[Pomp-commits] r914 - in pkg/pomp: . inst/doc tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 31 13:58:41 CEST 2014
Author: kingaa
Date: 2014-03-31 13:58:40 +0200 (Mon, 31 Mar 2014)
New Revision: 914
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/inst/doc/manual.pdf
pkg/pomp/tests/abc.Rout.save
pkg/pomp/tests/bbs-trajmatch.Rout.save
pkg/pomp/tests/bbs.Rout.save
pkg/pomp/tests/blowflies.Rout.save
pkg/pomp/tests/dacca.R
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-bsmc.Rout.save
pkg/pomp/tests/ou2-forecast.Rout.save
pkg/pomp/tests/ou2-kalman.Rout.save
pkg/pomp/tests/ou2-mif-fp.R
pkg/pomp/tests/ou2-mif-fp.Rout.save
pkg/pomp/tests/ou2-mif.R
pkg/pomp/tests/ou2-mif.Rout.save
pkg/pomp/tests/ou2-mif2.R
pkg/pomp/tests/ou2-mif2.Rout.save
pkg/pomp/tests/ou2-nlf.Rout.save
pkg/pomp/tests/ou2-pmcmc.R
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.R
pkg/pomp/tests/ricker-bsmc.Rout.save
pkg/pomp/tests/ricker-probe.R
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:
- put tests back in for R-Forge version
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/DESCRIPTION 2014-03-31 11:58:40 UTC (rev 914)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.49-2
-Date: 2014-03-25
+Version: 0.49-3
+Date: 2014-03-31
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/inst/doc/manual.pdf
===================================================================
(Binary files differ)
Modified: pkg/pomp/tests/abc.Rout.save
===================================================================
--- pkg/pomp/tests/abc.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/abc.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -124,4 +124,4 @@
>
> proc.time()
user system elapsed
- 7.816 0.084 8.154
+ 7.884 0.052 8.120
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -82,4 +82,4 @@
>
> proc.time()
user system elapsed
- 2.14 0.04 2.21
+ 2.396 0.048 2.469
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/bbs.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -65,4 +65,4 @@
>
> proc.time()
user system elapsed
- 2.908 0.064 3.003
+ 2.888 0.064 3.011
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/blowflies.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> pompExample(blowflies)
@@ -71,4 +72,4 @@
>
> proc.time()
user system elapsed
- 1.196 0.032 1.249
+ 1.216 0.036 1.283
Modified: pkg/pomp/tests/dacca.R
===================================================================
--- pkg/pomp/tests/dacca.R 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/dacca.R 2014-03-31 11:58:40 UTC (rev 914)
@@ -1,89 +1,85 @@
-if (Sys.getenv("POMP_FULL_TESTS")=="yes") {
+library(pomp)
- library(pomp)
+set.seed(1420306530L)
- set.seed(1420306530L)
+pompExample(dacca)
- pompExample(dacca)
+x <- as.data.frame(dacca)
+x <- simulate(dacca,nsim=3,as.data.frame=TRUE)
- x <- as.data.frame(dacca)
- x <- simulate(dacca,nsim=3,as.data.frame=TRUE)
+pf <- pfilter(dacca,Np=1000,seed=5886855L)
+pf1 <- pfilter(simulate(dacca),Np=1000,seed=5886855L)
- pf <- pfilter(dacca,Np=1000,seed=5886855L)
- pf1 <- pfilter(simulate(dacca),Np=1000,seed=5886855L)
