[Pomp-commits] r981 - in pkg/pomp: . R inst man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 25 19:38:58 CEST 2014
Author: kingaa
Date: 2014-06-25 19:38:58 +0200 (Wed, 25 Jun 2014)
New Revision: 981
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/NAMESPACE
pkg/pomp/R/abc-methods.R
pkg/pomp/R/bsmc.R
pkg/pomp/R/generics.R
pkg/pomp/R/mif-methods.R
pkg/pomp/R/pmcmc-methods.R
pkg/pomp/R/probe.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/man/abc-methods.Rd
pkg/pomp/man/mif-methods.Rd
pkg/pomp/man/pmcmc-methods.Rd
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
Log:
- new 'mifList' class
- define plot methods for 'mifList'
- warn on ignored 'y' in 'plot(x,y)'
- deprecate 'compare.mif'
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/DESCRIPTION 2014-06-25 17:38:58 UTC (rev 981)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.51-4
-Date: 2014-06-23
+Version: 0.52-1
+Date: 2014-06-26
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/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/NAMESPACE 2014-06-25 17:38:58 UTC (rev 981)
@@ -43,7 +43,7 @@
exportClasses(
pomp,
pfilterd.pomp,
- mif,
+ mif,mifList,
pmcmc,pmcmcList,
traj.matched.pomp,
probed.pomp,probe.matched.pomp,
Modified: pkg/pomp/R/abc-methods.R
===================================================================
--- pkg/pomp/R/abc-methods.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/R/abc-methods.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -1,12 +1,12 @@
## this file contains short definitions of methods for the 'abc' class
-## extract the convergence record
+## extract the convergence record as an 'mcmc' object
setMethod(
'conv.rec',
'abc',
function (object, pars, ...) {
if (missing(pars)) pars <- colnames(object at conv.rec)
- coda::mcmc(object at conv.rec[,pars,drop=FALSE])
+ coda::mcmc(object at conv.rec[,pars,drop=FALSE],...)
}
)
@@ -21,6 +21,8 @@
## } else {
## plot.ts(conv.rec(x,pars),xlab="iteration",...)
## }
+ if (!missing(y))
+ warning(sQuote("y")," is ignored")
abc.diagnostics(c(x),pars=pars,scatter=scatter,...)
}
)
@@ -98,6 +100,7 @@
}
)
+## extract the convergence record as an 'mcmc.list' object
setMethod(
'conv.rec',
signature=signature(object='abcList'),
@@ -109,7 +112,9 @@
setMethod(
"plot",
signature=signature(x='abcList'),
- definition=function (x, y = NULL, ...) {
+ definition=function (x, y, ...) {
+ if (!missing(y))
+ warning(sQuote("y")," is ignored")
abc.diagnostics(x,...)
}
)
Modified: pkg/pomp/R/bsmc.R
===================================================================
--- pkg/pomp/R/bsmc.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/R/bsmc.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -367,17 +367,17 @@
setMethod(
"bsmc",
- "pomp",
- function (object, params, Np, est,
- smooth = 0.1,
- ntries = 1,
- tol = 1e-17,
- lower = -Inf, upper = Inf,
- seed = NULL,
- verbose = getOption("verbose"),
- max.fail = 0,
- transform = FALSE,
- ...) {
+ signature=signature(object="pomp"),
+ definition = function (object, params, Np, est,
+ smooth = 0.1,
+ ntries = 1,
+ tol = 1e-17,
+ lower = -Inf, upper = Inf,
+ seed = NULL,
+ verbose = getOption("verbose"),
+ max.fail = 0,
+ transform = FALSE,
+ ...) {
bsmc.internal(
object=object,
params=params,
@@ -397,7 +397,10 @@
