[Pomp-commits] r666 - in pkg/pompExamples: . data inst/data-R inst/doc man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 17 23:37:51 CEST 2012
Author: kingaa
Date: 2012-04-17 23:37:50 +0200 (Tue, 17 Apr 2012)
New Revision: 666
Removed:
pkg/pompExamples/inst/data-R/budmoth-params.csv
pkg/pompExamples/inst/data-R/pertussis-params.csv
Modified:
pkg/pompExamples/.Rinstignore
pkg/pompExamples/DESCRIPTION
pkg/pompExamples/NAMESPACE
pkg/pompExamples/data/budmoth.sim.rda
pkg/pompExamples/data/pertussis.sim.rda
pkg/pompExamples/inst/data-R/budmoth-simdata.rda
pkg/pompExamples/inst/data-R/budmoth.sim.R
pkg/pompExamples/inst/data-R/pertussis-simdata.rda
pkg/pompExamples/inst/data-R/pertussis.sim.R
pkg/pompExamples/inst/doc/budmoth-model-slices.rda
pkg/pompExamples/inst/doc/budmoth-model-true-loglik.rda
pkg/pompExamples/inst/doc/budmoth-model.Rnw
pkg/pompExamples/inst/doc/budmoth-model.pdf
pkg/pompExamples/inst/doc/pertussis-model.Rnw
pkg/pompExamples/inst/doc/pertussis-model.pdf
pkg/pompExamples/man/budmoth.Rd
pkg/pompExamples/tests/budmoth.R
pkg/pompExamples/tests/pertussis.R
Log:
- fix loads of bugs
Modified: pkg/pompExamples/.Rinstignore
===================================================================
--- pkg/pompExamples/.Rinstignore 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/.Rinstignore 2012-04-17 21:37:50 UTC (rev 666)
@@ -1,2 +1,3 @@
inst/doc/Makefile
-inst/doc/fullnat.bst
+inst/data-R/Makefile
+inst/doc/(.+?)\.bst$
Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/DESCRIPTION 2012-04-17 21:37:50 UTC (rev 666)
@@ -10,3 +10,4 @@
License: GPL (>= 2)
LazyLoad: true
LazyData: false
+BuildVignettes: no
Modified: pkg/pompExamples/NAMESPACE
===================================================================
--- pkg/pompExamples/NAMESPACE 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/NAMESPACE 2012-04-17 21:37:50 UTC (rev 666)
@@ -1,11 +1,2 @@
-useDynLib(pomp.devel)
+useDynLib(pompExamples)
importFrom(pomp)
-export(
- logit,
- expit,
- rlogitnorm,
- dlogitnorm,
- mult.norm.ts,
- spsainb,
- sainb
- )
Modified: pkg/pompExamples/data/budmoth.sim.rda
===================================================================
(Binary files differ)
Modified: pkg/pompExamples/data/pertussis.sim.rda
===================================================================
(Binary files differ)
Deleted: pkg/pompExamples/inst/data-R/budmoth-params.csv
===================================================================
--- pkg/pompExamples/inst/data-R/budmoth-params.csv 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/inst/data-R/budmoth-params.csv 2012-04-17 21:37:50 UTC (rev 666)
@@ -1,5 +0,0 @@
-"seed";"alpha";"sig.alpha";"gam";"lambda";"sig.lambda";"g";"delta";"a";"sig.a";"w";"beta0";"beta1";"u";"sigQobs";"sigNobs";"sigSobs";"Q.0";"N.0";"S.0"
-"tri.1";1691699385.71224;0.5;0.1;50;22;0.25;0.08;10;1.7;0.1;0.15;0;35;0.9;0.03;0.5;0.1;0.96;0.02;0.22
-"para.1";1116757478.97997;0.5;0.1;50;22;0.25;0.08;0.5;1.7;0.1;0.15;0;35;0.9;0.03;0.5;0.1;0.96;0.02;0.22
-"food.1";1054866677.50879;0.5;0.1;20;5;0.25;0.02;10;1;0.1;0;0;35;0.9;0.03;0.5;0.1;0.96;0.02;0.22
-"para.2";1361101458.86619;0.5;0.1;50;10;5;0.08;0.5;1.7;1;0.15;0;35;0.9;0.03;0.5;0.1;0.96;0.02;0.22
