[Pomp-commits] r577 - in pkg: . R data inst inst/data-R inst/doc man src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jan 7 17:05:13 CET 2012
Author: kingaa
Date: 2012-01-07 17:05:13 +0100 (Sat, 07 Jan 2012)
New Revision: 577
Modified:
pkg/DESCRIPTION
pkg/R/pomp.R
pkg/R/trajectory-pomp.R
pkg/data/blowflies.rda
pkg/data/dacca.rda
pkg/data/euler.sir.rda
pkg/data/gillespie.sir.rda
pkg/data/gompertz.rda
pkg/data/ou2.rda
pkg/data/ricker.rda
pkg/data/rw2.rda
pkg/data/verhulst.rda
pkg/inst/NEWS
pkg/inst/data-R/blowflies.R
pkg/inst/data-R/dacca.R
pkg/inst/data-R/euler.sir.R
pkg/inst/data-R/gillespie.sir.R
pkg/inst/data-R/gompertz.R
pkg/inst/data-R/ou2.R
pkg/inst/data-R/ricker.R
pkg/inst/data-R/rw2.R
pkg/inst/data-R/verhulst.R
pkg/inst/doc/advanced_topics_in_pomp.pdf
pkg/inst/doc/gompertz-multi-mif.rda
pkg/inst/doc/gompertz-trajmatch.rda
pkg/inst/doc/intro_to_pomp.Rnw
pkg/inst/doc/intro_to_pomp.pdf
pkg/inst/doc/manual.pdf
pkg/inst/doc/nlf-block-boot.rda
pkg/inst/doc/nlf-boot.rda
pkg/inst/doc/nlf-fit-from-truth.rda
pkg/inst/doc/nlf-fits.rda
pkg/inst/doc/nlf-lag-tests.rda
pkg/inst/doc/nlf-multi-short.rda
pkg/inst/doc/ricker-mif.rda
pkg/inst/doc/ricker-probe-match.rda
pkg/man/pomp-class.Rd
pkg/man/pomp.Rd
pkg/src/trajectory.c
Log:
- add 'skelmap.delta.t' as a slot in the basic 'pomp' object
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/DESCRIPTION 2012-01-07 16:05:13 UTC (rev 577)
@@ -2,7 +2,7 @@
Type: Package
Title: Statistical inference for partially observed Markov processes
Version: 0.40-1
-Date: 2012-01-06
+Date: 2012-01-08
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
Modified: pkg/R/pomp.R
===================================================================
--- pkg/R/pomp.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/R/pomp.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -11,6 +11,7 @@
rmeasure = 'pomp.fun',
skeleton.type = 'character',
skeleton = 'pomp.fun',
+ skelmap.delta.t = 'numeric',
initializer = 'function',
states = 'array',
params = 'numeric',
@@ -46,6 +47,7 @@
pomp.constructor <- function (data, times, t0, ..., rprocess, dprocess,
rmeasure, dmeasure, measurement.model,
skeleton = NULL, skeleton.type = c("map","vectorfield"),
+ skelmap.delta.t = 1,
initializer, covar, tcovar,
obsnames, statenames, paramnames, covarnames,
PACKAGE, parameter.transform, parameter.inv.transform) {
@@ -103,6 +105,9 @@
dmeasure <- function(y,x,t,params,log,covars,...)stop(sQuote("dmeasure")," not specified")
skeleton.type <- match.arg(skeleton.type)
+ skelmap.delta.t <- as.numeric(skelmap.delta.t)
+ if (skelmap.delta.t <= 0)
+ stop(sQuote("skelmap.delta.t")," must be positive")
if (is.null(skeleton)) {
skeleton <- pomp.fun(f=function(x,t,params,covars,...)stop(sQuote("skeleton")," not specified"))
@@ -262,8 +267,9 @@
dprocess = dprocess,
dmeasure = dmeasure,
rmeasure = rmeasure,
- skeleton.type = skeleton.type,
skeleton = skeleton,
+ skeleton.type = skeleton.type,
+ skelmap.delta.t=skelmap.delta.t,
data = data,
times = times,
t0 = t0,
@@ -360,25 +366,16 @@
)
}
-## for backward compatibility
-skeleton.jigger <- function (skeleton = NULL, skeleton.type) {
- list(fn=skeleton,type=skeleton.type)
-}
-
-
setMethod(
"pomp",
signature(data="data.frame"),
function (data, times, t0, ..., rprocess, dprocess,
rmeasure, dmeasure, measurement.model,
skeleton = NULL, skeleton.type = c("map","vectorfield"),
+ skelmap.delta.t = 1,
initializer, covar, tcovar,
obsnames, statenames, paramnames, covarnames,
PACKAGE, parameter.transform, parameter.inv.transform) {
- skel <- skeleton.jigger(
- skeleton=skeleton,
