[Pomp-commits] r801 - in pkg/pomp: . data inst inst/examples man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 9 21:17:00 CET 2013
Author: kingaa
Date: 2013-01-09 21:16:59 +0100 (Wed, 09 Jan 2013)
New Revision: 801
Added:
pkg/pomp/inst/examples/bbs.R
pkg/pomp/inst/examples/euler.sir.R
pkg/pomp/inst/examples/gillespie.sir.R
pkg/pomp/man/example.Rd
Removed:
pkg/pomp/data/bbs.rda
pkg/pomp/data/blowflies.rda
pkg/pomp/data/dacca.rda
pkg/pomp/data/euler.sir.rda
pkg/pomp/data/gillespie.sir.rda
pkg/pomp/data/gompertz.rda
pkg/pomp/data/ou2.rda
pkg/pomp/data/ricker.rda
pkg/pomp/data/rw2.rda
pkg/pomp/data/verhulst.rda
pkg/pomp/inst/examples/sir.R
Modified:
pkg/pomp/.Rbuildignore
pkg/pomp/DESCRIPTION
pkg/pomp/inst/NEWS
pkg/pomp/man/blowflies.Rd
pkg/pomp/man/dacca.Rd
pkg/pomp/man/gompertz.Rd
pkg/pomp/man/init.state-pomp.Rd
pkg/pomp/man/ou2.Rd
pkg/pomp/man/parmat.Rd
pkg/pomp/man/probe.Rd
pkg/pomp/man/ricker.Rd
pkg/pomp/man/rw2.Rd
pkg/pomp/man/simulate-pomp.Rd
pkg/pomp/man/sir.Rd
pkg/pomp/man/spect.Rd
pkg/pomp/man/traj-match.Rd
pkg/pomp/man/trajectory-pomp.Rd
pkg/pomp/man/verhulst.Rd
pkg/pomp/tests/bbs-trajmatch.R
pkg/pomp/tests/bbs-trajmatch.Rout.save
pkg/pomp/tests/bbs.R
pkg/pomp/tests/bbs.Rout.save
pkg/pomp/tests/blowflies.R
pkg/pomp/tests/blowflies.Rout.save
pkg/pomp/tests/dacca.R
pkg/pomp/tests/dacca.Rout.save
pkg/pomp/tests/dimchecks.R
pkg/pomp/tests/dimchecks.Rout.save
pkg/pomp/tests/fhn.Rout.save
pkg/pomp/tests/filtfail.Rout.save
pkg/pomp/tests/gillespie.R
pkg/pomp/tests/gillespie.Rout.save
pkg/pomp/tests/gompertz.R
pkg/pomp/tests/gompertz.Rout.save
pkg/pomp/tests/logistic.Rout.save
pkg/pomp/tests/ou2-bsmc.R
pkg/pomp/tests/ou2-bsmc.Rout.save
pkg/pomp/tests/ou2-forecast.R
pkg/pomp/tests/ou2-forecast.Rout.save
pkg/pomp/tests/ou2-icfit.R
pkg/pomp/tests/ou2-icfit.Rout.save
pkg/pomp/tests/ou2-kalman.R
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-nlf.R
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.R
pkg/pomp/tests/ou2-probe.Rout.save
pkg/pomp/tests/ou2-procmeas.R
pkg/pomp/tests/ou2-procmeas.Rout.save
pkg/pomp/tests/ou2-simulate.R
pkg/pomp/tests/ou2-simulate.Rout.save
pkg/pomp/tests/ou2-trajmatch.R
pkg/pomp/tests/ou2-trajmatch.Rout.save
pkg/pomp/tests/partrans.R
pkg/pomp/tests/partrans.Rout.save
pkg/pomp/tests/pfilter.R
pkg/pomp/tests/pfilter.Rout.save
pkg/pomp/tests/pomppomp.R
pkg/pomp/tests/pomppomp.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.R
pkg/pomp/tests/ricker-spect.Rout.save
pkg/pomp/tests/ricker.R
pkg/pomp/tests/ricker.Rout.save
pkg/pomp/tests/rw2.R
pkg/pomp/tests/rw2.Rout.save
pkg/pomp/tests/sir.R
pkg/pomp/tests/sir.Rout.save
pkg/pomp/tests/skeleton.R
pkg/pomp/tests/skeleton.Rout.save
pkg/pomp/tests/steps.R
pkg/pomp/tests/steps.Rout.save
pkg/pomp/tests/synlik.R
pkg/pomp/tests/synlik.Rout.save
pkg/pomp/tests/verhulst.R
pkg/pomp/tests/verhulst.Rout.save
Log:
- get rid of all data()-loadable pomp objects, replacing them with the new 'pompExample' facility
Modified: pkg/pomp/.Rbuildignore
===================================================================
--- pkg/pomp/.Rbuildignore 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/.Rbuildignore 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,6 +1,4 @@
inst/doc/Makefile
-inst/data-R/Makefile
-inst/data-R/make.R
inst/doc/(.+?)\.bst$
inst/doc/(.+?)\.R$
inst/doc/(.+?)\.png$
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/DESCRIPTION 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.43-6
-Date: 2013-01-08
+Version: 0.44-1
+Date: 2013-01-09
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
Deleted: pkg/pomp/data/bbs.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/blowflies.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/dacca.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/euler.sir.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/gillespie.sir.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/gompertz.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/ou2.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/ricker.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/rw2.rda
===================================================================
(Binary files differ)
Deleted: pkg/pomp/data/verhulst.rda
===================================================================
(Binary files differ)
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/inst/NEWS 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,4 +1,9 @@
NEWS
+0.44-1
+ o Remove all data()-loadable pomp objects.
