- acf.0.y acf.1.y acf.2.y acf.3.y acf.4.y acf.5.y
-0.8171828 0.1358641 0.6313686 0.1878122 0.2897103 0.6853147
-
-$synth.loglik
-[1] -12.45474
-
+> invisible(pb at datvals)
+> invisible(summary(pb))
> plot(pb)
>
> pb <- probe(
@@ -457,28 +216,8 @@
+ nsim=1000,
+ seed=838775L
+ )
-> pb at datvals
- acf.1.y acf.2.y acf.3.y acf.4.y acf.5.y
--0.33177095 -0.22838933 0.14242173 -0.12971720 0.06926033
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
-acf.1.y acf.2.y acf.3.y acf.4.y acf.5.y
- 0.152 0.317 0.896 0.143 0.653
-
-$pvals
- acf.1.y acf.2.y acf.3.y acf.4.y acf.5.y
-0.3056943 0.6353646 0.2097902 0.2877123 0.6953047
-
-$synth.loglik
-[1] 5.174849
-
+> invisible(pb at datvals)
+> invisible(summary(pb))
> plot(pb)
>
> pb <- probe(
@@ -501,28 +240,8 @@
+ nsim=1000,
+ seed=838775L
+ )
-> pb at datvals
- v acf.0.y acf.1.y acf.2.y nlar.1^1 nlar.2^1
-22.1986212 21.7633541 -7.2204486 -4.9705179 -0.4637368 -0.3923487
-> summary(pb)
-$coef
- r sigma phi N.0 e.0
-44.70118 0.30000 10.00000 7.00000 0.00000
-
-$nsim
-[1] 1000
-
-$quantiles
- v acf.0.y acf.1.y acf.2.y nlar.1^1 nlar.2^1
- 0.592 0.592 0.067 0.315 0.105 0.133
-
-$pvals
- v acf.0.y acf.1.y acf.2.y nlar.1^1 nlar.2^1
-0.8171828 0.8171828 0.1358641 0.6313686 0.2117882 0.2677323
-
-$synth.loglik
-[1] 29.82456
-
+> invisible(pb at datvals)
+> invisible(summary(pb))
> plot(pb)
>
> try(
@@ -577,4 +296,4 @@
>
> proc.time()
user system elapsed
- 13.044 0.064 13.327
+ 12.404 0.060 12.659
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