Modified: pkg/pompExamples/inst/data-R/budmoth-simdata.rda
===================================================================
(Binary files differ)
Modified: pkg/pompExamples/inst/data-R/budmoth.sim.R
===================================================================
--- pkg/pompExamples/inst/data-R/budmoth.sim.R 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/inst/data-R/budmoth.sim.R 2012-04-17 21:37:50 UTC (rev 666)
@@ -1,31 +1,30 @@
-require(pomp.devel)
+require(pompExamples)
-params <- read.csv("budmoth-params.csv",sep=";")
-datasets <- rownames(params)
-params <- params[!(names(params)%in%c("seed"))]
-
load("budmoth-simdata.rda")
+datasets <- rownames(params)
+params <- subset(params,select=-seed)
+
budmoth.sim <- list()
for (d in datasets) {
po <- pomp(
- data=subset(budmoth.sim.data,dataset==d,select=c(time,Qobs,Nobs,Sobs)),
+ data=subset(simdata,dataset==d,select=c(time,Qobs,Nobs,Sobs)),
time="time",
t0=0,
rprocess=euler.sim(
step.fun="budmoth_map",
delta.t=1,
- PACKAGE="pomp.devel"
+ PACKAGE="pompExamples"
),
dprocess=onestep.dens(
dens.fun="budmoth_density",
- PACKAGE="pomp.devel"
+ PACKAGE="pompExamples"
),
rmeasure="budmoth_rmeasure",
dmeasure="budmoth_dmeasure",
skeleton.type="map",
skeleton="budmoth_skeleton",
- PACKAGE="pomp.devel",
+ PACKAGE="pompExamples",
paramnames=c(
"alpha","sig.alpha","gam","lambda","sig.lambda",
"g","delta","a","sig.a",
Deleted: pkg/pompExamples/inst/data-R/pertussis-params.csv
===================================================================
--- pkg/pompExamples/inst/data-R/pertussis-params.csv 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/inst/data-R/pertussis-params.csv 2012-04-17 21:37:50 UTC (rev 666)
@@ -1,9 +0,0 @@
-model;pop;seed;birthrate;deathrate;mean.beta;ampl.beta;imports;sigma;gamma;alpha.1;alpha.2;alpha.ratio;report.prob;boost.prob;polar.prob;vacc.prob;foi.mod;popsize;noise.sigma;tau;S.0;E.0;I.0;R1.0;R2.0;V.0
-SEIR;small;1489450081;0.02;0.02;450;0.15;10;46;26;0;0.1;1;0.3;0;0;0;0;500000;0;0.01;0.1;0.01;0.01;0.88;0;0
-SEIR;big;1385639311;0.02;0.02;450;0.15;10;46;26;0;0.1;1;0.3;0;0;0;0;5000000;0;0.01;0.1;0.01;0.01;0.88;0;0
-SEIRS;small;181048726;0.02;0.02;150;0.15;10;46;26;0.1;0.1;1;0.1;0;0;0;0;500000;0;0.01;0.1;0.01;0.01;0.88;0;0
-SEIRS;big;497318207;0.02;0.02;150;0.15;10;46;26;0.1;0.1;1;0.1;0;0;0;0;5000000;0;0.01;0.1;0.01;0.01;0.88;0;0
-SEIRR;small;1952854080;0.02;0.02;150;0.15;10;46;26;0.1;0.1;1;0.11;0.75;0;0;0.5;500000;0;0.01;0.1;0.01;0.01;0.88;0;0
-SEIRR;big;949351093;0.02;0.02;150;0.15;10;46;26;0.1;0.1;1;0.11;0.75;0;0;0.5;5000000;0;0.01;0.1;0.01;0.01;0.88;0;0
-full;small;744725040.5;0.02;0.02;150;0.15;10;46;26;0.1;0.1;1;0.1;0.75;0.1;0;0.5;500000;0.01;0.01;0.1;0.01;0.01;0.88;0;0
-full;big;1532950814;0.02;0.02;150;0.15;10;46;26;0.1;0.1;1;0.1;0.75;0.1;0;0.5;5000000;0.01;0.01;0.1;0.01;0.01;0.88;0;0
Modified: pkg/pompExamples/inst/data-R/pertussis-simdata.rda
===================================================================
(Binary files differ)
Modified: pkg/pompExamples/inst/data-R/pertussis.sim.R
===================================================================
--- pkg/pompExamples/inst/data-R/pertussis.sim.R 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/inst/data-R/pertussis.sim.R 2012-04-17 21:37:50 UTC (rev 666)