}
)
-setMethod("$",signature(x="bsmcd.pomp"),function (x,name) slot(x,name))
+setMethod("$",
+ signature(x="bsmcd.pomp"),
+ definition = function (x, name) slot(x,name)
+ )
bsmc.plot <- function (prior, post, pars, thin, ...) {
p1 <- sample.int(n=ncol(prior),size=min(thin,ncol(prior)))
@@ -437,7 +440,9 @@
setMethod(
"plot",
signature(x="bsmcd.pomp"),
- function (x, ..., pars, thin) {
+ function (x, y, ..., pars, thin) {
+ if (!missing(y))
+ warning(sQuote("y")," is ignored")
if (missing(pars)) pars <- names(coef(x,transform=!x at transform))
if (missing(thin)) thin <- Inf
bsmc.plot(
Modified: pkg/pomp/R/generics.R
===================================================================
--- pkg/pomp/R/generics.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/R/generics.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -45,7 +45,6 @@
setGeneric("eff.sample.size",function(object,...)standardGeneric("eff.sample.size"))
## convergence record
setGeneric("conv.rec",function(object,...)standardGeneric("conv.rec"))
-
## stochastic simulation
setGeneric("simulate",function(object,nsim=1,seed=NULL,...)standardGeneric("simulate"))
Modified: pkg/pomp/R/mif-methods.R
===================================================================
--- pkg/pomp/R/mif-methods.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/R/mif-methods.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -89,11 +89,108 @@
setMethod(
"plot",
"mif",
- function (x, y = NULL, ...) {
- compare.mif(x)
+ function (x, y, ...) {
+ if (!missing(y)) {
+ y <- substitute(y)
+ warning(sQuote(y)," is ignored")
+ }
+ mif.diagnostics(list(x))
}
)
+## mifList class
+setClass(
+ 'mifList',
+ contains='list',
+ validity=function (object) {
+ if (!all(sapply(object,is,'mif'))) {
+ retval <- paste0(
+ "error in ",sQuote("c"),
+ ": dissimilar objects cannot be combined"
+ )
+ return(retval)
+ }
+ d <- sapply(object,function(x)dim(x at conv.rec))
+ if (!all(apply(d,1,diff)==0)) {
+ retval <- paste0(
+ "error in ",sQuote("c"),
+ ": to be combined, ",sQuote("mif"),
+ " objects must equal numbers of iterations"
+ )
+ return(retval)
+ }
+ TRUE
+ }
+ )
+
+setMethod(
+ 'c',
+ signature=signature(x='mif'),
+ definition=function (x, ...) {
+ y <- list(...)
+ if (length(y)==0) {
+ new("mifList",list(x))
+ } else {
+ p <- sapply(y,is,'mif')
+ pl <- sapply(y,is,'mifList')
+ if (any(!(p||pl)))
+ stop("cannot mix ",sQuote("mif"),
+ " and non-",sQuote("mif")," objects")
+ y[p] <- lapply(y[p],list)
+ y[pl] <- lapply(y[pl],as,"list")
+ new("mifList",c(list(x),y,recursive=TRUE))
+ }
+ }
+ )
+
+setMethod(
+ 'c',
+ signature=signature(x='mifList'),
+ definition=function (x, ...) {
+ y <- list(...)
+ if (length(y)==0) {
+ x
+ } else {
+ p <- sapply(y,is,'mif')
+ pl <- sapply(y,is,'mifList')
+ if (any(!(p||pl)))
+ stop("cannot mix ",sQuote("mif"),
+ " and non-",sQuote("mif")," objects")
+ y[p] <- lapply(y[p],list)
+ y[pl] <- lapply(y[pl],as,"list")
+ new("mifList",c(as(x,"list"),y,recursive=TRUE))
+ }
+ }
+ )
+
+setMethod(
+ "[",
+ signature=signature(x="mifList"),
+ definition=function(x, i, ...) {
+ new('mifList',as(x,"list")[i])
+ }
+ )
+
+setMethod(
+ 'conv.rec',
+ signature=signature(object='mifList'),
+ definition=function (object, ...) {
+ lapply(object,conv.rec,...)