+ To load the prebuilt example pomp objects from previous versions, use the new 'pompExample' function.
+ E.g., instead of 'data(euler.sir)', do 'pompExample("euler.sir")'.
+
0.43-4
o Clean up tests.
Added: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R (rev 0)
+++ pkg/pomp/inst/examples/bbs.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -0,0 +1,87 @@
+require(pomp)
+
+tc <- textConnection("
+day;reports
+1;3
+2;8
+3;28
+4;76
+5;222
+6;293
+7;257
+8;237
+9;192
+10;126
+11;70
+12;28
+13;12
+14;5
+")
+
+flu <- read.csv2(file=tc)
+close(tc)
+
+po <- pomp(
+ data=flu,
+ times="day",
+ t0=0,
+ rprocess=euler.sim(
+ step.fun="_sir_euler_simulator",
+ delta.t=1/12,
+ PACKAGE="pomp"
+ ),
+ skeleton.type="vectorfield",
+ skeleton="_sir_ODE",
+ measurement.model=reports~norm(mean=rho*cases,sd=1+sigma*cases),
+ PACKAGE="pomp",
+ obsnames = c("reports"),
+ statenames=c("S","I","R","cases","W"),
+ paramnames=c(
+ "gamma","mu","iota",
+ "beta","beta.sd","pop","rho",
+ "S.0","I.0","R.0"
+ ),
+ zeronames=c("cases"),
+ comp.names=c("S","I","R"),
+ ic.names=c("S.0","I.0","R.0"),
+ nbasis=1L,
+ degree=0L,
+ period=1.0,
+ logvar=c(
+ "beta","gamma","mu","iota","sigma","beta.sd",
+ "S.0","I.0","R.0"
+ ),
+ logitvar="rho",
+ parameter.inv.transform=function (params, logvar, logitvar, ...) {
+ params[logvar] <- log(params[logvar])
+ params[logitvar] <- qlogis(params[logitvar])
+ params
+ },
+ parameter.transform=function (params, logvar, logitvar, ...) {
+ params[logvar] <- exp(params[logvar])
+ params[logitvar] <- plogis(params[logitvar])
+ params
+ },
+ initializer=function(params, t0, comp.names, ic.names, ...) {
+ snames <- c("S","I","R","cases","W")
+ fracs <- params[ic.names]
+ x0 <- numeric(length(snames))
+ names(x0) <- snames
+ x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
+ x0
+ }
+ )
+
+coef(po) <- c(
+ gamma=1/3,mu=0.0,iota=0.0,
+ beta=1.4,
+ beta.sd=0,
+ pop=1400,
+ rho=0.9,sigma=3.6,
+ S.0=0.999,I.0=0.001,R.0=0
+ )
+
+bbs <- po
+
+assign("bbs",bbs,envir=.GlobalEnv)
+c("bbs")
Added: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R (rev 0)
+++ pkg/pomp/inst/examples/euler.sir.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -0,0 +1,57 @@
+require(pomp)
+
+po <- pomp(
+ data=data.frame(
+ time=seq(from=1/52,to=4,by=1/52),
+ reports=NA
+ ),
+ times="time",
+ t0=0,
+ rprocess=euler.sim(
+ step.fun="_sir_euler_simulator",
+ delta.t=1/52/20,
+ PACKAGE="pomp"
+ ),
+ skeleton.type="vectorfield",
+ skeleton="_sir_ODE",
+ rmeasure="_sir_binom_rmeasure",
+ dmeasure="_sir_binom_dmeasure",
+ PACKAGE="pomp",
+ obsnames = c("reports"),
+ statenames=c("S","I","R","cases","W"),
+ paramnames=c(
+ "gamma","mu","iota",
+ "beta1","beta.sd","pop","rho",
+ "S.0","I.0","R.0"
+ ),
+ zeronames=c("cases"),
+ comp.names=c("S","I","R"),
+ ic.names=c("S.0","I.0","R.0"),
+ parameter.transform="_sir_par_trans",
+ parameter.inv.transform="_sir_par_untrans",
+ nbasis=3L,
+ degree=3L,
+ period=1.0,
+ initializer=function(params, t0, comp.names, ic.names, ...) {
+ snames <- c("S","I","R","cases","W")
+ fracs <- params[ic.names]
+ x0 <- numeric(length(snames))
+ names(x0) <- snames
+ x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