+## to investigate the rogue crash:
- ## to investigate the rogue crash:
+dacca.pars <- c("gamma","eps","deltaI","beta.trend",
+ "log.beta1","log.beta2","log.beta3",
+ "log.beta4","log.beta5","log.beta6",
+ "log.omega1","log.omega2","log.omega3",
+ "log.omega4","log.omega5","log.omega6",
+ "sd.beta","tau")
+dacca.ivps <- c("S.0","I.0","R1.0","R2.0","R3.0")
+dacca.rw.sd <- c(
+ rep(0.1,length(dacca.pars)),
+ rep(0.2,length(dacca.ivps))
+ )
+names(dacca.rw.sd) <- c(dacca.pars,dacca.ivps)
- dacca.pars <- c("gamma","eps","deltaI","beta.trend",
- "log.beta1","log.beta2","log.beta3",
- "log.beta4","log.beta5","log.beta6",
- "log.omega1","log.omega2","log.omega3",
- "log.omega4","log.omega5","log.omega6",
- "sd.beta","tau")
- dacca.ivps <- c("S.0","I.0","R1.0","R2.0","R3.0")
- dacca.rw.sd <- c(
- rep(0.1,length(dacca.pars)),
- rep(0.2,length(dacca.ivps))
- )
- names(dacca.rw.sd) <- c(dacca.pars,dacca.ivps)
-
- param.tab <- read.csv2(text='
+param.tab <- read.csv2(text='
"";"gamma";"eps";"rho";"delta";"deltaI";"clin";"alpha";"beta.trend";"log.beta1";"log.beta2";"log.beta3";"log.beta4";"log.beta5";"log.beta6";"log.omega1";"log.omega2";"log.omega3";"log.omega4";"log.omega5";"log.omega6";"sd.beta";"tau";"S.0";"I.0";"Rs.0";"R1.0";"R2.0";"R3.0";"nbasis";"nrstage"
"mle1";20,8;19,1;0;0,02;0,06;1;1;-0,00498;0,747;6,38;-3,44;4,23;3,33;4,55;-1,6928195214;-2,5433835795;-2,8404393891;-4,6918179927;-8,4779724783;-4,3900588064;3,13;0,23;0,621;0,378;0;0,000843;0,000972;1,16e-07;6;3
"box_min";10;0,2;0;0,02;0,03;1;1;-0,01;-4;0;-4;0;0;0;-10;-10;-10;-10;-10;-10;1;0,1;0;0;0;0;0;0;6;3
"box_max";40;30;0;0,02;0,6;1;1;0;4;8;4;8;8;8;0;0;0;0;0;0;5;0,5;1;1;0;1;1;1;6;3
',
- row.names=1
- )
+ row.names=1
+ )
- dacca.hyperparams <- list(
- min=unlist(param.tab["box_min",]),
- max=unlist(param.tab["box_max",])
- )
+dacca.hyperparams <- list(
+ min=unlist(param.tab["box_min",]),
+ max=unlist(param.tab["box_max",])
+ )
- dacca.rprior <- function (hyperparams, ...) {
- r <- runif(length(hyperparams$min),min=hyperparams$min,max=hyperparams$max)
- names(r) <- names(hyperparams$min)
- r
- }
+dacca.rprior <- function (hyperparams, ...) {
+ r <- runif(length(hyperparams$min),min=hyperparams$min,max=hyperparams$max)
+ names(r) <- names(hyperparams$min)
+ r
+}
- op <- options(warn=-1)
-
- set.seed(7777+7)
- params.tricky <- dacca.rprior(dacca.hyperparams)
- m7 <- mif(
- dacca,
- Nmif=2,
- start=params.tricky,
- pars=dacca.pars,
- ivps=dacca.ivps,
- Np=100,
- method="mif2",
- rw.sd=dacca.rw.sd,
- cooling.type="geometric",
- cooling.fraction=sqrt(0.1),
- var.factor=2,
- transform=TRUE
- )
- m7 <- continue(m7)
+op <- options(warn=-1)
- set.seed(12350)
- th.draw <- dacca.rprior(dacca.hyperparams)
- m1 <- mif(
- dacca,
- Nmif=10,
- Np=100,
- start=th.draw,
- pars=dacca.pars,
- ivps=dacca.ivps,
- method="mif2",
- rw.sd=dacca.rw.sd,
- cooling.type="geometric",
- cooling.fraction=sqrt(0.1),
- var.factor=2,
- transform=TRUE
- )
+set.seed(7777+7)
+params.tricky <- dacca.rprior(dacca.hyperparams)
+m7 <- mif(
+ dacca,
+ Nmif=2,
+ start=params.tricky,
+ pars=dacca.pars,