@@ -3,29 +3,27 @@
## and states. Simulations from the process model are approximated using
## an Euler approximation.
-require(pomp.devel)
+require(pompExamples)
-params <- read.csv("pertussis-params.csv",sep=";")
-datasets <- with(params,paste(model,pop,sep="."))
-params <- params[!(names(params)%in%c("model","pop","seed"))]
-rownames(params) <- datasets
-
load("pertussis-simdata.rda")
+datasets <- rownames(params)
+params <- subset(params,select=-c(model,pop,seed))
+
pertussis.sim <- list()
for (d in datasets) {
po <- pomp(
- data=subset(pertussis.sim.data,dataset==d,select=c(time,reports)),
+ data=subset(simdata,dataset==d,select=c(time,reports)),
times="time",
t0=-1/52,
rprocess = euler.sim(
step.fun="pertussis_sveirr_EM",
- delta.t=1/52/7, # Euler stepsize
- PACKAGE="pomp.devel"
+ delta.t=1/52/7, # Euler stepsize
+ PACKAGE="pompExamples"
),
skeleton.type="vectorfield",
skeleton="pertussis_sveirr_skel",
- PACKAGE="pomp.devel", # name of the dynamically loadable library where the C functions are
+ PACKAGE="pompExamples",
paramnames=c(
"birthrate","deathrate","mean.beta","ampl.beta",
"imports","sigma","gamma","alpha.1","alpha.2","alpha.ratio",
Modified: pkg/pompExamples/inst/doc/budmoth-model-slices.rda
===================================================================
(Binary files differ)
Modified: pkg/pompExamples/inst/doc/budmoth-model-true-loglik.rda
===================================================================
(Binary files differ)
Modified: pkg/pompExamples/inst/doc/budmoth-model.Rnw
===================================================================
--- pkg/pompExamples/inst/doc/budmoth-model.Rnw 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/inst/doc/budmoth-model.Rnw 2012-04-17 21:37:50 UTC (rev 666)
@@ -35,7 +35,7 @@
\maketitle
<<options,echo=F,results=hide>>=
-require(pomp.devel)
+require(pompExamples)
require(xtable)
glop <- options(keep.source=TRUE,width=60,continue=" ",prompt=" ")
options(
@@ -68,7 +68,7 @@
Note: $X$ is $\mathrm{LogitNormal}(\mu,\sigma^2)$ if $\logit(X)$ is $\mathrm{Normal}(\mu,\sigma^2)$.
The inverse of $\logit$ is $\expit$.
-R functions \texttt{logit}, \texttt{expit}, \texttt{rlogitnorm}, \texttt{dlogitnorm} are part of \texttt{pomp.devel}.
+R functions \texttt{logit}, \texttt{expit}, \texttt{rlogitnorm}, \texttt{dlogitnorm} are part of \texttt{pompExamples}.
The state process, for $t=1,\ldots,T$:
\begin{eqnarray}
@@ -120,7 +120,7 @@
@
The parameters at which the simulated data are generated can be extracted via
<<true-params>>=
-true.pars <- sapply(budmoth.sim[c("food.1","para.1","para.2","tri.1")],coef)
+true.pars <- sapply(budmoth.sim[c("food","para1","para2","tri")],coef)
@
and are displayed in Table~\ref{tab:sim-params}.
