[Pomp-commits] r347 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 29 17:48:49 CEST 2010
Author: kingaa
Date: 2010-09-29 17:48:48 +0200 (Wed, 29 Sep 2010)
New Revision: 347
Added:
pkg/tests/ou2-probe.R
pkg/tests/ou2-probe.Rout.save
Removed:
pkg/tests/ou2-probe-match.R
pkg/tests/ou2-probe-match.Rout.save
Log:
- change name of file
- add in a test of probe.acf and probe.nlar
Deleted: pkg/tests/ou2-probe-match.R
===================================================================
--- pkg/tests/ou2-probe-match.R 2010-09-29 15:38:12 UTC (rev 346)
+++ pkg/tests/ou2-probe-match.R 2010-09-29 15:48:48 UTC (rev 347)
@@ -1,56 +0,0 @@
-library(pomp)
-set.seed(1066L)
-
-data(ou2)
-po <- ou2
-coef(po,c("x1.0","x2.0","alpha.1","alpha.4")) <- c(0,0,0.1,0.2)
-
-pm.ou2 <- probe(
- ou2,
- probes=list(
- y1.mean=probe.mean(var="y1"),
- y2.mean=probe.mean(var="y2"),
- y1.sd=probe.sd(var="y1"),
- y2.sd=probe.sd(var="y2")
- ),
- nsim=500
- )
-pm.po <- probe(
- po,
- probes=list(
- y1.mean=probe.mean(var="y1"),
- y2.mean=probe.mean(var="y2"),
- y1.sd=probe.sd(var="y1"),
- y2.sd=probe.sd(var="y2")
- ),
- nsim=500
- )
-
-summary(pm.ou2)
-summary(pm.po)
-
-plot(pm.ou2)
-plot(pm.po)
-
-pm.ou2 <- probe(
- ou2,
- probes=list(
- y1acf=probe.acf(var="y1",lag.max=2,type="corr"),
- y2.cov12=probe.cov(vars=c("y1"),lag=12,method="spearman"),
- y12.cov8=probe.cov(vars=c("y2","y1"),lag=8,method="pearson")
- ),
- nsim=500
- )
-
-summary(pm.ou2)
-
-pb <- probe(
- ou2,
- probes=list(
- y1=probe.quantile(var="y1",prob=seq(0.1,0.9,by=0.1)),
- probe.acf(var=c("y1","y2"),lag.max=4,transform=identity),
- pd=probe.period(var="y1",kernel.width=3)
- ),
- nsim=200
- )
-summary(pb)
Deleted: pkg/tests/ou2-probe-match.Rout.save
===================================================================
--- pkg/tests/ou2-probe-match.Rout.save 2010-09-29 15:38:12 UTC (rev 346)
+++ pkg/tests/ou2-probe-match.Rout.save 2010-09-29 15:48:48 UTC (rev 347)
@@ -1,142 +0,0 @@
-
-R version 2.11.1 (2010-05-31)
-Copyright (C) 2010 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> library(pomp)
-> set.seed(1066L)
->
-> data(ou2)
-> po <- ou2
-> coef(po,c("x1.0","x2.0","alpha.1","alpha.4")) <- c(0,0,0.1,0.2)
->
-> pm.ou2 <- probe(
-+ ou2,
-+ probes=list(
-+ y1.mean=probe.mean(var="y1"),
-+ y2.mean=probe.mean(var="y2"),
-+ y1.sd=probe.sd(var="y1"),
-+ y2.sd=probe.sd(var="y2")
-+ ),
-+ nsim=500
-+ )
-> pm.po <- probe(
-+ po,
-+ probes=list(
-+ y1.mean=probe.mean(var="y1"),
