[Pomp-commits] r961 - in pkg/pomp: . R man src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri May 23 18:23:09 CEST 2014
Author: kingaa
Date: 2014-05-23 18:23:09 +0200 (Fri, 23 May 2014)
New Revision: 961
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/NAMESPACE
pkg/pomp/R/abc-methods.R
pkg/pomp/R/pmcmc-methods.R
pkg/pomp/R/pomp-methods.R
pkg/pomp/man/pmcmc-methods.Rd
pkg/pomp/src/Makevars
pkg/pomp/tests/ou2-pmcmc.R
pkg/pomp/tests/ou2-pmcmc.Rout.save
pkg/pomp/tests/rw2.Rout.save
pkg/pomp/tests/sir.Rout.save
Log:
- change 'show' method for 'pomp' objects to be somewhat less verbose
- add 'pmcmcList' class and associated methods to facilitate multiple-chain algorithms
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/DESCRIPTION 2014-05-23 16:23:09 UTC (rev 961)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.50-9
-Date: 2014-05-18
+Version: 0.51-1
+Date: 2014-05-21
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")),
@@ -18,7 +18,7 @@
)
URL: http://pomp.r-forge.r-project.org
Description: Inference methods for partially-observed Markov processes
-Depends: R(>= 3.0.0), stats, graphics, methods, mvtnorm, subplex, nloptr, deSolve
+Depends: R(>= 3.0.0), stats, graphics, methods, mvtnorm, subplex, nloptr, deSolve, coda
Suggests: knitr
License: GPL(>= 2)
LazyData: true
Modified: pkg/pomp/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/NAMESPACE 2014-05-23 16:23:09 UTC (rev 961)
@@ -38,12 +38,13 @@
importFrom(subplex,subplex)
importFrom(deSolve,ode)
importFrom(nloptr,nloptr)
+importFrom(coda,mcmc,mcmc.list)
exportClasses(
pomp,
pfilterd.pomp,
mif,
- pmcmc,
+ pmcmc,pmcmcList,
traj.matched.pomp,
probed.pomp,probe.matched.pomp,
spect.pomp,spect.matched.pomp,
@@ -87,7 +88,7 @@
profileDesign,
bspline.basis,
periodic.bspline.basis,
- compare.mif,compare.pmcmc,compare.abc,
+ compare.mif,
nlf,
parmat,
logmeanexp,
Modified: pkg/pomp/R/abc-methods.R
===================================================================
--- pkg/pomp/R/abc-methods.R 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/R/abc-methods.R 2014-05-23 16:23:09 UTC (rev 961)
@@ -6,18 +6,18 @@
'abc',
function (object, pars, ...) {
if (missing(pars)) pars <- colnames(object at conv.rec)
- object at conv.rec[,pars]
+ coda::mcmc(object at conv.rec[,pars])
}
)
-## plot pmcmc object
+## plot abc object
setMethod(
"plot",
"abc",
function (x, y, pars, scatter = FALSE, ...) {
if (missing(pars)) pars <- x at pars
if (scatter) {
- pairs(conv.rec(x, pars))
+ pairs(as.matrix(conv.rec(x, pars)))
} else {
plot.ts(conv.rec(x,pars),xlab="iteration",...)
}
Modified: pkg/pomp/R/pmcmc-methods.R
===================================================================
--- pkg/pomp/R/pmcmc-methods.R 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/R/pmcmc-methods.R 2014-05-23 16:23:09 UTC (rev 961)
@@ -3,41 +3,133 @@
## extract the estimated log likelihood
setMethod('logLik','pmcmc',function(object,...)object at loglik)
-## extract the filtering means
-setMethod(
- 'filter.mean',
- 'pmcmc',
- function (object, pars, ...) {
- if (missing(pars)) pars <- rownames(object at filter.mean)
- object at filter.mean[pars,]
- }
- )
-
## extract the convergence record
setMethod(
'conv.rec',
- 'pmcmc',
+ signature=signature(object='pmcmc'),
function (object, pars, ...) {
if (missing(pars)) pars <- colnames(object at conv.rec)
- object at conv.rec[,pars]
+ coda::mcmc(object at conv.rec[,pars])
}
)
## plot pmcmc object
setMethod(
"plot",
- "pmcmc",
+ signature=signature(x='pmcmc'),
function (x, y = NULL, ...) {
- compare.pmcmc(x)
+ pmcmc.diagnostics(list(x))
}
)
-compare.pmcmc <- function (z) {
+
+## pmcmcList class
+setClass(
+ 'pmcmcList',
+ slots=c(
+ list = 'list'
+ ),
+ prototype=prototype(
+ list = list()
+ ),
+ validity=function (object) {
+ if (!all(sapply(object at list,is,'pmcmc'))) {
+ retval <- paste0(
+ "error in ",sQuote("c"),
+ ": dissimilar objects cannot be combined"
+ )
+ return(retval)
+ }
+ d <- sapply(object at list,function(x)dim(x at conv.rec))
+ if (!all(apply(d,1,diff)==0)) {
+ retval <- paste0(
+ "error in ",sQuote("c"),
+ ": to be combined, ",sQuote("pmcmc"),
+ " objects must have chains of equal length"
+ )
+ return(retval)
+ }
+ TRUE
+ }
+ )
+
+setMethod(
+ 'c',
+ signature=signature(x='pmcmc'),
+ definition=function (x, ...) {
+ y <- list(...)