+ x0
+ }
+ )
+
+coef(po) <- c(
+ gamma=26,mu=0.02,iota=0.01,
+ beta1=400,beta2=480,beta3=320,
+ beta.sd=1e-3,
+ pop=2.1e6,
+ rho=0.6,
+ S.0=26/400,I.0=0.001,R.0=1-26/400
+ )
+
+simulate(po,nsim=1,seed=329343545L) -> euler.sir
+
+assign("euler.sir",euler.sir,envir=.GlobalEnv)
+c("euler.sir")
Added: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R (rev 0)
+++ pkg/pomp/inst/examples/gillespie.sir.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -0,0 +1,75 @@
+require(pomp)
+
+po <- pomp(
+ data=data.frame(
+ time=seq(from=0,to=10,by=1/52),
+ reports=NA
+ ),
+ times="time",
+ t0=0,
+ rprocess=gillespie.sim(
+ rate.fun="_sir_rates",
+ PACKAGE="pomp",
+ v=cbind(
+ birth=c(1,0,0,1,0),
+ sdeath=c(-1,0,0,-1,0),
+ infection=c(-1,1,0,0,0),
+ ideath=c(0,-1,0,-1,0),
+ recovery=c(0,-1,1,0,1),
+ rdeath=c(0,0,-1,-1,0)
+ ),
+ d=cbind(
+ birth=c(0,0,0,1,0),
+ sdeath=c(1,0,0,0,0),
+ infection=c(1,1,0,1,0),
+ ideath=c(0,1,0,0,0),
+ recovery=c(0,1,0,0,0),
+ rdeath=c(0,0,1,0,0)
+ )
+ ),
+ skeleton.type="vectorfield",
+ skeleton="_sir_ODE",
+ measurement.model=reports~binom(size=cases,prob=rho),
+ PACKAGE="pomp",
+ obsnames = c("reports"),
+ statenames=c("S","I","R","N","cases"),
+ paramnames=c(
+ "gamma","mu","iota",
+ "beta1","beta.sd","pop","rho",
+ "S.0","I.0","R.0"
+ ),
+ zeronames=c("cases"),
+ comp.names=c("S","I","R"),
+ ic.names=c("S.0","I.0","R.0"),
+ parameter.transform="_sir_par_trans",
+ parameter.inv.transform="_sir_par_untrans",
+ nbasis=3L,
+ degree=3L,
+ period=1.0,
+ initializer=function(params, t0, comp.names, ic.names, ...) {
+ x0 <- numeric(5)
+ names(x0) <- c("S","I","R","N","cases")
+ fracs <- params[ic.names]
+ x0["N"] <- params["pop"]
+ x0[comp.names] <- round(params["pop"]*fracs/sum(fracs))
+ x0
+ }
+ )
+
+coef(po) <- c(
+ gamma=24,mu=1/70,iota=0.1,
+ beta1=330,beta2=410,beta3=490,
+ rho=0.1,
+ S.0=0.05,I.0=1e-4,R.0=0.95,
+ pop=1000000,
+ beta.sd=0
+ )
+
+simulate(
+ po,
+ nsim=1,
+ seed=1165270654L
+ ) -> gillespie.sir
+
+assign("gillespie.sir",gillespie.sir,envir=.GlobalEnv)
+c("gillespie.sir")
Deleted: pkg/pomp/inst/examples/sir.R
===================================================================
--- pkg/pomp/inst/examples/sir.R 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/inst/examples/sir.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,196 +0,0 @@
-require(pomp)
-
-po <- pomp(
- data=data.frame(
- time=seq(from=1/52,to=4,by=1/52),
- reports=NA
- ),
- times="time",
- t0=0,
- rprocess=euler.sim(
- step.fun="_sir_euler_simulator",
- delta.t=1/52/20,
- PACKAGE="pomp"
- ),
- skeleton.type="vectorfield",
- skeleton="_sir_ODE",
- rmeasure="_sir_binom_rmeasure",
- dmeasure="_sir_binom_dmeasure",
- PACKAGE="pomp",
- obsnames = c("reports"),
- statenames=c("S","I","R","cases","W"),
- paramnames=c(
- "gamma","mu","iota",
- "beta1","beta.sd","pop","rho",
- "S.0","I.0","R.0"
- ),
- zeronames=c("cases"),
- comp.names=c("S","I","R"),
- ic.names=c("S.0","I.0","R.0"),
- parameter.transform="_sir_par_trans",
- parameter.inv.transform="_sir_par_untrans",
- nbasis=3L,
- degree=3L,
- period=1.0,
- initializer=function(params, t0, comp.names, ic.names, ...) {
- snames <- c("S","I","R","cases","W")