+ }
+ )
+
+setMethod(
+ "plot",
+ signature=signature(x='mifList'),
+ definition=function (x, y, ...) {
+ if (!missing(y)) {
+ y <- substitute(y)
+ warning(sQuote(y)," is ignored")
+ }
+ mif.diagnostics(x)
+ }
+ )
+
predvarplot.mif <- function (object, pars, type = 'l', mean = FALSE, ...) {
if (!is(object,'mif'))
stop("predvarplot error: ",sQuote("object")," must be of class ",sQuote("mif"),call.=FALSE)
@@ -112,10 +209,12 @@
}
compare.mif <- function (z) {
- ## assumes that x is a list of mifs with identical structure
- if (!is.list(z)) z <- list(z)
- if (!all(sapply(z,function(x)is(x,'mif'))))
- stop("compare.mif error: ",sQuote("z")," must be a mif object or a list of mif objects",call.=FALSE)
+ stop(sQuote("compare.mif")," has been deprecated in favor of ",
+ sQuote("plot"))
+}
+
+mif.diagnostics <- function (z) {
+ ## assumes that z is a list of mifs with identical structure
mar.multi <- c(0,5.1,0,2.1)
oma.multi <- c(6,0,5,0)
xx <- z[[1]]
Modified: pkg/pomp/R/pmcmc-methods.R
===================================================================
--- pkg/pomp/R/pmcmc-methods.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/R/pmcmc-methods.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -9,7 +9,7 @@
signature=signature(object='pmcmc'),
function (object, pars, ...) {
if (missing(pars)) pars <- colnames(object at conv.rec)
- coda::mcmc(object at conv.rec[,pars,drop=FALSE])
+ coda::mcmc(object at conv.rec[,pars,drop=FALSE],...)
}
)
@@ -17,7 +17,9 @@
setMethod(
"plot",
signature=signature(x='pmcmc'),
- function (x, y = NULL, ...) {
+ function (x, y, ...) {
+ if (!missing(y))
+ warning(sQuote("y")," is ignored")
pmcmc.diagnostics(list(x))
}
)
@@ -96,6 +98,7 @@
}
)
+## extract the convergence records as a coda::mcmc.list object
setMethod(
'conv.rec',
signature=signature(object='pmcmcList'),
@@ -107,7 +110,9 @@
setMethod(
"plot",
signature=signature(x='pmcmcList'),
- definition=function (x, y = NULL, ...) {
+ definition=function (x, y, ...) {
+ if (!missing(y))
+ warning(sQuote("y")," is ignored")
pmcmc.diagnostics(x)
}
)
Modified: pkg/pomp/R/probe.R
===================================================================
--- pkg/pomp/R/probe.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/R/probe.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -104,7 +104,7 @@
}
)
-probeplot.internal <- function (x, y, ...) {
+probeplot.internal <- function (x, ...) {
##function for plotting diagonal panels
diag.panel.hist <- function(x, ...) {
##plot a histogram for the simulations
@@ -170,9 +170,12 @@
}
}
-setMethod("plot","probed.pomp",
- function (x, y, ...) {
- probeplot.internal(x=x,y=y,...)
+setMethod("plot",
+ signature=signature(x="probed.pomp"),
+ definition=function (x, y, ...) {
+ if (!missing(y))
+ warning(sQuote("y")," is ignored")
+ probeplot.internal(x=x,...)
}
)
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/inst/NEWS 2014-06-25 17:38:58 UTC (rev 981)
@@ -1,5 +1,14 @@
_N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_2-_1:
+
+ • The new ‘mifList’ class facilitates approaches based on
+ multiple ‘mif’ runs. The ‘c’ method constructs ‘mifList’s
+ from ‘mif’s. The ‘plot’ method produces diagnostic plots.
+
+ • ‘compare.mif’ is now deprecated in favor of ‘plot’ applied to
+ a ‘mif’ or ‘mifList’.
+
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_1-_3:
• ‘transform’ argument for ‘pmcmc’ and ‘abc’ has been removed.
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/inst/NEWS.Rd 2014-06-25 17:38:58 UTC (rev 981)
@@ -1,5 +1,13 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.52-1}{
+ \itemize{
+ \item The new \code{mifList} class facilitates approaches based on multiple \code{mif} runs.
+ The \code{c} method constructs \code{mifList}s from \code{mif}s.
+ The \code{plot} method produces diagnostic plots.
+ \item \code{compare.mif} is now deprecated in favor of \code{plot} applied to a \code{mif} or \code{mifList}.
+ }
+}
\section{Changes in \pkg{pomp} version 0.51-3}{
\itemize{
\item \code{transform} argument for \code{pmcmc} and \code{abc} has been removed.