+ if (length(y)==0) {
+ new("pmcmcList",list=list(x))
+ } else {
+ p <- sapply(y,is,'pmcmc')
+ q <- sapply(y,is,'pmcmcList')
+ if (any(!(p||q)))
+ stop("cannot mix ",sQuote("pmcmc"),
+ " and non-",sQuote("pmcmc")," objects")
+ y[p] <- lapply(y[p],list)
+ y[q] <- lapply(y[q],slot,"list")
+ new("pmcmcList",list=c(list(x),y,recursive=TRUE))
+ }
+ }
+ )
+
+setMethod(
+ 'c',
+ signature=signature(x='pmcmcList'),
+ definition=function (x, ...) {
+ y <- list(...)
+ if (length(y)==0) {
+ x
+ } else {
+ x <- x at list
+ p <- sapply(y,is,'pmcmc')
+ pl <- sapply(y,is,'pmcmcList')
+ if (any(!(p||pl)))
+ stop("cannot mix ",sQuote("pmcmc"),
+ " and non-",sQuote("pmcmc")," objects")
+ y[p] <- lapply(y[p],list)
+ y[pl] <- lapply(y[pl],slot,"list")
+ new("pmcmcList",list=c(x,y,recursive=TRUE))
+ }
+ }
+ )
+
+setMethod(
+ "[",
+ signature=signature(x="pmcmcList"),
+ definition=function(x, i, ...) {
+ y <- x
+ y at list <- x at list[i]
+ y
+ }
+ )
+
+setMethod(
+ "[[",
+ signature=signature(x="pmcmcList"),
+ definition=function(x, i, ...) {
+ x at list[[i]]
+ }
+ )
+
+setMethod(
+ 'conv.rec',
+ signature=signature(object='pmcmcList'),
+ definition=function (object, ...) {
+ coda::mcmc.list(lapply(object at list,conv.rec,...))
+ }
+ )
+
+setMethod(
+ "plot",
+ signature=signature(x='pmcmcList'),
+ definition=function (x, y = NULL, ...) {
+ pmcmc.diagnostics(x at list)
+ }
+ )
+
+pmcmc.diagnostics <- function (z) {
## assumes that x is a list of pmcmcs with identical structure
- if (!is.list(z)) z <- list(z)
- if (!all(sapply(z,function(x)is(x,'pmcmc'))))
- stop("compare.pmcmc error: ",sQuote("z"),
- " must be a pmcmc object or a list of pmcmc objects",call.=FALSE)
mar.multi <- c(0,5.1,0,2.1)
oma.multi <- c(6,0,5,0)
xx <- z[[1]]
@@ -81,3 +173,13 @@
}
invisible(NULL)
}
+
+compare.pmcmc <- function (z) {
+ if (!is.list(z)) z <- list(z)
+ if (!all(sapply(z,function(x)is(x,'pmcmc'))))
+ stop("compare.pmcmc error: ",sQuote("z"),
+ " must be a pmcmc object or a list of pmcmc objects",call.=FALSE)
+ warning(sQuote("compare.pmcmc")," is deprecated.\n",
+ "Use ",sQuote("diagnostics")," instead.",call.=FALSE)
+ pmcmc.diagnostics(z)
+}
Modified: pkg/pomp/R/pomp-methods.R
===================================================================
--- pkg/pomp/R/pomp-methods.R 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/R/pomp-methods.R 2014-05-23 16:23:09 UTC (rev 961)
@@ -243,7 +243,7 @@
"print",
"pomp",
function (x, ...) {
- cat("data and states:\n")
+ cat("data, states, and covariates:\n")
print(as(x,"data.frame"))
invisible(x)
}
@@ -253,13 +253,20 @@
"show",
"pomp",
function (object) {
- print(object)
+ cat(length(object at times),"records of",
+ nrow(obs(object)),"observables,",
+ "recorded from t =",
+ min(object at times),"to",max(object at times),"\n")
+ cat("summary of data:\n")
+ print(summary(as.data.frame(t(obs(object)))))
cat("zero time, t0 = ",object at t0,"\n",sep="")
- if (length(coef(object))>0) {
- cat("parameter(s):\n")
- print(coef(object))
- } else {
- cat ("parameter(s) unspecified\n");
+ if (length(object at tcovar)>0) {
+ cat(nrow(object at covar),"records of",
+ ncol(object at covar),"covariates,",
+ "recorded from t =",min(object at tcovar),
+ "to",max(object at tcovar),"\n")
+ cat("summary of covariates:\n")
+ print(summary(as.data.frame(object at covar)))
}
cat("process model simulator, rprocess = \n")