+ ivps=dacca.ivps,
+ Np=100,
+ method="mif2",
+ rw.sd=dacca.rw.sd,
+ cooling.type="geometric",
+ cooling.fraction=sqrt(0.1),
+ var.factor=2,
+ transform=TRUE
+ )
+m7 <- continue(m7)
- options(op)
+set.seed(12350)
+th.draw <- dacca.rprior(dacca.hyperparams)
+m1 <- mif(
+ dacca,
+ Nmif=10,
+ Np=100,
+ start=th.draw,
+ pars=dacca.pars,
+ ivps=dacca.ivps,
+ method="mif2",
+ rw.sd=dacca.rw.sd,
+ cooling.type="geometric",
+ cooling.fraction=sqrt(0.1),
+ var.factor=2,
+ transform=TRUE
+ )
-}
+options(op)
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/dacca.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -15,102 +15,98 @@
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
-> if (Sys.getenv("POMP_FULL_TESTS")=="yes") {
-+
-+ library(pomp)
-+
-+ set.seed(1420306530L)
-+
-+ pompExample(dacca)
-+
-+ x <- as.data.frame(dacca)
-+ x <- simulate(dacca,nsim=3,as.data.frame=TRUE)
-+
-+ pf <- pfilter(dacca,Np=1000,seed=5886855L)
-+ pf1 <- pfilter(simulate(dacca),Np=1000,seed=5886855L)
-+
-+ ## to investigate the rogue crash:
-+
-+ dacca.pars <- c("gamma","eps","deltaI","beta.trend",
-+ "log.beta1","log.beta2","log.beta3",
-+ "log.beta4","log.beta5","log.beta6",
-+ "log.omega1","log.omega2","log.omega3",
-+ "log.omega4","log.omega5","log.omega6",
-+ "sd.beta","tau")
-+ dacca.ivps <- c("S.0","I.0","R1.0","R2.0","R3.0")
-+ dacca.rw.sd <- c(
-+ rep(0.1,length(dacca.pars)),
-+ rep(0.2,length(dacca.ivps))
-+ )
-+ names(dacca.rw.sd) <- c(dacca.pars,dacca.ivps)
-+
-+ param.tab <- read.csv2(text='
-+ "";"gamma";"eps";"rho";"delta";"deltaI";"clin";"alpha";"beta.trend";"log.beta1";"log.beta2";"log.beta3";"log.beta4";"log.beta5";"log.beta6";"log.omega1";"log.omega2";"log.omega3";"log.omega4";"log.omega5";"log.omega6";"sd.beta";"tau";"S.0";"I.0";"Rs.0";"R1.0";"R2.0";"R3.0";"nbasis";"nrstage"
-+ "mle1";20,8;19,1;0;0,02;0,06;1;1;-0,00498;0,747;6,38;-3,44;4,23;3,33;4,55;-1,6928195214;-2,5433835795;-2,8404393891;-4,6918179927;-8,4779724783;-4,3900588064;3,13;0,23;0,621;0,378;0;0,000843;0,000972;1,16e-07;6;3
-+ "box_min";10;0,2;0;0,02;0,03;1;1;-0,01;-4;0;-4;0;0;0;-10;-10;-10;-10;-10;-10;1;0,1;0;0;0;0;0;0;6;3
-+ "box_max";40;30;0;0,02;0,6;1;1;0;4;8;4;8;8;8;0;0;0;0;0;0;5;0,5;1;1;0;1;1;1;6;3
-+ ',
-+ row.names=1
-+ )
-+
-+ dacca.hyperparams <- list(
-+ min=unlist(param.tab["box_min",]),
-+ max=unlist(param.tab["box_max",])
-+ )
-+
-+ dacca.rprior <- function (hyperparams, ...) {
-+ r <- runif(length(hyperparams$min),min=hyperparams$min,max=hyperparams$max)
-+ names(r) <- names(hyperparams$min)
-+ r
-+ }
-+
-+ op <- options(warn=-1)
-+
-+ set.seed(7777+7)
-+ params.tricky <- dacca.rprior(dacca.hyperparams)
-+ m7 <- mif(
-+ dacca,
-+ Nmif=2,
-+ start=params.tricky,
-+ pars=dacca.pars,
-+ ivps=dacca.ivps,
-+ Np=100,
-+ method="mif2",
-+ rw.sd=dacca.rw.sd,
-+ cooling.type="geometric",
-+ cooling.fraction=sqrt(0.1),
-+ var.factor=2,
-+ transform=TRUE
-+ )
-+ m7 <- continue(m7)
-+
-+ set.seed(12350)
-+ th.draw <- dacca.rprior(dacca.hyperparams)
-+ m1 <- mif(
-+ dacca,
-+ Nmif=10,
-+ Np=100,
-+ start=th.draw,
-+ pars=dacca.pars,
-+ ivps=dacca.ivps,