Modified: pkg/pomp/man/abc-methods.Rd
===================================================================
--- pkg/pomp/man/abc-methods.Rd 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/man/abc-methods.Rd 2014-06-25 17:38:58 UTC (rev 981)
@@ -45,6 +45,9 @@
\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.
}
+ \item{c}{
+ Concatenates \code{abc} objects into an \code{abcList}.
+ }
\item{plot}{
Diagnostic plots.
}
Modified: pkg/pomp/man/mif-methods.Rd
===================================================================
--- pkg/pomp/man/mif-methods.Rd 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/man/mif-methods.Rd 2014-06-25 17:38:58 UTC (rev 981)
@@ -6,22 +6,37 @@
\alias{conv.rec}
\alias{conv.rec,mif-method}
\alias{conv.rec-mif}
+\alias{conv.rec,mifList-method}
+\alias{conv.rec-mifList}
\alias{plot-mif}
\alias{plot,mif-method}
+\alias{plot-mifList}
+\alias{plot,mifList-method}
+\alias{mifList-class}
+\alias{c-mif}
+\alias{c,mif-method}
+\alias{c-mifList}
+\alias{c,mifList-method}
+\alias{[-mifList}
+\alias{[,mifList-method}
\alias{compare.mif}
\title{Methods of the "mif" class}
\description{Methods of the \code{mif} class.}
\usage{
\S4method{logLik}{mif}(object, \dots)
\S4method{conv.rec}{mif}(object, pars, transform = FALSE, \dots)
-\S4method{plot}{mif}(x, y = NULL, \dots)
+\S4method{conv.rec}{mifList}(object, \dots)
+\S4method{plot}{mif}(x, y, \dots)
+\S4method{plot}{mifList}(x, y, \dots)
+\S4method{c}{mif}(x, \dots, recursive = FALSE)
+\S4method{c}{mifList}(x, \dots, recursive = FALSE)
compare.mif(z)
}
\arguments{
\item{object}{The \code{mif} object.}
\item{pars}{Names of parameters.}
\item{x}{The \code{mif} object.}
- \item{y}{Ignored.}
+ \item{y, recursive}{Ignored.}
\item{z}{A \code{mif} object or list of \code{mif} objects.}
\item{transform}{
optional logical;
@@ -41,13 +56,15 @@
\item{logLik}{
Returns the value in the \code{loglik} slot.
}
- \item{compare.mif}{
- Given a \code{mif} object or a list of \code{mif} objects, \code{compare.mif} produces a set of diagnostic plots.
+ \item{c}{
+ Concatenates \code{mif} objects into an \code{mifList}.
}
\item{plot}{
Plots a series of diagnostic plots.
- When \code{x} is a \code{mif} object, \code{plot(x)} is equivalent to \code{compare.mif(list(x))}.
}
+ \item{compare.mif}{
+ Deprecated: use \code{plot} instead.
+ }
}
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
Modified: pkg/pomp/man/pmcmc-methods.Rd
===================================================================
--- pkg/pomp/man/pmcmc-methods.Rd 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/man/pmcmc-methods.Rd 2014-06-25 17:38:58 UTC (rev 981)
@@ -24,7 +24,7 @@
\S4method{logLik}{pmcmc}(object, \dots)
\S4method{conv.rec}{pmcmc}(object, pars, \dots)
\S4method{conv.rec}{pmcmcList}(object, \dots)
-\S4method{plot}{pmcmc}(x, y = NULL, \dots)
+\S4method{plot}{pmcmc}(x, y, \dots)
\S4method{plot}{pmcmcList}(x, y, \dots)
\S4method{c}{pmcmc}(x, \dots, recursive = FALSE)
\S4method{c}{pmcmcList}(x, \dots, recursive = FALSE)
Modified: pkg/pomp/tests/ou2-mif-fp.R
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/tests/ou2-mif-fp.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -41,6 +41,6 @@
method="fp"
)
-compare.mif(list(mif1,mif2))
+plot(c(mif1,mif2))
dev.off()