-+ y2.mean=probe.mean(var="y2"),
-+ y1.sd=probe.sd(var="y1"),
-+ y2.sd=probe.sd(var="y2")
-+ ),
-+ nsim=500
-+ )
->
-> summary(pm.ou2)
-$coef
-alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3 tau x1.0 x2.0
- 0.8 -0.5 0.3 0.9 3.0 -0.5 2.0 1.0 -3.0 4.0
-
-$nsim
-[1] 500
-
-$quantiles
-y1.mean y2.mean y1.sd y2.sd
- 0.100 0.530 0.024 0.052
-
-$pvals
- y1.mean y2.mean y1.sd y2.sd
-0.20359281 0.94211577 0.05189621 0.10778443
-
-> summary(pm.po)
-$coef
-alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3 tau x1.0 x2.0
- 0.1 -0.5 0.3 0.2 3.0 -0.5 2.0 1.0 0.0 0.0
-
-$nsim
-[1] 500
-
-$quantiles
-y1.mean y2.mean y1.sd y2.sd
- 0.054 0.644 1.000 1.000
-
-$pvals
- y1.mean y2.mean y1.sd y2.sd
-0.111776447 0.714570858 0.003992016 0.003992016
-
->
-> plot(pm.ou2)
-> plot(pm.po)
->
-> pm.ou2 <- probe(
-+ ou2,
-+ probes=list(
-+ y1acf=probe.acf(var="y1",lag.max=2,type="corr"),
-+ y2.cov12=probe.cov(vars=c("y1"),lag=12,method="spearman"),
-+ y12.cov8=probe.cov(vars=c("y2","y1"),lag=8,method="pearson")
-+ ),
-+ nsim=500
-+ )
->
-> summary(pm.ou2)
-$coef
-alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3 tau x1.0 x2.0
- 0.8 -0.5 0.3 0.9 3.0 -0.5 2.0 1.0 -3.0 4.0
-
-$nsim
-[1] 500
-
-$quantiles
-y1acf.acf.1.y1 y1acf.acf.2.y1 y2.cov12 y12.cov8
- 0.092 0.054 0.726 0.462
-
-$pvals
-y1acf.acf.1.y1 y1acf.acf.2.y1 y2.cov12 y12.cov8
- 0.1876248 0.1117764 0.5508982 0.9261477
-
->
-> pb <- probe(
-+ ou2,
-+ probes=list(
-+ y1=probe.quantile(var="y1",prob=seq(0.1,0.9,by=0.1)),
-+ probe.acf(var=c("y1","y2"),lag.max=4,transform=identity),
-+ pd=probe.period(var="y1",kernel.width=3)
-+ ),
-+ nsim=200
-+ )
-> summary(pb)
-$coef
-alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3 tau x1.0 x2.0
- 0.8 -0.5 0.3 0.9 3.0 -0.5 2.0 1.0 -3.0 4.0
-
-$nsim
-[1] 200
-
-$quantiles
- y1.10% y1.20% y1.30% y1.40% y1.50% y1.60% y1.70% y1.80%
- 0.755 0.790 0.765 0.555 0.335 0.115 0.035 0.025
- y1.90% acf.0.y1 acf.1.y1 acf.2.y1 acf.3.y1 acf.4.y1 acf.0.y2 acf.1.y2
- 0.010 0.035 0.045 0.030 0.115 0.790 0.065 0.060
-acf.2.y2 acf.3.y2 acf.4.y2 pd
- 0.080 0.110 0.445 0.060
-
-$pvals
- y1.10% y1.20% y1.30% y1.40% y1.50% y1.60% y1.70%
-0.49751244 0.42786070 0.47761194 0.89552239 0.67661692 0.23880597 0.07960199
- y1.80% y1.90% acf.0.y1 acf.1.y1 acf.2.y1 acf.3.y1 acf.4.y1
-0.05970149 0.02985075 0.07960199 0.09950249 0.06965174 0.23880597 0.42786070
- acf.0.y2 acf.1.y2 acf.2.y2 acf.3.y2 acf.4.y2 pd
-0.13930348 0.12935323 0.16915423 0.22885572 0.89552239 0.12935323
-