- fracs <- params[ic.names]
- x0 <- numeric(length(snames))
- names(x0) <- snames
- x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
- x0
- }
- )
-
-coef(po) <- c(
- gamma=26,mu=0.02,iota=0.01,
- beta1=400,beta2=480,beta3=320,
- beta.sd=1e-3,
- pop=2.1e6,
- rho=0.6,
- S.0=26/400,I.0=0.001,R.0=1-26/400
- )
-
-simulate(po,nsim=1,seed=329343545L) -> euler.sir
-
-time(po) <- seq(from=0,to=10,by=1/52)
-
-po <- pomp(
- po,
- statenames=c("S","I","R","N","cases"),
- rprocess=gillespie.sim(
- rate.fun="_sir_rates",
- PACKAGE="pomp",
- v=cbind(
- birth=c(1,0,0,1,0),
- sdeath=c(-1,0,0,-1,0),
- infection=c(-1,1,0,0,0),
- ideath=c(0,-1,0,-1,0),
- recovery=c(0,-1,1,0,1),
- rdeath=c(0,0,-1,-1,0)
- ),
- d=cbind(
- birth=c(0,0,0,1,0),
- sdeath=c(1,0,0,0,0),
- infection=c(1,1,0,1,0),
- ideath=c(0,1,0,0,0),
- recovery=c(0,1,0,0,0),
- rdeath=c(0,0,1,0,0)
- )
- ),
- measurement.model=reports~binom(size=cases,prob=rho),
- comp.names=c("S","I","R"),
- ic.names=c("S.0","I.0","R.0"),
- initializer=function(params, t0, comp.names, ic.names, ...) {
- x0 <- numeric(5)
- names(x0) <- c("S","I","R","N","cases")
- fracs <- params[ic.names]
- x0["N"] <- params["pop"]
- x0[comp.names] <- round(params["pop"]*fracs/sum(fracs))
- x0
- }
- )
-
-coef(po) <- c(
- gamma=24,mu=1/70,iota=0.1,
- beta1=330,beta2=410,beta3=490,
- rho=0.1,
- S.0=0.05,I.0=1e-4,R.0=0.95,
- pop=1000000,
- beta.sd=0
- )
-
-simulate(
- po,
- nsim=1,
- seed=1165270654L
- ) -> gillespie.sir
-
-
-tc <- textConnection("
-day;reports
-1;3
-2;8
-3;28
-4;76
-5;222
-6;293
-7;257
-8;237
-9;192
-10;126
-11;70
-12;28
-13;12
-14;5
-")
-
-flu <- read.csv2(file=tc)
-close(tc)
-
-po <- pomp(
- data=flu,
- times="day",
- t0=0,
- rprocess=euler.sim(
- step.fun="_sir_euler_simulator",
- delta.t=1/12,
- PACKAGE="pomp"
- ),
- skeleton.type="vectorfield",
- skeleton="_sir_ODE",
- measurement.model=reports~norm(mean=rho*cases,sd=1+sigma*cases),
- PACKAGE="pomp",
- obsnames = c("reports"),
- statenames=c("S","I","R","cases","W"),
- paramnames=c(
- "gamma","mu","iota",
- "beta","beta.sd","pop","rho",
- "S.0","I.0","R.0"
- ),
- zeronames=c("cases"),
- comp.names=c("S","I","R"),
- ic.names=c("S.0","I.0","R.0"),
- nbasis=1L,
- degree=0L,
- period=1.0,
- logvar=c(
- "beta","gamma","mu","iota","sigma","beta.sd",
- "S.0","I.0","R.0"
- ),
- logitvar="rho",
- parameter.inv.transform=function (params, logvar, logitvar, ...) {
- params[logvar] <- log(params[logvar])
- params[logitvar] <- qlogis(params[logitvar])
- params
- },
- parameter.transform=function (params, logvar, logitvar, ...) {
- params[logvar] <- exp(params[logvar])
- params[logitvar] <- plogis(params[logitvar])
- params
- },
- initializer=function(params, t0, comp.names, ic.names, ...) {
- snames <- c("S","I","R","cases","W")
- fracs <- params[ic.names]
- x0 <- numeric(length(snames))
- names(x0) <- snames
- x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
- x0
- }
- )
-
-coef(po) <- c(
- gamma=1/3,mu=0.0,iota=0.0,
- beta=1.4,
- beta.sd=0,
- pop=1400,
- rho=0.9,sigma=3.6,
- S.0=0.999,I.0=0.001,R.0=0
- )
-
-bbs <- po
-
-assign("euler.sir",euler.sir,envir=.GlobalEnv)
-assign("gillespie.sir",gillespie.sir,envir=.GlobalEnv)