-+ method="mif2",
-+ rw.sd=dacca.rw.sd,
-+ cooling.type="geometric",
-+ cooling.fraction=sqrt(0.1),
-+ var.factor=2,
-+ transform=TRUE
-+ )
-+
-+ options(op)
-+
-+ }
+> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+>
+> set.seed(1420306530L)
+>
+> pompExample(dacca)
newly created pomp object(s):
dacca
>
+> x <- as.data.frame(dacca)
+> x <- simulate(dacca,nsim=3,as.data.frame=TRUE)
+>
+> pf <- pfilter(dacca,Np=1000,seed=5886855L)
+> pf1 <- pfilter(simulate(dacca),Np=1000,seed=5886855L)
+>
+> ## to investigate the rogue crash:
+>
+> dacca.pars <- c("gamma","eps","deltaI","beta.trend",
++ "log.beta1","log.beta2","log.beta3",
++ "log.beta4","log.beta5","log.beta6",
++ "log.omega1","log.omega2","log.omega3",
++ "log.omega4","log.omega5","log.omega6",
++ "sd.beta","tau")
+> dacca.ivps <- c("S.0","I.0","R1.0","R2.0","R3.0")
+> dacca.rw.sd <- c(
++ rep(0.1,length(dacca.pars)),
++ rep(0.2,length(dacca.ivps))
++ )
+> names(dacca.rw.sd) <- c(dacca.pars,dacca.ivps)
+>
+> param.tab <- read.csv2(text='
++ "";"gamma";"eps";"rho";"delta";"deltaI";"clin";"alpha";"beta.trend";"log.beta1";"log.beta2";"log.beta3";"log.beta4";"log.beta5";"log.beta6";"log.omega1";"log.omega2";"log.omega3";"log.omega4";"log.omega5";"log.omega6";"sd.beta";"tau";"S.0";"I.0";"Rs.0";"R1.0";"R2.0";"R3.0";"nbasis";"nrstage"
++ "mle1";20,8;19,1;0;0,02;0,06;1;1;-0,00498;0,747;6,38;-3,44;4,23;3,33;4,55;-1,6928195214;-2,5433835795;-2,8404393891;-4,6918179927;-8,4779724783;-4,3900588064;3,13;0,23;0,621;0,378;0;0,000843;0,000972;1,16e-07;6;3
++ "box_min";10;0,2;0;0,02;0,03;1;1;-0,01;-4;0;-4;0;0;0;-10;-10;-10;-10;-10;-10;1;0,1;0;0;0;0;0;0;6;3
++ "box_max";40;30;0;0,02;0,6;1;1;0;4;8;4;8;8;8;0;0;0;0;0;0;5;0,5;1;1;0;1;1;1;6;3
++ ',
++ row.names=1
++ )
+>
+> dacca.hyperparams <- list(
++ min=unlist(param.tab["box_min",]),
++ max=unlist(param.tab["box_max",])
++ )
+>
+> dacca.rprior <- function (hyperparams, ...) {
++ r <- runif(length(hyperparams$min),min=hyperparams$min,max=hyperparams$max)
++ names(r) <- names(hyperparams$min)
++ r
++ }
+>
+> op <- options(warn=-1)
+>
+> set.seed(7777+7)
+> params.tricky <- dacca.rprior(dacca.hyperparams)
+> m7 <- mif(
++ dacca,
++ Nmif=2,
++ start=params.tricky,
++ pars=dacca.pars,
++ ivps=dacca.ivps,
++ Np=100,
++ method="mif2",
++ rw.sd=dacca.rw.sd,
++ cooling.type="geometric",
++ cooling.fraction=sqrt(0.1),
++ var.factor=2,
++ transform=TRUE
++ )
+> m7 <- continue(m7)
+>
+> set.seed(12350)
+> th.draw <- dacca.rprior(dacca.hyperparams)
+> m1 <- mif(
++ dacca,
++ Nmif=10,
++ Np=100,
++ start=th.draw,
++ pars=dacca.pars,
++ ivps=dacca.ivps,
++ method="mif2",
++ rw.sd=dacca.rw.sd,
++ cooling.type="geometric",
++ cooling.fraction=sqrt(0.1),
++ var.factor=2,
++ transform=TRUE
++ )
+>
+> options(op)
+>
> proc.time()
user system elapsed
- 11.068 0.104 11.227
+ 11.056 0.036 11.143
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/dimchecks.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> set.seed(1420306530L)
@@ -163,4 +164,4 @@
>
> proc.time()
user system elapsed
- 0.520 0.036 0.574
+ 0.504 0.064 0.591
Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/fhn.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> pdf.options(useDingbats=FALSE)
@@ -92,4 +93,4 @@
>
> proc.time()
user system elapsed
- 1.028 0.052 1.292
+ 1.024 0.064 1.220
Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/filtfail.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> set.seed(834454394L)
@@ -117,4 +118,4 @@
>
> proc.time()
user system elapsed
- 0.520 0.052 0.582
+ 0.552 0.036 0.605
Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/gillespie.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> params <- c(
@@ -132,4 +133,4 @@
>
> proc.time()
user system elapsed
- 2.436 0.048 2.503
+ 2.664 0.068 2.758
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/gompertz.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
> options(digits=4)
>
@@ -134,4 +135,4 @@
>
> proc.time()
user system elapsed
- 1.504 0.068 1.585
+ 1.552 0.048 1.622
Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/logistic.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> po <- pomp(
@@ -123,4 +124,4 @@
>
> proc.time()
user system elapsed
- 0.896 0.048 1.087
+ 0.916 0.044 1.078
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> set.seed(398585L)
@@ -63,7 +64,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 2.921494 secs
+Time difference of 2.999716 secs
>
> print(
+ cbind(
@@ -105,4 +106,4 @@
>
> proc.time()
user system elapsed
- 4.788 0.072 4.889
+ 4.896 0.068 4.995
Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/ou2-forecast.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> set.seed(921625222L)
@@ -62,4 +63,4 @@
>
> proc.time()
user system elapsed
- 1.576 0.060 1.751
+ 1.580 0.068 1.753
Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/ou2-kalman.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -18,6 +18,7 @@
> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
>
> set.seed(577639485L)
@@ -165,7 +166,7 @@
117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 3.442711 secs
+Time difference of 3.437749 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
@@ -189,4 +190,4 @@
>
> proc.time()
user system elapsed
- 3.960 0.056 4.038
+ 4.004 0.056 4.089
Modified: pkg/pomp/tests/ou2-mif-fp.R
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.R 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/ou2-mif-fp.R 2014-03-31 11:58:40 UTC (rev 914)
@@ -1,50 +1,46 @@
-if (Sys.getenv("POMP_FULL_TESTS")=="yes") {
+library(pomp)
- library(pomp)
+pompExample(ou2)
- pompExample(ou2)
+set.seed(64857673L)
- set.seed(64857673L)
+pdf(file="ou2-mif-fp.pdf")
- pdf(file="ou2-mif-fp.pdf")
+p.truth <- coef(ou2)
+guess2 <- guess1 <- p.truth
+guess1[c('x1.0','x2.0','alpha.2','alpha.3')] <- 0.25*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
+guess2[c('x1.0','x2.0','alpha.2','alpha.3')] <- 4*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
- p.truth <- coef(ou2)
- guess2 <- guess1 <- p.truth
- guess1[c('x1.0','x2.0','alpha.2','alpha.3')] <- 0.25*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