->
Copied: pkg/tests/ou2-probe.R (from rev 324, pkg/tests/ou2-probe-match.R)
===================================================================
--- pkg/tests/ou2-probe.R (rev 0)
+++ pkg/tests/ou2-probe.R 2010-09-29 15:48:48 UTC (rev 347)
@@ -0,0 +1,74 @@
+library(pomp)
+set.seed(1066L)
+
+data(ou2)
+po <- ou2
+coef(po,c("x1.0","x2.0","alpha.1","alpha.4")) <- c(0,0,0.1,0.2)
+
+pm.ou2 <- probe(
+ ou2,
+ probes=list(
+ y1.mean=probe.mean(var="y1"),
+ y2.mean=probe.mean(var="y2"),
+ y1.sd=probe.sd(var="y1"),
+ y2.sd=probe.sd(var="y2")
+ ),
+ nsim=500
+ )
+pm.po <- probe(
+ po,
+ probes=list(
+ y1.mean=probe.mean(var="y1"),
+ y2.mean=probe.mean(var="y2"),
+ y1.sd=probe.sd(var="y1"),
+ y2.sd=probe.sd(var="y2")
+ ),
+ nsim=500
+ )
+
+summary(pm.ou2)
+summary(pm.po)
+
+plot(pm.ou2)
+plot(pm.po)
+
+pm.ou2 <- probe(
+ ou2,
+ probes=list(
+ y1acf=probe.acf(var="y1",lag.max=2,type="corr"),
+ y2.cov12=probe.cov(vars=c("y1"),lag=12,method="spearman"),
+ y12.cov8=probe.cov(vars=c("y2","y1"),lag=8,method="pearson")
+ ),
+ nsim=500
+ )
+
+summary(pm.ou2)
+
+pb <- probe(
+ ou2,
+ probes=list(
+ y1=probe.quantile(var="y1",prob=seq(0.1,0.9,by=0.1)),
+ probe.acf(var=c("y1","y2"),lag.max=4,transform=identity),
+ pd=probe.period(var="y1",kernel.width=3)
+ ),
+ nsim=200
+ )
+summary(pb)
+
+po <- ou2
+coef(po,c("alpha.2","alpha.3")) <- c(0,0)
+coef(po,c("sigma.2","sigma.1","sigma.3")) <- c(0,0.0,0.0)
+coef(po,c("tau")) <- c(0.0)
+po <- simulate(po)
+pb <- probe(
+ po,
+ probes=list(
+ probe.acf(var=c("y1","y2"),lag.max=1,type="cor"),
+ probe.nlar("y1",lags=1,powers=1),
+ probe.nlar("y2",lags=1,powers=1)
+ ),
+ nsim=1000,
+ seed=1066L
+ )
+summary(pb)
+pb at datvals
Copied: pkg/tests/ou2-probe.Rout.save (from rev 324, pkg/tests/ou2-probe-match.Rout.save)
===================================================================
--- pkg/tests/ou2-probe.Rout.save (rev 0)
+++ pkg/tests/ou2-probe.Rout.save 2010-09-29 15:48:48 UTC (rev 347)
@@ -0,0 +1,142 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(pomp)
+> set.seed(1066L)
+>
+> data(ou2)
+> po <- ou2
+> coef(po,c("x1.0","x2.0","alpha.1","alpha.4")) <- c(0,0,0.1,0.2)
+>
+> pm.ou2 <- probe(
++ ou2,
++ probes=list(
++ y1.mean=probe.mean(var="y1"),
++ y2.mean=probe.mean(var="y2"),
++ y1.sd=probe.sd(var="y1"),
++ y2.sd=probe.sd(var="y2")
++ ),
++ nsim=500
++ )
+> pm.po <- probe(
++ po,
++ probes=list(
++ y1.mean=probe.mean(var="y1"),
++ y2.mean=probe.mean(var="y2"),
++ y1.sd=probe.sd(var="y1"),