-assign("bbs",bbs,envir=.GlobalEnv)
-c("euler.sir","gillespie.sir","bbs")
Modified: pkg/pomp/man/blowflies.Rd
===================================================================
--- pkg/pomp/man/blowflies.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/blowflies.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -7,9 +7,8 @@
\description{
\code{blowflies1} and \code{blowflies2} are \code{pomp} objects encoding stochastic delay-difference models.
}
-\usage{data(blowflies)}
\examples{
-data(blowflies)
+pompExample("blowflies")
plot(blowflies1)
plot(blowflies2)
}
@@ -34,7 +33,7 @@
Do
- \code{file.show(system.file("data-R","blowflies.R",package="pomp"))}
+ \code{file.show(system.file("examples","blowflies.R",package="pomp"))}
to view the code that constructs these pomp objects.
}
Modified: pkg/pomp/man/dacca.Rd
===================================================================
--- pkg/pomp/man/dacca.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/dacca.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -9,9 +9,6 @@
Data are provided courtesy of Dr. Menno J. Bouma, London School of Tropical Medicine and Hygiene.
}
-\usage{
-data(dacca)
-}
\details{
\code{dacca} is a \code{pomp} object containing the model, data, and MLE parameters.
Parameters that naturally range over the positive reals are log-transformed;
@@ -19,7 +16,7 @@
parameters that are naturally unbounded or take integer values are not transformed.
}
\examples{
-data(dacca)
+pompExample("dacca")
plot(dacca)
#MLEs on the natural scale
coef(dacca)
Added: pkg/pomp/man/example.Rd
===================================================================
--- pkg/pomp/man/example.Rd (rev 0)
+++ pkg/pomp/man/example.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -0,0 +1,23 @@
+\name{pompExample}
+\alias{pompExample}
+\title{Pre-built examples of pomp objects.}
+\description{
+ \code{pompExample} loads pre-built example \code{pomp} objects.
+}
+\usage{
+pompExample(example)
+}
+\arguments{
+ \item{example}{
+ character; name of the example to load.
+ Evoked without an argument, \code{pompExample} lists all available examples.
+ }
+}
+\value{
+ \code{pompExample} has the side effect of creating one or more \code{pomp} objects in the global workspace.
+}
+\author{Aaron A. King \email{kingaa at umich dot edu}}
+\examples{
+ pompExample()
+ pompExample("euler.sir")
+}
Modified: pkg/pomp/man/gompertz.Rd
===================================================================
--- pkg/pomp/man/gompertz.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/gompertz.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -5,7 +5,6 @@
\description{
\code{gompertz} is a \code{pomp} object encoding a stochastic Gompertz population model with log-normal measurement error.
}
-\usage{data(gompertz)}
\details{
The state process is \eqn{X_{t+1} = K^{1-S} X_{t}^S \epsilon_{t}}{X[t+1]=K^(1-S) X[t]^S eps[t]}, where \eqn{S=e^{-r}}{S=e^{-r}} and the \eqn{\epsilon_t}{eps[t]} are i.i.d. lognormal random deviates with variance \eqn{\sigma^2}{sigma^2}.
The observed variables \eqn{Y_t} are distributed as \eqn{\mathrm{lognormal}(\log{X_t},\tau)}{lognormal(log(X[t]),tau)}.