- skeleton.type=skeleton.type
- )
pomp.constructor(
data=data,
times=times,
@@ -388,8 +385,9 @@
rmeasure=rmeasure,
dmeasure=dmeasure,
measurement.model=measurement.model,
- skeleton=skel$fn,
- skeleton.type=skel$type,
+ skeleton=skeleton,
+ skeleton.type=skeleton.type,
+ skelmap.delta.t=skelmap.delta.t,
initializer=initializer,
covar=covar,
tcovar=tcovar,
@@ -411,13 +409,10 @@
function (data, times, t0, ..., rprocess, dprocess,
rmeasure, dmeasure, measurement.model,
skeleton = NULL, skeleton.type = c("map","vectorfield"),
+ skelmap.delta.t = 1,
initializer, covar, tcovar,
obsnames, statenames, paramnames, covarnames,
PACKAGE, parameter.transform, parameter.inv.transform) {
- skel <- skeleton.jigger(
- skeleton=skeleton,
- skeleton.type=skeleton.type
- )
pomp.constructor(
data=data,
times=times,
@@ -427,8 +422,9 @@
rmeasure=rmeasure,
dmeasure=dmeasure,
measurement.model=measurement.model,
- skeleton=skel$fn,
- skeleton.type=skel$type,
+ skeleton=skeleton,
+ skeleton.type=skeleton.type,
+ skelmap.delta.t=skelmap.delta.t,
initializer=initializer,
covar=covar,
tcovar=tcovar,
@@ -451,13 +447,10 @@
function (data, times, t0, ..., rprocess, dprocess,
rmeasure, dmeasure, measurement.model,
skeleton = NULL, skeleton.type = c("map","vectorfield"),
+ skelmap.delta.t = 1,
initializer, covar, tcovar,
obsnames, statenames, paramnames, covarnames,
PACKAGE, parameter.transform, parameter.inv.transform) {
- skel <- skeleton.jigger(
- skeleton=skeleton,
- skeleton.type=skeleton.type
- )
pomp.constructor(
data=matrix(data,nrow=1,ncol=length(data)),
times=times,
@@ -467,8 +460,9 @@
rmeasure=rmeasure,
dmeasure=dmeasure,
measurement.model=measurement.model,
- skeleton=skel$fn,
- skeleton.type=skel$type,
+ skeleton=skeleton,
+ skeleton.type=skeleton.type,
+ skelmap.delta.t=skelmap.delta.t,
initializer=initializer,
covar=covar,
tcovar=tcovar,
@@ -489,7 +483,7 @@
signature(data="pomp"),
function (data, times, t0, ..., rprocess, dprocess,
rmeasure, dmeasure, measurement.model,
- skeleton, skeleton.type,
+ skeleton, skeleton.type, skelmap.delta.t,
initializer, covar, tcovar,
obsnames, statenames, paramnames, covarnames,
PACKAGE, parameter.transform, parameter.inv.transform) {
@@ -523,6 +517,7 @@
if (missing(PACKAGE)) PACKAGE <- data at PACKAGE
if (missing(skeleton.type)) skeleton.type <- data at skeleton.type
if (missing(skeleton)) skeleton <- data at skeleton
+ if (missing(skelmap.delta.t)) skelmap.delta.t <- data at skelmap.delta.t
if (missing(parameter.transform)) {
if (missing(parameter.inv.transform)) {
@@ -558,6 +553,7 @@
dmeasure=dmeasure,
skeleton=skeleton,
skeleton.type=skeleton.type,
+ skelmap.delta.t=skelmap.delta.t,
initializer=initializer,
covar=covar,
tcovar=tcovar,
@@ -574,4 +570,3 @@
)
}
)
-
Modified: pkg/R/trajectory-pomp.R
===================================================================
--- pkg/R/trajectory-pomp.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/R/trajectory-pomp.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -66,12 +66,7 @@
if (type=="map") {
- if ("skelmap.delta.t"%in%names(object at userdata))
- dt <- as.numeric(object at userdata$skelmap.delta.t)
- else
- dt <- 1
-
- x <- .Call(iterate_map,object,times,t0,x0,params,dt,znames)
+ x <- .Call(iterate_map,object,times,t0,x0,params,znames)
} else if (type=="vectorfield") {
Modified: pkg/data/blowflies.rda
===================================================================
(Binary files differ)
Modified: pkg/data/dacca.rda
===================================================================
(Binary files differ)