show(object at rprocess)
@@ -283,6 +290,12 @@
show(object at par.trans)
cat("parameter inverse transform function = \n")
show(object at par.untrans)
+ if (length(coef(object))>0) {
+ cat("parameter(s):\n")
+ print(coef(object))
+ } else {
+ cat ("parameter(s) unspecified\n");
+ }
if (length(object at userdata)>0) {
cat("userdata = \n")
show(object at userdata)
Modified: pkg/pomp/man/pmcmc-methods.Rd
===================================================================
--- pkg/pomp/man/pmcmc-methods.Rd 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/man/pmcmc-methods.Rd 2014-05-23 16:23:09 UTC (rev 961)
@@ -5,25 +5,35 @@
\alias{logLik-pmcmc}
\alias{conv.rec,pmcmc-method}
\alias{conv.rec-pmcmc}
-\alias{filter.mean,pmcmc-method}
-\alias{filter.mean-pmcmc}
+\alias{conv.rec,pmcmcList-method}
+\alias{conv.rec-pmcmcList}
\alias{plot-pmcmc}
\alias{plot,pmcmc-method}
-\alias{compare.pmcmc}
+\alias{plot-pmcmcList}
+\alias{plot,pmcmcList-method}
+\alias{pmcmcList-class}
+\alias{c-pmcmc}
+\alias{c,pmcmc-method}
+\alias{c-pmcmcList}
+\alias{c,pmcmcList-method}
+\alias{[-pmcmcList}
+\alias{[,pmcmcList-method}
+\alias{[[-pmcmcList}
+\alias{[[,pmcmcList-method}
\title{Methods of the "pmcmc" class}
\description{Methods of the "pmcmc" class.}
\usage{
\S4method{logLik}{pmcmc}(object, \dots)
\S4method{conv.rec}{pmcmc}(object, pars, \dots)
-\S4method{filter.mean}{pmcmc}(object, pars, \dots)
+\S4method{conv.rec}{pmcmcList}(object, \dots)
\S4method{plot}{pmcmc}(x, y = NULL, \dots)
-compare.pmcmc(z)
+\S4method{c}{pmcmc}(x, \dots, recursive = FALSE)
+\S4method{c}{pmcmcList}(x, \dots, recursive = FALSE)
}
\arguments{
- \item{object, x}{The \code{pmcmc} object.}
+ \item{object, x}{The \code{pmcmc} or \code{pmcmcList} object.}
\item{pars}{Names of parameters.}
- \item{y}{Ignored.}
- \item{z}{A \code{pmcmc} object or list of \code{pmcmc} objects.}
+ \item{y, recursive}{Ignored.}
\item{\dots}{
Further arguments (either ignored or passed to underlying functions).
}
@@ -31,36 +41,18 @@
\section{Methods}{
\describe{
\item{conv.rec}{
- \code{conv.rec(object, pars)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars}.
- By default, all rows are returned.
+ \code{conv.rec(object, pars)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars} as an object of class \code{\link[coda]{mcmc}} or \code{\link[coda]{mcmc.list}}.
}
+ \item{plot}{
+ Plots density- and trace-plots.
+ This uses package \pkg{coda}'s default plots.
+ }
\item{logLik}{
Returns the value in the \code{loglik} slot.
}
- \item{pmcmc}{
- Re-runs the PMCMC iterations.
- See the documentation for \code{\link{pmcmc}}.
+ \item{c}{
+ Concatenates \code{pmcmc} objects into a \code{pmcmcList}.
}
- \item{compare.pmcmc}{
- Given a \code{pmcmc} object or a list of \code{pmcmc} objects, \code{compare.pmcmc} produces a set of diagnostic plots.
- }
- \item{plot}{
- Plots a series of diagnostic plots.
- When \code{x} is a \code{pmcmc} object, \code{plot(x)} is equivalent to \code{compare.pmcmc(list(x))}.
- }
- \item{filter.mean}{
- \code{filter.mean(object, pars = NULL)} returns the rows of the filtering-mean matrix corresponding to the names in \code{pars}.
- By default, all rows are returned.
- }
- \item{print}{
- Prints a summary of the \code{pmcmc} object.
- }
- \item{show}{
- Displays the \code{pmcmc} object.
- }
- \item{pfilter}{
- See \code{\link{pfilter}}.