@@ -13,7 +12,7 @@
The \code{pomp} object includes parameter transformations that log-transform the parameters for estimation purposes.
}
\examples{
-data(gompertz)
+pompExample("gompertz")
plot(gompertz)
coef(gompertz)
coef(gompertz,transform=TRUE)
Modified: pkg/pomp/man/init.state-pomp.Rd
===================================================================
--- pkg/pomp/man/init.state-pomp.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/init.state-pomp.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -25,11 +25,11 @@
Returns a matrix of initial states (with rownames).
}
\examples{
-data(ou2)
+pompExample("ou2")
coef(ou2)
init.state(ou2)
-data(euler.sir)
+pompExample("euler.sir")
coef(euler.sir)
init.state(euler.sir)
}
Modified: pkg/pomp/man/ou2.Rd
===================================================================
--- pkg/pomp/man/ou2.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/ou2.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -5,7 +5,6 @@
\description{
\code{ou2} is a \code{pomp} object encoding a bivariate discrete-time Ornstein-Uhlenbeck process.
}
-\usage{data(ou2)}
\details{
If the state process is \eqn{X(t) = (x_{1}(t),x_{2}(t))}, then
\deqn{X(t+1) = \alpha X(t) + \sigma \epsilon(t),}
@@ -16,7 +15,7 @@
This object is demonstrated in the vignette "Advanced topics in pomp".
}
\examples{
-data(ou2)
+pompExample("ou2")
plot(ou2)
coef(ou2)
x <- simulate(ou2)
Modified: pkg/pomp/man/parmat.Rd
===================================================================
--- pkg/pomp/man/parmat.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/parmat.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -21,7 +21,7 @@
\author{Aaron A. King \email{kingaa at umich dot edu}}
\examples{
## generate a bifurcation diagram for the Ricker map
- data(ricker)
+ pompExample("ricker")
p <- parmat(coef(ricker),nrep=500)
p["r",] <- exp(seq(from=1.5,to=4,length=500))
x <- trajectory(ricker,times=seq(from=1000,to=2000,by=1),params=p)
Modified: pkg/pomp/man/probe.Rd
===================================================================
--- pkg/pomp/man/probe.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/probe.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -166,7 +166,7 @@
Aaron A. King (kingaa at umich dot edu)
}
\examples{
-data(ou2)
+pompExample("ou2")
good <- probe(
ou2,
probes=list(
Modified: pkg/pomp/man/ricker.Rd
===================================================================
--- pkg/pomp/man/ricker.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/ricker.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -5,13 +5,12 @@
\description{
\code{ricker} is a \code{pomp} object encoding a stochastic Ricker model with Poisson measurement error.
}
-\usage{data(ricker)}
\details{
The state process is \eqn{N_{t+1} = r N_{t} \exp(-N_{t}+e_{t})}{N[t+1] = r N[t] exp(-N[t]+e[t])}, where the \eqn{e_t}{e[t]} are i.i.d. normal random deviates with zero mean and variance \eqn{\sigma^2}{sigma^2}.
The observed variables \eqn{y_t}{y[t]} are distributed as \eqn{\mathrm{Poisson}(\phi N_t)}{Poisson(phi N[t])}.
}
\examples{
-data(ricker)
+pompExample("ricker")
plot(ricker)
coef(ricker)
}
Modified: pkg/pomp/man/rw2.Rd
===================================================================
--- pkg/pomp/man/rw2.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/rw2.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -5,12 +5,11 @@
\description{
\code{rw2} is a \code{pomp} object encoding a 2-D normal random walk.
}
-\usage{data(rw2)}
\details{
The random-walk process is fully but noisily observed.
}
\examples{
-data(rw2)
+pompExample("rw2")
plot(rw2)
x <- simulate(rw2,nsim=10,seed=20348585L,params=c(x1.0=0,x2.0=0,s1=1,s2=3,tau=1))
plot(x[[1]])
Modified: pkg/pomp/man/simulate-pomp.Rd
===================================================================
--- pkg/pomp/man/simulate-pomp.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/simulate-pomp.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -61,7 +61,7 @@
This makes it possible for the user to write highly optimized code for these potentially expensive computations.
}
\examples{
-data(ou2)
+pompExample("ou2")
x <- simulate(ou2,seed=3495485,nsim=10)
x <- simulate(ou2,seed=3495485,nsim=10,states=TRUE,obs=TRUE)
}
Modified: pkg/pomp/man/sir.Rd
===================================================================
--- pkg/pomp/man/sir.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/sir.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -10,33 +10,28 @@
\code{gillespie.sir} has the same model implemented using Gillespie's algorithm.