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2014-06-25 17:38:58 UTC (rev 981)
@@ -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):
@@ -64,7 +66,7 @@
+ method="fp"
+ )
>
-> compare.mif(list(mif1,mif2))
+> plot(c(mif1,mif2))
>
> dev.off()
null device
@@ -72,4 +74,4 @@
>
> proc.time()
user system elapsed
- 19.269 0.064 19.562
+ 22.609 0.039 22.668
Modified: pkg/pomp/tests/ou2-mif.R
===================================================================
--- pkg/pomp/tests/ou2-mif.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/tests/ou2-mif.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -49,9 +49,9 @@
pdf(file="ou2-mif.pdf")
plot(mif1)
-compare.mif(mif2)
-try(compare.mif(mif1,mif2))
-compare.mif(list(mif1,mif2))
+plot(mif2)
+try(plot(mif1,mif2))
+plot(c(mif1,mif2))
dev.off()
set.seed(33848585L)
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2014-06-25 17:38:58 UTC (rev 981)
@@ -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):
@@ -85,10 +87,11 @@
>
> pdf(file="ou2-mif.pdf")
> plot(mif1)
-> compare.mif(mif2)
-> try(compare.mif(mif1,mif2))
-Error in compare.mif(mif1, mif2) : unused argument (mif2)
-> compare.mif(list(mif1,mif2))
+> plot(mif2)
+> try(plot(mif1,mif2))
+Warning message:
+In plot(mif1, mif2) : 'mif2' is ignored
+> plot(c(mif1,mif2))
> dev.off()
null device
1
@@ -282,4 +285,4 @@
>
> proc.time()
user system elapsed
- 11.828 0.036 12.014
+ 14.306 0.041 14.344
Modified: pkg/pomp/tests/ou2-mif2.R
===================================================================
--- pkg/pomp/tests/ou2-mif2.R 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/tests/ou2-mif2.R 2014-06-25 17:38:58 UTC (rev 981)
@@ -41,7 +41,7 @@
tol=1e-8
)
-compare.mif(list(mif1a,mif2a))
+plot(c(mif1a,mif2a))
set.seed(64857673L)
mif1b <- mif(ou2,Nmif=50,start=guess1,
@@ -91,11 +91,16 @@
)
mif2c <- continue(mif2c,Nmif=50)
-compare.mif(list(mif1b,mif2b))
+plot(c(mif1b,mif2b))
-compare.mif(list(mif1a,mif1b))
-compare.mif(list(mif2a,mif2b))
+plot(c(mif1a,mif1b))
+plot(c(mif2a,mif2b))
-compare.mif(list(mif1b,mif2c))
+plot(mfl1 <- c(mif1b,mif2c))
+mfl2 <- c(mfl1,mif2c)
+mfl3 <- c(mif2a,mfl1)
+
+try(c(mif2a,continue(mif2b,Nmif=1)))
+
dev.off()
Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save 2014-06-23 14:13:43 UTC (rev 980)
+++ pkg/pomp/tests/ou2-mif2.Rout.save 2014-06-25 17:38:58 UTC (rev 981)
@@ -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):
@@ -64,7 +66,7 @@
+ tol=1e-8
+ )
>
-> compare.mif(list(mif1a,mif2a))
+> plot(c(mif1a,mif2a))
>
> set.seed(64857673L)
> mif1b <- mif(ou2,Nmif=50,start=guess1,
@@ -117,17 +119,24 @@
+ )
> mif2c <- continue(mif2c,Nmif=50)
>
-> compare.mif(list(mif1b,mif2b))
+> plot(c(mif1b,mif2b))
>
-> compare.mif(list(mif1a,mif1b))
-> compare.mif(list(mif2a,mif2b))
+> plot(c(mif1a,mif1b))
+> plot(c(mif2a,mif2b))
>
-> compare.mif(list(mif1b,mif2c))
+> plot(mfl1 <- c(mif1b,mif2c))
>
+> mfl2 <- c(mfl1,mif2c)
+> mfl3 <- c(mif2a,mfl1)
+>
+> try(c(mif2a,continue(mif2b,Nmif=1)))
+Error in validObject(.Object) :
+ invalid class "mifList" object: error in 'c': to be combined, 'mif' objects must equal numbers of iterations
+>
> dev.off()
null device
1
>
> proc.time()
user system elapsed
- 50.335 0.068 50.772
+ 59.213 0.057 59.317
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