- guess2[c('x1.0','x2.0','alpha.2','alpha.3')] <- 4*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
+mif1 <- mif(ou2,Nmif=100,start=guess1,
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=5,x2.0=5,
+ alpha.2=0.1,alpha.3=0.1
+ ),
+ Np=1000,
+ var.factor=1,
+ ic.lag=10,
+ cooling.type="geometric",
+ cooling.fraction=0.95^50,
+ max.fail=100,
+ method="fp"
+ )
- mif1 <- mif(ou2,Nmif=100,start=guess1,
- pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
- rw.sd=c(
- x1.0=5,x2.0=5,
- alpha.2=0.1,alpha.3=0.1
- ),
- Np=1000,
- var.factor=1,
- ic.lag=10,
- cooling.type="geometric",
- cooling.fraction=0.95^50,
- max.fail=100,
- method="fp"
- )
-
- mif2 <- mif(ou2,Nmif=100,start=guess2,
- pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
- rw.sd=c(
- x1.0=5,x2.0=5,
- alpha.2=0.1,alpha.3=0.1
- ),
- Np=1000,
- var.factor=1,
- ic.lag=10,
- cooling.type="geometric",
- cooling.fraction=0.95^50,
- max.fail=100,
- method="fp"
- )
-
- compare.mif(list(mif1,mif2))
+mif2 <- mif(ou2,Nmif=100,start=guess2,
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=5,x2.0=5,
+ alpha.2=0.1,alpha.3=0.1
+ ),
+ Np=1000,
+ var.factor=1,
+ ic.lag=10,
+ cooling.type="geometric",
+ cooling.fraction=0.95^50,
+ max.fail=100,
+ method="fp"
+ )
- dev.off()
+compare.mif(list(mif1,mif2))
-}
+dev.off()
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2014-03-31 11:58:40 UTC (rev 914)
@@ -15,64 +15,61 @@
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
-> if (Sys.getenv("POMP_FULL_TESTS")=="yes") {
-+
-+ library(pomp)
-+
-+ pompExample(ou2)
-+
-+ set.seed(64857673L)
-+
-+ pdf(file="ou2-mif-fp.pdf")
-+
-+ p.truth <- coef(ou2)
-+ guess2 <- guess1 <- p.truth
-+ guess1[c('x1.0','x2.0','alpha.2','alpha.3')] <- 0.25*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
-+ guess2[c('x1.0','x2.0','alpha.2','alpha.3')] <- 4*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
-+
-+ mif1 <- mif(ou2,Nmif=100,start=guess1,
-+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
-+ rw.sd=c(
-+ x1.0=5,x2.0=5,
-+ alpha.2=0.1,alpha.3=0.1
-+ ),
-+ Np=1000,
-+ var.factor=1,
-+ ic.lag=10,
-+ cooling.type="geometric",
-+ cooling.fraction=0.95^50,
-+ max.fail=100,
-+ method="fp"
-+ )
-+
-+ mif2 <- mif(ou2,Nmif=100,start=guess2,
-+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
-+ rw.sd=c(
-+ x1.0=5,x2.0=5,
-+ alpha.2=0.1,alpha.3=0.1
-+ ),
-+ Np=1000,
-+ var.factor=1,
-+ ic.lag=10,
-+ cooling.type="geometric",
-+ cooling.fraction=0.95^50,
-+ max.fail=100,
-+ method="fp"
-+ )
-+
-+ compare.mif(list(mif1,mif2))
-+
-+ dev.off()
-+
-+ }
+> library(pomp)
Loading required package: mvtnorm
Loading required package: subplex
+Loading required package: nloptr
Loading required package: deSolve
+>
+> pompExample(ou2)
newly created pomp object(s):
ou2
+>
+> set.seed(64857673L)
+>
+> pdf(file="ou2-mif-fp.pdf")
+>
+> p.truth <- coef(ou2)
+> guess2 <- guess1 <- p.truth
+> guess1[c('x1.0','x2.0','alpha.2','alpha.3')] <- 0.25*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
+> guess2[c('x1.0','x2.0','alpha.2','alpha.3')] <- 4*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
+>
+> mif1 <- mif(ou2,Nmif=100,start=guess1,