@@ -136,8 +136,8 @@
"$\\beta_{0}$","$\\beta_{1}$",
"$u$","$\\sigma_{Q}$","$\\sigma_{N}$","$\\sigma_{S}$",
"$Q_{0}$","$N_{0}$","$S_{0}$")
-params <- params[c("math","name","food.1","para.1","para.2","tri.1")]
-names(params) <- c("parameter","R name","food.1","para.1","para.2","tri.1")
+params <- params[c("math","name","food","para1","para2","tri")]
+names(params) <- c("parameter","R name","food","para1","para2","tri")
print(
xtable(
params,
@@ -157,7 +157,7 @@
\begin{figure}
<<data-plot,fig=T,height=6,width=8,pdf=T,png=F,echo=F>>=
-require(pomp.devel)
+require(pompExamples)
require(plyr)
require(reshape)
require(ggplot2)
@@ -177,7 +177,7 @@
<<true-loglik-calc,echo=F,eval=F>>=
require(Rmpi)
require(mpifarm)
-require(pomp.devel)
+require(pompExamples)
data(budmoth.sim)
@@ -192,27 +192,23 @@
mpi.farmer(
chunk=5,
- seeds=as.integer(floor(runif(n=10000,1,2^31))),
+ seeds=as.integer(floor(runif(n=nrep,1,2^31))),
jobs={
- joblist <- vector(mode='list',length=nrep*length(budmoth.sim))
- k <- 0
- for (q in names(budmoth.sim)) {
- for (r in seq_len(nrep)) {
- k <- k+1
- joblist[[k]] <- list(
- seed=seeds[k],
- dataset=q
- )
- }
- }
- joblist
+ require(plyr)
+ dlply(
+ expand.grid(
+ seed=seeds,
+ dataset=names(budmoth.sim)
+ ),
+ ~dataset+seed
+ )
},
common=list(
pomps=budmoth.sim,
Np=Np
),
main={
- require(pomp.devel)
+ require(pompExamples)
save.seed <- .Random.seed
set.seed(seed)
tic <- Sys.time()
@@ -298,7 +294,7 @@
To get some sense of the shape of the likelihood surface, we can construct slices through each of the true parameter points.
These likelihood slices are shown in Fig.~\ref{fig:slices}.
<<slices-calc,eval=F,echo=F>>=
-require(pomp.devel)
+require(pompExamples)
require(Rmpi)
require(mpifarm)
@@ -312,7 +308,8 @@
estnames <- c("gam","lambda","g","delta","a","w")
par.range <- t(apply(true.pars[estnames,],1,function(x)c(0.5*min(x),1.5*max(x))))
-ncpus <- as.integer(Sys.getenv("PBS_NP"))
+##ncpus <- as.integer(Sys.getenv("PBS_NP"))
+ncpus <- 6
slices <- lapply(
budmoth.sim,
@@ -369,7 +366,7 @@
estnames=estnames
),
main={
- require(pomp.devel)
+ require(pompExamples)
po <- pomps[[dataset]]
save.seed <- .Random.seed
set.seed(seed)
Modified: pkg/pompExamples/inst/doc/budmoth-model.pdf
===================================================================
(Binary files differ)
Modified: pkg/pompExamples/inst/doc/pertussis-model.Rnw
===================================================================
--- pkg/pompExamples/inst/doc/pertussis-model.Rnw 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/inst/doc/pertussis-model.Rnw 2012-04-17 21:37:50 UTC (rev 666)
@@ -59,7 +59,7 @@
\begin{document}
<<options,echo=F,results=hide>>=
-require(pomp.devel)
+require(pompExamples)
require(xtable)
.glop <- options(keep.source=TRUE,width=60,continue=" ",prompt=" ")
on.exit(options(.glop))
@@ -305,7 +305,7 @@
Details on the implementation of this algorithm are given in \citet[][Box~1]{He2010}.