Modified: pkg/data/euler.sir.rda
===================================================================
(Binary files differ)
Modified: pkg/data/gillespie.sir.rda
===================================================================
(Binary files differ)
Modified: pkg/data/gompertz.rda
===================================================================
(Binary files differ)
Modified: pkg/data/ou2.rda
===================================================================
(Binary files differ)
Modified: pkg/data/ricker.rda
===================================================================
(Binary files differ)
Modified: pkg/data/rw2.rda
===================================================================
(Binary files differ)
Modified: pkg/data/verhulst.rda
===================================================================
(Binary files differ)
Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/NEWS 2012-01-07 16:05:13 UTC (rev 577)
@@ -2,6 +2,9 @@
0.40-1
o It is now possible for discrete-time determistic skeletons to have a general step-size.
Before, the stepsize was always forced to be 1.
+ The new argument 'skelmap.delta.t' in 'pomp' (default value 1) sets this step-size.
+ NB: in implementing this feature, a new slot has been added to the basic 'pomp' class.
+ 'pomp' objects created with versions <0.40-1 will not therefore work with this version and must be re-created.
o The deterministic skeleton trajectory functions now look for variables named in 'zeronames' and treat these variables as accumulators.
This brings the behavior of the deterministic skeleton functions into line with 'rprocess'.
Modified: pkg/inst/data-R/blowflies.R
===================================================================
--- pkg/inst/data-R/blowflies.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/blowflies.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -118,4 +118,4 @@
}
-save(blowflies1,blowflies2,file="blowflies.rda")
+save(blowflies1,blowflies2,file="blowflies.rda",compress=TRUE)
Modified: pkg/inst/data-R/dacca.R
===================================================================
--- pkg/inst/data-R/dacca.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/dacca.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -188,4 +188,4 @@
}
coef(dacca) <- dacca.transform(mle,dir="forward")
-save(dacca,file="dacca.rda")
+save(dacca,file="dacca.rda",compress=TRUE)
Modified: pkg/inst/data-R/euler.sir.R
===================================================================
--- pkg/inst/data-R/euler.sir.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/euler.sir.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -62,4 +62,4 @@
simulate(po,nsim=1,seed=329348545L) -> euler.sir
-save(euler.sir,file="euler.sir.rda")
+save(euler.sir,file="euler.sir.rda",compress=TRUE)
Modified: pkg/inst/data-R/gillespie.sir.R
===================================================================
--- pkg/inst/data-R/gillespie.sir.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/gillespie.sir.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -88,4 +88,4 @@
seed=1165270654L
) -> gillespie.sir
-save(gillespie.sir,file="gillespie.sir.rda")
+save(gillespie.sir,file="gillespie.sir.rda",compress=TRUE)
Modified: pkg/inst/data-R/gompertz.R
===================================================================
--- pkg/inst/data-R/gompertz.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/gompertz.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -30,4 +30,4 @@
simulate(po,nsim=1,seed=299438676L) -> gompertz
-save(gompertz,file="gompertz.rda")