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
++ rw.sd=c(
++ x1.0=5,x2.0=5,
++ alpha.2=0.1,alpha.3=0.1
++ ),
++ Np=1000,
++ var.factor=1,
++ ic.lag=10,
++ cooling.type="geometric",
++ cooling.fraction=0.95^50,
++ max.fail=100,
++ method="fp"
++ )
+>
+> mif2 <- mif(ou2,Nmif=100,start=guess2,
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
++ rw.sd=c(
++ x1.0=5,x2.0=5,
++ alpha.2=0.1,alpha.3=0.1
++ ),
++ Np=1000,
++ var.factor=1,
++ ic.lag=10,
++ cooling.type="geometric",
++ cooling.fraction=0.95^50,
++ max.fail=100,
++ method="fp"
++ )
+>
+> compare.mif(list(mif1,mif2))
+>
+> dev.off()
null device
1
>
> proc.time()
user system elapsed
- 19.229 0.092 19.539
+ 19.269 0.064 19.562
Modified: pkg/pomp/tests/ou2-mif.R
===================================================================
--- pkg/pomp/tests/ou2-mif.R 2014-03-27 12:31:51 UTC (rev 913)
+++ pkg/pomp/tests/ou2-mif.R 2014-03-31 11:58:40 UTC (rev 914)
@@ -1,212 +1,209 @@
-if (Sys.getenv("POMP_FULL_TESTS")=="yes") {
+library(pomp)
- library(pomp)
+pompExample(ou2)
- pompExample(ou2)
+set.seed(64857673L)
- set.seed(64857673L)
+obs(window(ou2,end=20,start=15))
+obs(window(ou2,end=5),"y1")
- obs(window(ou2,end=20,start=15))
- obs(window(ou2,end=5),"y1")
+fit1.pfilter <- pfilter(ou2,Np=1000)
+cat("coefficients at `truth'\n")
+print(coef(ou2,c('x1.0','x2.0','alpha.2','alpha.3')),digits=4)
+cat("particle filter log likelihood at truth\n")
+print(fit1.pfilter$loglik,digits=4)
- fit1.pfilter <- pfilter(ou2,Np=1000)
- cat("coefficients at `truth'\n")
- print(coef(ou2,c('x1.0','x2.0','alpha.2','alpha.3')),digits=4)
- cat("particle filter log likelihood at truth\n")
- print(fit1.pfilter$loglik,digits=4)
+p.truth <- coef(ou2)
+guess2 <- guess1 <- p.truth
+guess1[c('x1.0','x2.0','alpha.2','alpha.3')] <- 0.5*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
+guess2[c('x1.0','x2.0','alpha.2','alpha.3')] <- 1.5*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
- p.truth <- coef(ou2)
- guess2 <- guess1 <- p.truth
- guess1[c('x1.0','x2.0','alpha.2','alpha.3')] <- 0.5*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
- guess2[c('x1.0','x2.0','alpha.2','alpha.3')] <- 1.5*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
+mif1 <- mif(ou2,Nmif=30,start=guess1,
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=5,x2.0=5,
+ alpha.2=0.1,alpha.3=0.1
+ ),
+ Np=1000,
+ var.factor=1,
+ ic.lag=10,
+ cooling.type="geometric",
+ cooling.factor=0.95,
+ max.fail=100
+ )
- mif1 <- mif(ou2,Nmif=30,start=guess1,
- pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
- rw.sd=c(
- x1.0=5,x2.0=5,
- alpha.2=0.1,alpha.3=0.1
- ),
- Np=1000,
- var.factor=1,
- ic.lag=10,
- cooling.type="geometric",
- cooling.factor=0.95,
- max.fail=100
- )
+mif2 <- mif(ou2,Nmif=30,start=guess2,
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ transform=TRUE,
+ rw.sd=c(
+ x1.0=5,x2.0=5,
+ alpha.2=0.1,alpha.3=0.1
+ ),
+ Np=1000,
+ var.factor=1,
+ ic.lag=10,
+ cooling.type="geometric",
+ cooling.fraction=0.95^50,
+ max.fail=100
+ )
- mif2 <- mif(ou2,Nmif=30,start=guess2,
- pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
- transform=TRUE,
- rw.sd=c(
- x1.0=5,x2.0=5,
- alpha.2=0.1,alpha.3=0.1
- ),
- Np=1000,
- var.factor=1,
- ic.lag=10,
- cooling.type="geometric",
- cooling.fraction=0.95^50,
- max.fail=100
- )
+pdf(file="ou2-mif.pdf")
+plot(mif1)
+compare.mif(mif2)
+try(compare.mif(mif1,mif2))
+compare.mif(list(mif1,mif2))
+dev.off()
- pdf(file="ou2-mif.pdf")
- plot(mif1)
- compare.mif(mif2)
- try(compare.mif(mif1,mif2))
- compare.mif(list(mif1,mif2))
- dev.off()
+set.seed(33848585L)
- set.seed(33848585L)
+try(
+ mif(
+ ou2,
+ Nmif=1,
+ pars=c("alpha.1","alpha.4","x1.0"),
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
+ Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+ )
- try(
- mif(
- ou2,
- Nmif=1,
- pars=c("alpha.1","alpha.4","x1.0"),
- ivps=c("x1.0","x2.0"),
- rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
- Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
- ic.lag=10,var.factor=1
- )
- )
+try(
+ mif(
+ ou2,
+ Nmif=1,
+ pars=c("alpha.1","alpha.4"),
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
+ Np=100,
+ cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+ )
- try(
- mif(
- ou2,
- Nmif=1,
- pars=c("alpha.1","alpha.4"),
- ivps=c("x1.0","x2.0"),
- rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
- Np=100,
- cooling.type="geometric",cooling.fraction=0.95^50,
- ic.lag=10,var.factor=1
- )
- )
+try(
+ mif(
+ ou2,
+ Nmif=1,
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(alpha.1=0.1,alpha.4=0.2,alpha.3=0),
+ Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
+ cooling.factor=0.95,ic.lag=10,var.factor=1
+ )
+ )
- try(
- mif(
- ou2,
- Nmif=1,
- ivps=c("x1.0","x2.0"),
- rw.sd=c(alpha.1=0.1,alpha.4=0.2,alpha.3=0),
- Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
- cooling.factor=0.95,ic.lag=10,var.factor=1
- )
- )
+try(
+ mif(
+ ou2,
+ Nmif=1,
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
+ Np=100,ic.lag=10,var.factor=1
+ )
+ )
- try(
- mif(
- ou2,
- Nmif=1,
- ivps=c("x1.0","x2.0"),
- rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
- Np=100,ic.lag=10,var.factor=1
- )
- )
+try(
+ mif(
+ ou2,
+ Nmif=1,
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
+ Np=-10,cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+ )
- try(
- mif(
- ou2,
- Nmif=1,
- ivps=c("x1.0","x2.0"),
- rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
- Np=-10,cooling.type="geometric",cooling.fraction=0.95^50,
- ic.lag=10,var.factor=1
- )
- )
+try(
+ mif(
+ ou2,
+ Nmif=-3,
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
+ Np=11.6,cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+ )
- try(
- mif(
- ou2,
- Nmif=-3,
- ivps=c("x1.0","x2.0"),
- rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
- Np=11.6,cooling.type="geometric",cooling.fraction=0.95^50,
- ic.lag=10,var.factor=1
- )
- )
+try(
+ mif(
+ ou2,
+ Nmif=2,
+ start=c(alpha.1=0.9,alpha.2=0,alpha.3=0,alpha.4=-Inf,sigma.1=1,sigma.2=0,sigma.3=2,tau=1,x1.0=50,x2.0=-50),
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 914
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