\code{bbs} is a nonseasonal SIR model together with data from a 1978 outbreak of influenza in a British boarding school.
}
-\usage{
-data(euler.sir)
-data(gillespie.sir)
-data(bbs)
-}
\details{
This example is discussed extensively in the \dQuote{Introduction to \pkg{pomp}} and \dQuote{Advanced topics in \pkg{pomp}} vignettes.
- The codes that construct these \code{pomp} objects can be found in the \dQuote{data-R} directory in the installed package.
- Do \code{file.show(system.file("data-R/sir.R",package="pomp"))} to view these codes.
+ The codes that construct these \code{pomp} objects can be found in the \dQuote{examples} directory in the installed package.
+ Do \code{system.file("examples",package="pomp"))} to find this directory.
For the basic \code{rprocess}, \code{dmeasure}, \code{rmeasure}, and \code{skeleton} functions, these codes use compiled native routines built into the package's library.
View \dQuote{src/sir.c} in the package source or \code{file.show("examples/sir.c")} from an \R session to view these codes.
The boarding school influenza outbreak is described in Anonymous (1978).
}
\examples{
-data(euler.sir)
+pompExample("euler.sir")
plot(euler.sir)
plot(simulate(euler.sir,seed=20348585))
coef(euler.sir)
-data(gillespie.sir)
+pompExample("gillespie.sir")
plot(gillespie.sir)
plot(simulate(gillespie.sir,seed=20348585))
coef(gillespie.sir)
-data(bbs)
+pompExample("bbs")
plot(bbs)
coef(bbs)
}
Modified: pkg/pomp/man/spect.Rd
===================================================================
--- pkg/pomp/man/spect.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/spect.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -154,7 +154,7 @@
Aaron A. King (kingaa at umich dot edu)
}
\examples{
-data(ou2)
+pompExample("ou2")
good <- spect(
ou2,
vars=c("y1","y2"),
Modified: pkg/pomp/man/traj-match.Rd
===================================================================
--- pkg/pomp/man/traj-match.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/traj-match.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -111,7 +111,7 @@
\code{traj.match.objfun} returns a function suitable for use as an objective function in an \code{\link{optim}}-like optimizer.
}
\examples{
- data(ou2)
+ pompExample("ou2")
true.p <- c(
alpha.1=0.9,alpha.2=0,alpha.3=-0.4,alpha.4=0.99,
sigma.1=2,sigma.2=0.1,sigma.3=2,
@@ -137,11 +137,11 @@
lines(x1~time,data=as(res,"data.frame"),col='blue')
lines(x2~time,data=as(res,"data.frame"),col='red')
- data(ricker)
+ pompExample("ricker")
ofun <- traj.match.objfun(ricker,est=c("r","phi"),transform=TRUE)
optim(fn=ofun,par=c(2,0),method="BFGS")
- data(bbs)
+ pompExample("bbs")
ofun <- traj.match.objfun(bbs,est=c("beta","gamma"),transform=TRUE,hmax=0.001)
optim(fn=ofun,par=c(0,-1),method="Nelder-Mead")
}
Modified: pkg/pomp/man/trajectory-pomp.Rd
===================================================================
--- pkg/pomp/man/trajectory-pomp.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/trajectory-pomp.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -48,7 +48,7 @@
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
\examples{
-data(euler.sir)
+pompExample("euler.sir")
x <- trajectory(euler.sir)
plot(time(euler.sir),x["I",1,],type='l',xlab='time',ylab='I')
lines(time(euler.sir),x["cases",1,],col='red')
Modified: pkg/pomp/man/verhulst.Rd
===================================================================
--- pkg/pomp/man/verhulst.Rd 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/man/verhulst.Rd 2013-01-09 20:16:59 UTC (rev 801)
@@ -5,13 +5,12 @@
\description{
\code{verhulst} is a \code{pomp} object encoding a univariate stochastic logistic model with measurement error.
}
-\usage{data(verhulst)}
\details{
The model is written as an Ito diffusion, \eqn{dn = r n (1-n/K) dt + \sigma n dW}, where \eqn{W} is a Wiener process.
It is implemented using the \code{\link{euler.sim}} plug-in.