- }
}
}
\references{
Property changes on: pkg/pomp/src/Makevars
___________________________________________________________________
Deleted: svn:executable
- *
Modified: pkg/pomp/tests/ou2-pmcmc.R
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.R 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/tests/ou2-pmcmc.R 2014-05-23 16:23:09 UTC (rev 961)
@@ -17,7 +17,7 @@
max.fail=100,
verbose=FALSE
)
-f1 <- continue(f1,Nmcmc=200,max.fail=100)
+f1 <- continue(f1,Nmcmc=20,max.fail=100)
plot(f1)
ff <- pfilter(f1)
@@ -29,44 +29,55 @@
verbose=FALSE
)
-f3 <- pmcmc(
- ff,
- Nmcmc=20,
- transform=TRUE,
- rw.sd=c(alpha.2=0.01,alpha.3=0.01),
- max.fail=100,
- verbose=FALSE
- )
-f4 <- pmcmc(f3)
-f4 <- continue(f4,Nmcmc=100)
+f3 <- pmcmc(f2)
+f4 <- continue(f3,Nmcmc=20)
-if (FALSE) {
- f2 <- pmcmc(
- f1,Nmcmc=1000,Np=500,max.fail=100,
- verbose=FALSE
- )
- plot(f2)
- runs <- rle(conv.rec(f2)[,'loglik'])$lengths
- plot(runs)
- acf(conv.rec(f2)[,c("alpha.2","alpha.3")])
-}
+plot(c(f2,f3))
-dprior.ou2 <- function (params, log, ...) {
- f <- sum(dnorm(params,mean=coef(ou2),sd=1,log=TRUE))
- if (log) f else exp(f)
+try(ff <- c(f3,f4))
+
+if (Sys.getenv("POMP_FULL_TESTS")=="yes") {
+ f2a <- pmcmc(
+ f1,Nmcmc=1000,Np=100,max.fail=100,
+ verbose=FALSE
+ )
+ plot(f2a)
+ runs <- rle(as.numeric(conv.rec(f2a,'loglik')))$lengths
+ plot(sort(runs))
+ acf(conv.rec(f2a,c("alpha.2","alpha.3")))
}
f5 <- pmcmc(
- ou2,
- start=coef(ou2),
+ pomp(ou2,
+ dprior=function (params, log, ...) {
+ f <- sum(dnorm(params,mean=coef(ou2),sd=1,log=TRUE))
+ if (log) f else exp(f)
+ }
+ ),
Nmcmc=20,
rw.sd=c(alpha.2=0.001,alpha.3=0.001),
Np=100,
max.fail=100,
verbose=FALSE
)
-f5 <- continue(f5,Nmcmc=200,max.fail=100)
-plot(f5)
+f6 <- continue(f5,Nmcmc=20,max.fail=100)
+plot(f6)
+ff <- c(f4,f6)
+plot(ff)
+plot(conv.rec(ff,c("alpha.2","alpha.3","loglik")))
+
+ff <- c(f2,f3)
+
+try(ff <- c(ff,f4,f6))
+try(ff <- c(f4,ou2))
+try(ff <- c(ff,ou2))
+
+plot(ff <- c(ff,f5))
+plot(conv.rec(c(f2,ff),c("alpha.2","alpha.3")))
+plot(conv.rec(ff[2],c("alpha.2")))
+plot(conv.rec(ff[2:3],c("alpha.3")))
+plot(conv.rec(ff[[3]],c("alpha.3")))
+
dev.off()
Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save 2014-05-23 16:23:09 UTC (rev 961)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.0 (2014-04-10) -- "Spring Dance"
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):
@@ -40,7 +42,7 @@
+ max.fail=100,
+ verbose=FALSE
+ )
-> f1 <- continue(f1,Nmcmc=200,max.fail=100)
+> f1 <- continue(f1,Nmcmc=20,max.fail=100)
> plot(f1)
>
> ff <- pfilter(f1)
@@ -52,45 +54,62 @@
+ verbose=FALSE
+ )
>
-> f3 <- pmcmc(
-+ ff,
-+ Nmcmc=20,
-+ transform=TRUE,
-+ rw.sd=c(alpha.2=0.01,alpha.3=0.01),
-+ max.fail=100,
-+ verbose=FALSE
-+ )
-> f4 <- pmcmc(f3)
-> f4 <- continue(f4,Nmcmc=100)
+> f3 <- pmcmc(f2)
+> f4 <- continue(f3,Nmcmc=20)
>
-> if (FALSE) {
-+ f2 <- pmcmc(
-+ f1,Nmcmc=1000,Np=500,max.fail=100,
-+ verbose=FALSE
-+ )
-+ plot(f2)
-+ runs <- rle(conv.rec(f2)[,'loglik'])$lengths
-+ plot(runs)
-+ acf(conv.rec(f2)[,c("alpha.2","alpha.3")])
-+ }
+> plot(c(f2,f3))
>
-> dprior.ou2 <- function (params, log, ...) {
-+ f <- sum(dnorm(params,mean=coef(ou2),sd=1,log=TRUE))
-+ if (log) f else exp(f)
+> try(ff <- c(f3,f4))
+Error in validObject(.Object) :
+ invalid class "pmcmcList" object: error in 'c': to be combined, 'pmcmc' objects must have chains of equal length
+>