++ y2.sd=probe.sd(var="y2")
++ ),
++ nsim=500
++ )
+>
+> summary(pm.ou2)
+$coef
+alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3 tau x1.0 x2.0
+ 0.8 -0.5 0.3 0.9 3.0 -0.5 2.0 1.0 -3.0 4.0
+
+$nsim
+[1] 500
+
+$quantiles
+y1.mean y2.mean y1.sd y2.sd
+ 0.100 0.530 0.024 0.052
+
+$pvals
+ y1.mean y2.mean y1.sd y2.sd
+0.20359281 0.94211577 0.05189621 0.10778443
+
+> summary(pm.po)
+$coef
+alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3 tau x1.0 x2.0
+ 0.1 -0.5 0.3 0.2 3.0 -0.5 2.0 1.0 0.0 0.0
+
+$nsim
+[1] 500
+
+$quantiles
+y1.mean y2.mean y1.sd y2.sd
+ 0.054 0.644 1.000 1.000
+
+$pvals
+ y1.mean y2.mean y1.sd y2.sd
+0.111776447 0.714570858 0.003992016 0.003992016
+
+>
+> plot(pm.ou2)
+> plot(pm.po)
+>
+> pm.ou2 <- probe(
++ ou2,
++ probes=list(
++ y1acf=probe.acf(var="y1",lag.max=2,type="corr"),
++ y2.cov12=probe.cov(vars=c("y1"),lag=12,method="spearman"),
++ y12.cov8=probe.cov(vars=c("y2","y1"),lag=8,method="pearson")
++ ),
++ nsim=500
++ )
+>
+> summary(pm.ou2)
+$coef
+alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3 tau x1.0 x2.0
+ 0.8 -0.5 0.3 0.9 3.0 -0.5 2.0 1.0 -3.0 4.0
+
+$nsim
+[1] 500
+
+$quantiles
+y1acf.acf.1.y1 y1acf.acf.2.y1 y2.cov12 y12.cov8
+ 0.092 0.054 0.726 0.462
+
+$pvals
+y1acf.acf.1.y1 y1acf.acf.2.y1 y2.cov12 y12.cov8
+ 0.1876248 0.1117764 0.5508982 0.9261477
+
+>
+> pb <- probe(
++ ou2,
++ probes=list(
++ y1=probe.quantile(var="y1",prob=seq(0.1,0.9,by=0.1)),
++ probe.acf(var=c("y1","y2"),lag.max=4,transform=identity),
++ pd=probe.period(var="y1",kernel.width=3)
++ ),
++ nsim=200
++ )
+> summary(pb)
+$coef
+alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3 tau x1.0 x2.0
+ 0.8 -0.5 0.3 0.9 3.0 -0.5 2.0 1.0 -3.0 4.0
+
+$nsim
+[1] 200
+
+$quantiles
+ y1.10% y1.20% y1.30% y1.40% y1.50% y1.60% y1.70% y1.80%
+ 0.755 0.790 0.765 0.555 0.335 0.115 0.035 0.025
+ y1.90% acf.0.y1 acf.1.y1 acf.2.y1 acf.3.y1 acf.4.y1 acf.0.y2 acf.1.y2
+ 0.010 0.035 0.045 0.030 0.115 0.790 0.065 0.060
+acf.2.y2 acf.3.y2 acf.4.y2 pd
+ 0.080 0.110 0.445 0.060
+
+$pvals
+ y1.10% y1.20% y1.30% y1.40% y1.50% y1.60% y1.70%
+0.49751244 0.42786070 0.47761194 0.89552239 0.67661692 0.23880597 0.07960199
+ y1.80% y1.90% acf.0.y1 acf.1.y1 acf.2.y1 acf.3.y1 acf.4.y1
+0.05970149 0.02985075 0.07960199 0.09950249 0.06965174 0.23880597 0.42786070
+ acf.0.y2 acf.1.y2 acf.2.y2 acf.3.y2 acf.4.y2 pd
+0.13930348 0.12935323 0.16915423 0.22885572 0.89552239 0.12935323
+
+>
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