}
\examples{
-data(verhulst)
+pompExample("verhulst")
plot(verhulst)
coef(verhulst)
params <- cbind(
Modified: pkg/pomp/tests/bbs-trajmatch.R
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.R 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/bbs-trajmatch.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,6 +1,6 @@
library(pomp)
-data(bbs)
+pompExample("bbs")
guess <- c(
mu=0,gamma=1/3,beta=1,beta.sd=0,iota=0,
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,5 +1,5 @@
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -21,7 +21,9 @@
Loading required package: subplex
Loading required package: deSolve
>
-> data(bbs)
+> pompExample("bbs")
+newly created pomp objects:
+ bbs
>
> guess <- c(
+ mu=0,gamma=1/3,beta=1,beta.sd=0,iota=0,
@@ -68,4 +70,4 @@
>
> proc.time()
user system elapsed
- 2.180 0.032 2.236
+ 2.424 0.060 2.516
Modified: pkg/pomp/tests/bbs.R
===================================================================
--- pkg/pomp/tests/bbs.R 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/bbs.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,6 +1,6 @@
library(pomp)
-data(bbs)
+pompExample("bbs")
set.seed(48857734L)
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/bbs.Rout.save 2013-01-09 20:16:59 UTC (rev 801)
@@ -21,7 +21,9 @@
Loading required package: subplex
Loading required package: deSolve
>
-> data(bbs)
+> pompExample("bbs")
+newly created pomp objects:
+ bbs
>
> set.seed(48857734L)
>
@@ -58,4 +60,4 @@
>
> proc.time()
user system elapsed
- 2.656 0.056 2.736
+ 2.704 0.100 2.827
Modified: pkg/pomp/tests/blowflies.R
===================================================================
--- pkg/pomp/tests/blowflies.R 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/blowflies.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,6 +1,6 @@
library(pomp)
-data(blowflies)
+pompExample("blowflies")
init.state(blowflies1)
x1 <- simulate(blowflies1)
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/blowflies.Rout.save 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,5 +1,5 @@
-R version 2.14.2 (2012-02-29)
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -21,7 +21,9 @@
Loading required package: subplex
Loading required package: deSolve
>
-> data(blowflies)
+> pompExample("blowflies")
+newly created pomp objects:
+ blowflies1 blowflies2
>
> init.state(blowflies1)
[,1]
@@ -68,3 +70,6 @@
> logLik(f2)
[1] -1471.781
>
+> proc.time()
+ user system elapsed
+ 1.316 0.064 1.397
Modified: pkg/pomp/tests/dacca.R
===================================================================
--- pkg/pomp/tests/dacca.R 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/dacca.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -2,7 +2,7 @@
set.seed(1420306530L)
-data(dacca)
+pompExample("dacca")
x <- as.data.frame(dacca)
print(names(x))
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/dacca.Rout.save 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,5 +1,5 @@
-R version 2.15.0 (2012-03-30)
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -23,7 +23,9 @@
>
> set.seed(1420306530L)
>
-> data(dacca)
+> pompExample("dacca")
+newly created pomp objects:
+ dacca
>
> x <- as.data.frame(dacca)
> print(names(x))
@@ -50,4 +52,4 @@
>
> proc.time()
user system elapsed
- 3.428 0.052 3.501
+ 3.544 0.096 3.661
Modified: pkg/pomp/tests/dimchecks.R
===================================================================
--- pkg/pomp/tests/dimchecks.R 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/dimchecks.R 2013-01-09 20:16:59 UTC (rev 801)
@@ -2,7 +2,7 @@
set.seed(1420306530L)
-data(ricker)
+pompExample("ricker")
po <- ricker
pars <- coef(po)
@@ -49,7 +49,7 @@
stopifnot(identical(g1,g3[,1:3,]))
stopifnot(identical(g1,g3[,4:6,]))
-data(gompertz)
+pompExample("gompertz")
p <- parmat(coef(gompertz),5)
f1 <- partrans(gompertz,p,"inv")
f2 <- parmat(coef(gompertz,transform=TRUE),5)
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2013-01-09 16:53:21 UTC (rev 800)
+++ pkg/pomp/tests/dimchecks.Rout.save 2013-01-09 20:16:59 UTC (rev 801)
@@ -1,5 +1,5 @@
-R version 2.15.0 (2012-03-30)
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -23,7 +23,9 @@
>
> set.seed(1420306530L)
>
-> data(ricker)
+> pompExample("ricker")
+newly created pomp objects:
+ ricker
> po <- ricker
>
> pars <- coef(po)
@@ -151,7 +153,9 @@
> stopifnot(identical(g1,g3[,1:3,]))
> stopifnot(identical(g1,g3[,4:6,]))
>
-> data(gompertz)
+> pompExample("gompertz")
+newly created pomp objects:
+ gompertz
> p <- parmat(coef(gompertz),5)
> f1 <- partrans(gompertz,p,"inv")
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 801
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