+> if (Sys.getenv("POMP_FULL_TESTS")=="yes") {
++ f2a <- pmcmc(
++ f1,Nmcmc=1000,Np=100,max.fail=100,
++ verbose=FALSE
++ )
++ plot(f2a)
++ runs <- rle(as.numeric(conv.rec(f2a,'loglik')))$lengths
++ plot(sort(runs))
++ acf(conv.rec(f2a,c("alpha.2","alpha.3")))
+ }
>
> f5 <- pmcmc(
-+ ou2,
-+ start=coef(ou2),
++ pomp(ou2,
++ dprior=function (params, log, ...) {
++ f <- sum(dnorm(params,mean=coef(ou2),sd=1,log=TRUE))
++ if (log) f else exp(f)
++ }
++ ),
+ Nmcmc=20,
+ rw.sd=c(alpha.2=0.001,alpha.3=0.001),
+ Np=100,
+ max.fail=100,
+ verbose=FALSE
+ )
-> f5 <- continue(f5,Nmcmc=200,max.fail=100)
-> plot(f5)
+> f6 <- continue(f5,Nmcmc=20,max.fail=100)
+> plot(f6)
>
+> ff <- c(f4,f6)
+> plot(ff)
+> plot(conv.rec(ff,c("alpha.2","alpha.3","loglik")))
+>
+> ff <- c(f2,f3)
+>
+> try(ff <- c(ff,f4,f6))
+Error in validObject(.Object) :
+ invalid class "pmcmcList" object: error in 'c': to be combined, 'pmcmc' objects must have chains of equal length
+> try(ff <- c(f4,ou2))
+Error in c(f4, ou2) : cannot mix 'pmcmc' and non-'pmcmc' objects
+> try(ff <- c(ff,ou2))
+Error in c(ff, ou2) : cannot mix 'pmcmc' and non-'pmcmc' objects
+>
+> plot(ff <- c(ff,f5))
+> plot(conv.rec(c(f2,ff),c("alpha.2","alpha.3")))
+> plot(conv.rec(ff[2],c("alpha.2")))
+> plot(conv.rec(ff[2:3],c("alpha.3")))
+> plot(conv.rec(ff[[3]],c("alpha.3")))
+>
> dev.off()
null device
1
@@ -98,4 +117,4 @@
>
> proc.time()
user system elapsed
- 13.904 0.052 14.145
+ 23.369 0.040 23.847
Modified: pkg/pomp/tests/rw2.Rout.save
===================================================================
--- pkg/pomp/tests/rw2.Rout.save 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/tests/rw2.Rout.save 2014-05-23 16:23:09 UTC (rev 961)
@@ -1,5 +1,5 @@
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+R version 3.1.0 (2014-04-10) -- "Spring Dance"
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(45768683)
>
@@ -113,110 +115,16 @@
+ )
>
> invisible(show(rw2))
-data and states:
- time y1 y2
-1 1 0 0
-2 2 0 0
-3 3 0 0
-4 4 0 0
-5 5 0 0
-6 6 0 0
-7 7 0 0
-8 8 0 0
-9 9 0 0
-10 10 0 0
-11 11 0 0
-12 12 0 0
-13 13 0 0
-14 14 0 0
-15 15 0 0
-16 16 0 0
-17 17 0 0
-18 18 0 0
-19 19 0 0
-20 20 0 0
-21 21 0 0
-22 22 0 0
-23 23 0 0
-24 24 0 0
-25 25 0 0
-26 26 0 0
-27 27 0 0
-28 28 0 0
-29 29 0 0
-30 30 0 0
-31 31 0 0
-32 32 0 0
-33 33 0 0
-34 34 0 0
-35 35 0 0
-36 36 0 0
-37 37 0 0
-38 38 0 0
-39 39 0 0
-40 40 0 0
-41 41 0 0
-42 42 0 0
-43 43 0 0
-44 44 0 0
-45 45 0 0
-46 46 0 0
-47 47 0 0
-48 48 0 0
-49 49 0 0
-50 50 0 0
-51 51 0 0
-52 52 0 0
-53 53 0 0
-54 54 0 0
-55 55 0 0
-56 56 0 0
-57 57 0 0
-58 58 0 0
-59 59 0 0
-60 60 0 0
-61 61 0 0
-62 62 0 0
-63 63 0 0
-64 64 0 0
-65 65 0 0
-66 66 0 0
-67 67 0 0
-68 68 0 0
-69 69 0 0
-70 70 0 0
-71 71 0 0
-72 72 0 0
-73 73 0 0
-74 74 0 0
-75 75 0 0
-76 76 0 0
-77 77 0 0
-78 78 0 0
-79 79 0 0
-80 80 0 0
-81 81 0 0
-82 82 0 0
-83 83 0 0
-84 84 0 0
-85 85 0 0
-86 86 0 0
-87 87 0 0
-88 88 0 0
-89 89 0 0
-90 90 0 0
-91 91 0 0
-92 92 0 0
-93 93 0 0
-94 94 0 0
-95 95 0 0
-96 96 0 0
-97 97 0 0
-98 98 0 0
-99 99 0 0
-100 100 0 0
+100 records of 2 observables, recorded from t = 1 to 100
+summary of data:
+ y1 y2
+ Min. :0 Min. :0
+ 1st Qu.:0 1st Qu.:0
+ Median :0 Median :0
+ Mean :0 Mean :0
+ 3rd Qu.:0 3rd Qu.:0
+ Max. :0 Max. :0
zero time, t0 = 0
-parameter(s) unspecified
process model simulator, rprocess =
function (params, xstart, times, ...)