<<format-params,echo=F,eval=F>>=
-require(pomp.devel)
+require(pompExamples)
require(plyr)
data(pertussis.sim)
true.pars <- sapply(pertussis.sim,coef)
@@ -528,7 +528,7 @@
\end{document}
<<wavelets,eval=F,echo=F,fig=T,clean=T>>=
-require(pomp.devel)
+require(pompExamples)
require(Rwave)
data(pertussis.sim)
x <- lapply(pertussis.sim,as,"data.frame")
Modified: pkg/pompExamples/inst/doc/pertussis-model.pdf
===================================================================
(Binary files differ)
Modified: pkg/pompExamples/man/budmoth.Rd
===================================================================
--- pkg/pompExamples/man/budmoth.Rd 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/man/budmoth.Rd 2012-04-17 21:37:50 UTC (rev 666)
@@ -1,29 +1,22 @@
\name{budmoth}
-\alias{budmoth.eng}
\alias{budmoth.sim}
\docType{data}
\title{Larch budmoth model POMPs with real and simulated data.}
\description{
- \code{budmoth.eng} is a \code{pomp} object containing the larch budmoth model, budmoth density, parasitism rate, and food quality (needle-length) data from the Engadine valley of Switzerland.
- \code{budmoth.sim} is a list of \code{pomp} objects:
- each encodes the larch budmoth model and contains simulated data.
- Three parameter regimes are represented, with a number of replicates for each.
+ \code{budmoth.sim} is a list of \code{pomp} objects containing the larch budmoth model, budmoth density, parasitism rate, and food quality (needle-length) simulated data.
+ Four parameter regimes are represented.
}
\usage{
-data(budmoth.eng)
data(budmoth.sim)
}
\examples{
-data(budmoth.eng)
-plot(budmoth.eng)
-
data(budmoth.sim)
names(budmoth.sim)
## three regimes, high and low noise regimes for parasitism and tritrophic
-plot(budmoth.sim[["food.1"]])
-plot(budmoth.sim[["para.1"]])
-plot(budmoth.sim[["para.2"]])
-plot(budmoth.sim[["tri.1"]])
+plot(budmoth.sim[["food"]])
+plot(budmoth.sim[["para1"]])
+plot(budmoth.sim[["para2"]])
+plot(budmoth.sim[["tri"]])
}
\seealso{the vignettes}
\keyword{datasets}
Modified: pkg/pompExamples/tests/budmoth.R
===================================================================
--- pkg/pompExamples/tests/budmoth.R 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/tests/budmoth.R 2012-04-17 21:37:50 UTC (rev 666)
@@ -1,4 +1,4 @@
-require(pomp.devel)
+require(pompExamples)
data(budmoth.sim)
@@ -6,3 +6,12 @@
x <- lapply(budmoth.sim,as,"data.frame")
print(lapply(x,tail))
+
+y <- simulate(budmoth.sim$food,seed=3434996L,as.data.frame=TRUE)
+tail(y)
+
+z <- trajectory(budmoth.sim$tri,as.data.frame=TRUE)
+tail(z)
+
+pf <- pfilter(budmoth.sim$food,seed=34348885L,Np=1000)
+logLik(pf)
Modified: pkg/pompExamples/tests/pertussis.R
===================================================================
--- pkg/pompExamples/tests/pertussis.R 2012-04-17 20:53:41 UTC (rev 665)
+++ pkg/pompExamples/tests/pertussis.R 2012-04-17 21:37:50 UTC (rev 666)
@@ -1,8 +1,20 @@
-require(pomp.devel)
+require(pompExamples)
data(pertussis.sim)
names(pertussis.sim)
-x <- lapply(pertussis.sim,as,"data.frame")
+x <- lapply(pertussis.sim,as.data.frame)
print(lapply(x,tail))
+
+x <- simulate(pertussis.sim$full.big,seed=395885L,as.data.frame=TRUE)
+tail(x)
+
+y <- trajectory(pertussis.sim$SEIRS.small,as.data.frame=TRUE)
+tail(y)
+
+x <- simulate(pertussis.sim$full.small,seed=395885L,times=100,states=TRUE)[1:6,,1]
+coef(pertussis.sim$full.small,paste0(names(x),".0")) <- x/sum(x)
+
+pf <- pfilter(pertussis.sim$full.small,seed=3445886L,Np=1000)
+logLik(pf)
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