[Pomp-commits] r105 - pkg/data
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Apr 26 18:04:58 CEST 2009
Author: kingaa
Date: 2009-04-26 18:04:56 +0200 (Sun, 26 Apr 2009)
New Revision: 105
Added:
pkg/data/euler.sir.rda
pkg/data/ou2.rda
Removed:
pkg/data/euler.sir.R
pkg/data/ou2.R
Log:
It turns out not to work to use R files in the 'data' directory if these involve actual computations. It appears that, during the package check process, the shared-object library is loaded *after* the data files are read. Consequently, the simulations used to generate the pomp objects in 'ou2.R' and 'euler.sir.R' will not work. As a temporary fix, I have replaced these with binary files containing the objects. I do not yet have a satisfactory way of including the code used to generate these into the package yet.
Deleted: pkg/data/euler.sir.R
===================================================================
--- pkg/data/euler.sir.R 2009-04-24 20:58:10 UTC (rev 104)
+++ pkg/data/euler.sir.R 2009-04-26 16:04:56 UTC (rev 105)
@@ -1,54 +0,0 @@
-require(pomp)
-
-euler.sir <- simulate(
- pomp(
- times=seq(1/52,4,by=1/52),
- data=rbind(measles=numeric(52*4)),
- t0=0,
- tcovar=seq(0,25,by=1/52),
- covar=matrix(
- periodic.bspline.basis(seq(0,25,by=1/52),nbasis=3,period=1,degree=3),
- ncol=3,
- dimnames=list(NULL,paste("seas",1:3,sep=''))
- ),
- delta.t=1/52/20,
- statenames=c("S","I","R","cases","W","B","dW"),
- paramnames=c("gamma","mu","iota","beta1","beta.sd","pop","rho"),
- covarnames=c("seas1"),
- zeronames=c("cases"),
- comp.names=c("S","I","R"),
- step.fun="sir_euler_simulator",
- rprocess=euler.simulate,
- dens.fun="sir_euler_density",
- dprocess=euler.density,
- skeleton.vectorfield="sir_ODE",
- rmeasure="binom_rmeasure",
- dmeasure="binom_dmeasure",
- PACKAGE="pomp",
- initializer=function(params, t0, comp.names, ...){
- p <- exp(params)
- snames <- c(
- "S","I","R","cases","W","B",
- "SI","SD","IR","ID","RD","dW"
- )
- fracs <- p[paste(comp.names,"0",sep=".")]
- x0 <- numeric(length(snames))
- names(x0) <- snames
- x0[comp.names] <- round(p['pop']*fracs/sum(fracs))
- x0
- }
- ),
- params=log(
- c(
- gamma=26,mu=0.02,iota=0.01,
- beta1=1200,beta2=1800,beta3=600,
- beta.sd=1e-3,
- pop=2.1e6,
- rho=0.6,
- S.0=26/1200,I.0=0.001,R.0=1-0.001-26/1200
- )
- ),
- nsim=1,
- seed=329348545L
- )
-euler.sir <- euler.sir[[1]]
Added: pkg/data/euler.sir.rda
===================================================================
(Binary files differ)
Property changes on: pkg/data/euler.sir.rda
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: pkg/data/ou2.R
===================================================================
--- pkg/data/ou2.R 2009-04-24 20:58:10 UTC (rev 104)
+++ pkg/data/ou2.R 2009-04-26 16:04:56 UTC (rev 105)
@@ -1,77 +0,0 @@
-require(pomp)
-ou2 <- pomp(
- times=seq(1,100),
- data=rbind(
- y1=rep(0,100),
- y2=rep(0,100)
- ),
- t0=0,
- rprocess = function (xstart, times, params, paramnames, ...) {
- nvar <- nrow(xstart)
- npar <- nrow(params)
- nrep <- ncol(xstart)
- ntimes <- length(times)
- ## get indices of the various parameters in the 'params' matrix
- ## C uses zero-based indexing!
- parindex <- match(paramnames,rownames(params))-1
- array(
- .C("ou2_adv",
- X = double(nvar*nrep*ntimes),
- xstart = as.double(xstart),
- par = as.double(params),
- times = as.double(times),
- n = as.integer(c(nvar,npar,nrep,ntimes)),
- parindex = as.integer(parindex),
- DUP = FALSE,
- NAOK = TRUE,
- PACKAGE = "pomp"
- )$X,
- dim=c(nvar,nrep,ntimes),
- dimnames=list(rownames(xstart),NULL,NULL)
- )
- },
- dprocess = function (x, times, params, log, ...) {
- nvar <- nrow(x)
- npar <- nrow(params)
- nrep <- ncol(x)
- ntimes <- length(times)
- parindex <- match(paramnames,rownames(params))-1
- array(
- .C("ou2_pdf",
- d = double(nrep*(ntimes-1)),
- X = as.double(x),
- par = as.double(params),
- times = as.double(times),
- n = as.integer(c(nvar,npar,nrep,ntimes)),
- parindex = as.integer(parindex),
- give_log=as.integer(log),
- DUP = FALSE,
- NAOK = TRUE,
- PACKAGE = "pomp"
- )$d,
- dim=c(nrep,ntimes-1)
- )
- },
- dmeasure = "normal_dmeasure",
- rmeasure = "normal_rmeasure",
- obsnames = c("y1","y2"),
- paramnames = c(
- "alpha.1","alpha.2","alpha.3","alpha.4",
- "sigma.1","sigma.2","sigma.3",
- "tau"
- ),
- statenames = c("x1","x2")
- )
-
-ou2 <- simulate(
- ou2,
- params=c(
- alpha.1=0.9,alpha.2=0,alpha.3=0,alpha.4=0.99,
- sigma.1=1,sigma.2=0,sigma.3=2,
- tau=1,x1.0=50,x2.0=-50
- ),
- nsim=1,
- seed=377456545L
- )
-
-ou2 <- ou2[[1]]
Added: pkg/data/ou2.rda
===================================================================
(Binary files differ)
Property changes on: pkg/data/ou2.rda
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
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