{
@@ -260,7 +168,7 @@
}
y
}
-<environment: 0x25f5b00>
+<environment: 0x310abf8>
measurement model density, dmeasure =
function (y, x, t, params, log, covars, ...)
{
@@ -273,7 +181,7 @@
f
else exp(f)
}
-<environment: 0x25f5b00>
+<environment: 0x310abf8>
prior simulator, rprior =
function not specified
prior density, dprior =
@@ -291,6 +199,7 @@
function not specified
parameter inverse transform function =
function not specified
+parameter(s) unspecified
userdata =
$useless
[1] 23
@@ -401,7 +310,7 @@
> invisible(timezero(new))
> timezero(new) <- 19
> print(simulate(new))
-data and states:
+data, states, and covariates:
time y1 y2 x1 x2
1 20 0.2438664 3.1093573 0.5247663 5.0741536
2 21 -2.4324990 4.5669427 -2.2582676 4.2250510
@@ -437,4 +346,4 @@
>
> proc.time()
user system elapsed
- 0.944 0.076 1.040
+ 0.968 0.064 1.059
Modified: pkg/pomp/tests/sir.Rout.save
===================================================================
--- pkg/pomp/tests/sir.Rout.save 2014-05-19 20:45:32 UTC (rev 960)
+++ pkg/pomp/tests/sir.Rout.save 2014-05-23 16:23:09 UTC (rev 961)
@@ -20,6 +20,8 @@
Loading required package: subplex
Loading required package: nloptr
Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
>
> tbasis <- seq(0,25,by=1/52)
> basis <- periodic.bspline.basis(tbasis,nbasis=3,names="seas%d")
@@ -166,222 +168,25 @@
+ )
>
> show(po)
-data and states:
- time reports seas1 seas2 seas3
-1 0.01923077 0 0.66343428 0.19708101 0.13948471
-2 0.03846154 0 0.65412115 0.23024769 0.11563116
-3 0.05769231 0 0.63930336 0.26559063 0.09510602
-4 0.07692308 0 0.61955697 0.30253376 0.07790927
-5 0.09615385 0 0.59545806 0.34050101 0.06404093
-6 0.11538462 0 0.56758269 0.37891633 0.05350099
-7 0.13461538 0 0.53650693 0.41720362 0.04628945
-8 0.15384615 0 0.50280686 0.45478683 0.04240631
-9 0.17307692 0 0.46705854 0.49108989 0.04185158
-10 0.19230769 0 0.42983804 0.52553672 0.04462525
-11 0.21153846 0 0.39172143 0.55755125 0.05072732
-12 0.23076923 0 0.35328478 0.58655743 0.06015779
-13 0.25000000 0 0.31510417 0.61197917 0.07291667
-14 0.26923077 0 0.27775565 0.63324040 0.08900394
-15 0.28846154 0 0.24181531 0.64976507 0.10841963
-16 0.30769231 0 0.20785920 0.66097709 0.13116371
-17 0.32692308 0 0.17646341 0.66630040 0.15723619
-18 0.34615385 0 0.14817554 0.66521582 0.18660863
-19 0.36538462 0 0.12321252 0.65786560 0.21892187
-20 0.38461538 0 0.10157791 0.64481869 0.25360340
-21 0.40384615 0 0.08327170 0.62665116 0.29007714
-22 0.42307692 0 0.06829389 0.60393908 0.32776703
-23 0.44230769 0 0.05664448 0.57725852 0.36609700
-24 0.46153846 0 0.04832347 0.54718556 0.40449097
-25 0.48076923 0 0.04333087 0.51429625 0.44237289
-26 0.50000000 0 0.04166667 0.47916667 0.47916667
-27 0.51923077 0 0.04333087 0.44237289 0.51429625
-28 0.53846154 0 0.04832347 0.40449097 0.54718556
-29 0.55769231 0 0.05664448 0.36609700 0.57725852
-30 0.57692308 0 0.06829389 0.32776703 0.60393908
-31 0.59615385 0 0.08327170 0.29007714 0.62665116
-32 0.61538462 0 0.10157791 0.25360340 0.64481869
-33 0.63461538 0 0.12321252 0.21892187 0.65786560
-34 0.65384615 0 0.14817554 0.18660863 0.66521582
-35 0.67307692 0 0.17646341 0.15723619 0.66630040
-36 0.69230769 0 0.20785920 0.13116371 0.66097709
-37 0.71153846 0 0.24181531 0.10841963 0.64976507
-38 0.73076923 0 0.27775565 0.08900394 0.63324040
-39 0.75000000 0 0.31510417 0.07291667 0.61197917
-40 0.76923077 0 0.35328478 0.06015779 0.58655743
-41 0.78846154 0 0.39172143 0.05072732 0.55755125
-42 0.80769231 0 0.42983804 0.04462525 0.52553672
-43 0.82692308 0 0.46705854 0.04185158 0.49108989
-44 0.84615385 0 0.50280686 0.04240631 0.45478683
-45 0.86538462 0 0.53650693 0.04628945 0.41720362
-46 0.88461538 0 0.56758269 0.05350099 0.37891633
-47 0.90384615 0 0.59545806 0.06404093 0.34050101
-48 0.92307692 0 0.61955697 0.07790927 0.30253376
-49 0.94230769 0 0.63930336 0.09510602 0.26559063
-50 0.96153846 0 0.65412115 0.11563116 0.23024769
-51 0.98076923 0 0.66343428 0.13948471 0.19708101
-52 1.00000000 0 0.66666667 0.16666667 0.16666667
-53 1.01923077 0 0.66343428 0.19708101 0.13948471
-54 1.03846154 0 0.65412115 0.23024769 0.11563116
-55 1.05769231 0 0.63930336 0.26559063 0.09510602
-56 1.07692308 0 0.61955697 0.30253376 0.07790927
-57 1.09615385 0 0.59545806 0.34050101 0.06404093
-58 1.11538462 0 0.56758269 0.37891633 0.05350099
-59 1.13461538 0 0.53650693 0.41720362 0.04628945
-60 1.15384615 0 0.50280686 0.45478683 0.04240631
-61 1.17307692 0 0.46705854 0.49108989 0.04185158
-62 1.19230769 0 0.42983804 0.52553672 0.04462525
-63 1.21153846 0 0.39172143 0.55755125 0.05072732
-64 1.23076923 0 0.35328478 0.58655743 0.06015779
-65 1.25000000 0 0.31510417 0.61197917 0.07291667
-66 1.26923077 0 0.27775565 0.63324040 0.08900394
-67 1.28846154 0 0.24181531 0.64976507 0.10841963
-68 1.30769231 0 0.20785920 0.66097709 0.13116371
-69 1.32692308 0 0.17646341 0.66630040 0.15723619
-70 1.34615385 0 0.14817554 0.66521582 0.18660863
-71 1.36538462 0 0.12321252 0.65786560 0.21892187
-72 1.38461538 0 0.10157791 0.64481869 0.25360340
-73 1.40384615 0 0.08327170 0.62665116 0.29007714
-74 1.42307692 0 0.06829389 0.60393908 0.32776703
-75 1.44230769 0 0.05664448 0.57725852 0.36609700
-76 1.46153846 0 0.04832347 0.54718556 0.40449097
-77 1.48076923 0 0.04333087 0.51429625 0.44237289
-78 1.50000000 0 0.04166667 0.47916667 0.47916667
-79 1.51923077 0 0.04333087 0.44237289 0.51429625
-80 1.53846154 0 0.04832347 0.40449097 0.54718556
-81 1.55769231 0 0.05664448 0.36609700 0.57725852
-82 1.57692308 0 0.06829389 0.32776703 0.60393908
-83 1.59615385 0 0.08327170 0.29007714 0.62665116
-84 1.61538462 0 0.10157791 0.25360340 0.64481869
-85 1.63461538 0 0.12321252 0.21892187 0.65786560
-86 1.65384615 0 0.14817554 0.18660863 0.66521582
-87 1.67307692 0 0.17646341 0.15723619 0.66630040
-88 1.69230769 0 0.20785920 0.13116371 0.66097709
-89 1.71153846 0 0.24181531 0.10841963 0.64976507
-90 1.73076923 0 0.27775565 0.08900394 0.63324040
-91 1.75000000 0 0.31510417 0.07291667 0.61197917
-92 1.76923077 0 0.35328478 0.06015779 0.58655743
-93 1.78846154 0 0.39172143 0.05072732 0.55755125
-94 1.80769231 0 0.42983804 0.04462525 0.52553672
-95 1.82692308 0 0.46705854 0.04185158 0.49108989
-96 1.84615385 0 0.50280686 0.04240631 0.45478683
-97 1.86538462 0 0.53650693 0.04628945 0.41720362
-98 1.88461538 0 0.56758269 0.05350099 0.37891633
-99 1.90384615 0 0.59545806 0.06404093 0.34050101
-100 1.92307692 0 0.61955697 0.07790927 0.30253376
-101 1.94230769 0 0.63930336 0.09510602 0.26559063
-102 1.96153846 0 0.65412115 0.11563116 0.23024769
-103 1.98076923 0 0.66343428 0.13948471 0.19708101
-104 2.00000000 0 0.66666667 0.16666667 0.16666667
-105 2.01923077 0 0.66343428 0.19708101 0.13948471
-106 2.03846154 0 0.65412115 0.23024769 0.11563116
-107 2.05769231 0 0.63930336 0.26559063 0.09510602
-108 2.07692308 0 0.61955697 0.30253376 0.07790927
-109 2.09615385 0 0.59545806 0.34050101 0.06404093
-110 2.11538462 0 0.56758269 0.37891633 0.05350099
-111 2.13461538 0 0.53650693 0.41720362 0.04628945
-112 2.15384615 0 0.50280686 0.45478683 0.04240631
-113 2.17307692 0 0.46705854 0.49108989 0.04185158
-114 2.19230769 0 0.42983804 0.52553672 0.04462525
-115 2.21153846 0 0.39172143 0.55755125 0.05072732
-116 2.23076923 0 0.35328478 0.58655743 0.06015779
-117 2.25000000 0 0.31510417 0.61197917 0.07291667
-118 2.26923077 0 0.27775565 0.63324040 0.08900394
-119 2.28846154 0 0.24181531 0.64976507 0.10841963
-120 2.30769231 0 0.20785920 0.66097709 0.13116371
-121 2.32692308 0 0.17646341 0.66630040 0.15723619
-122 2.34615385 0 0.14817554 0.66521582 0.18660863
-123 2.36538462 0 0.12321252 0.65786560 0.21892187
-124 2.38461538 0 0.10157791 0.64481869 0.25360340
-125 2.40384615 0 0.08327170 0.62665116 0.29007714
-126 2.42307692 0 0.06829389 0.60393908 0.32776703
-127 2.44230769 0 0.05664448 0.57725852 0.36609700
-128 2.46153846 0 0.04832347 0.54718556 0.40449097
-129 2.48076923 0 0.04333087 0.51429625 0.44237289
-130 2.50000000 0 0.04166667 0.47916667 0.47916667
-131 2.51923077 0 0.04333087 0.44237289 0.51429625
-132 2.53846154 0 0.04832347 0.40449097 0.54718556
-133 2.55769231 0 0.05664448 0.36609700 0.57725852
-134 2.57692308 0 0.06829389 0.32776703 0.60393908
-135 2.59615385 0 0.08327170 0.29007714 0.62665116
-136 2.61538462 0 0.10157791 0.25360340 0.64481869
-137 2.63461538 0 0.12321252 0.21892187 0.65786560
-138 2.65384615 0 0.14817554 0.18660863 0.66521582
-139 2.67307692 0 0.17646341 0.15723619 0.66630040
-140 2.69230769 0 0.20785920 0.13116371 0.66097709
-141 2.71153846 0 0.24181531 0.10841963 0.64976507
-142 2.73076923 0 0.27775565 0.08900394 0.63324040
-143 2.75000000 0 0.31510417 0.07291667 0.61197917
-144 2.76923077 0 0.35328478 0.06015779 0.58655743
-145 2.78846154 0 0.39172143 0.05072732 0.55755125
-146 2.80769231 0 0.42983804 0.04462525 0.52553672
-147 2.82692308 0 0.46705854 0.04185158 0.49108989
-148 2.84615385 0 0.50280686 0.04240631 0.45478683
-149 2.86538462 0 0.53650693 0.04628945 0.41720362
-150 2.88461538 0 0.56758269 0.05350099 0.37891633
-151 2.90384615 0 0.59545806 0.06404093 0.34050101
-152 2.92307692 0 0.61955697 0.07790927 0.30253376
-153 2.94230769 0 0.63930336 0.09510602 0.26559063
-154 2.96153846 0 0.65412115 0.11563116 0.23024769
-155 2.98076923 0 0.66343428 0.13948471 0.19708101
-156 3.00000000 0 0.66666667 0.16666667 0.16666667
-157 3.01923077 0 0.66343428 0.19708101 0.13948471
-158 3.03846154 0 0.65412115 0.23024769 0.11563116
-159 3.05769231 0 0.63930336 0.26559063 0.09510602
-160 3.07692308 0 0.61955697 0.30253376 0.07790927
-161 3.09615385 0 0.59545806 0.34050101 0.06404093
-162 3.11538462 0 0.56758269 0.37891633 0.05350099
-163 3.13461538 0 0.53650693 0.41720362 0.04628945
-164 3.15384615 0 0.50280686 0.45478683 0.04240631
-165 3.17307692 0 0.46705854 0.49108989 0.04185158
-166 3.19230769 0 0.42983804 0.52553672 0.04462525
-167 3.21153846 0 0.39172143 0.55755125 0.05072732
-168 3.23076923 0 0.35328478 0.58655743 0.06015779
-169 3.25000000 0 0.31510417 0.61197917 0.07291667
-170 3.26923077 0 0.27775565 0.63324040 0.08900394
-171 3.28846154 0 0.24181531 0.64976507 0.10841963
-172 3.30769231 0 0.20785920 0.66097709 0.13116371
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 961
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