+save(gompertz,file="gompertz.rda",compress=TRUE)
Modified: pkg/inst/data-R/ou2.R
===================================================================
--- pkg/inst/data-R/ou2.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/ou2.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -36,4 +36,4 @@
ou2 <- window(ou2,end=100)
timezero(ou2) <- 0
-save(ou2,file="ou2.rda")
+save(ou2,file="ou2.rda",compress=TRUE)
Modified: pkg/inst/data-R/ricker.R
===================================================================
--- pkg/inst/data-R/ricker.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/ricker.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -28,4 +28,4 @@
seed=73691676L
) -> ricker
-save(ricker,file="ricker.rda")
+save(ricker,file="ricker.rda",compress=TRUE)
Modified: pkg/inst/data-R/rw2.R
===================================================================
--- pkg/inst/data-R/rw2.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/rw2.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -39,4 +39,4 @@
seed=738377475L
) -> rw2
-save(rw2,file="rw2.rda")
+save(rw2,file="rw2.rda",compress=TRUE)
Modified: pkg/inst/data-R/verhulst.R
===================================================================
--- pkg/inst/data-R/verhulst.R 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/data-R/verhulst.R 2012-01-07 16:05:13 UTC (rev 577)
@@ -56,4 +56,4 @@
seed=73658676L
) -> verhulst
-save(verhulst,file="verhulst.rda")
+save(verhulst,file="verhulst.rda",compress=TRUE)
Modified: pkg/inst/doc/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/gompertz-multi-mif.rda
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/gompertz-trajmatch.rda
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/intro_to_pomp.Rnw
===================================================================
--- pkg/inst/doc/intro_to_pomp.Rnw 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/doc/intro_to_pomp.Rnw 2012-01-07 16:05:13 UTC (rev 577)
@@ -716,7 +716,8 @@
loglik.mif.est,loglik.true.est,
loglik.mif.se,loglik.true.se,
etime,
- file=binary.file
+ file=binary.file,
+ compress=TRUE
)
}
rbind(
@@ -839,7 +840,7 @@
load(binary.file)
} else {
<<gompertz-trajmatch-calc>>
- save(new.gompertz,tm,file=binary.file)
+ save(new.gompertz,tm,file=binary.file,compress=TRUE)
}
@
@@ -1013,7 +1014,7 @@
load(binary.file)
} else {
<<ricker-probe-match-calc>>
- save(pm,file=binary.file)
+ save(pm,file=binary.file,compress=TRUE)
}
@
@@ -1040,7 +1041,7 @@
load(binary.file)
} else {
<<ricker-mif-calc>>
- save(mf,file=binary.file)
+ save(mf,file=binary.file,compress=TRUE)
}
@
The following code compares parameters, likelihoods, and synthetic likelihoods (based on the probes in \code{plist}) at each of
@@ -1133,7 +1134,7 @@
} else {
<<nlf-gompertz-starts>>
<<nlf-gompertz-fits>>
- save(starts,out,fits,file=binary.file)
+ save(starts,out,fits,file=binary.file,compress=TRUE)
}
@
The results in this case are very encouraging,
@@ -1211,7 +1212,7 @@
<<nlf-my-pomp>>
<<nlf-lag-test-log.r>>
<<nlf-lag-test-log.K>>
- save(theta,lags,log.r.vals,log.K.vals,fvals,fvals2,file=binary.file)
+ save(theta,lags,log.r.vals,log.K.vals,fvals,fvals2,file=binary.file,compress=TRUE)
}
@
@@ -1281,7 +1282,7 @@
load(binary.file)
} else {
<<nlf-multi-short>>
- save(lags,nreps,ndata,fvals,file=binary.file)
+ save(lags,nreps,ndata,fvals,file=binary.file,compress=TRUE)
}
@
The last line above expresses the objective function as the geometric mean (quasi)likelihood per data point.
@@ -1308,7 +1309,7 @@
load(binary.file)
} else {
<<nlf-fit-from-truth>>
- save(true.fit,file=binary.file)
+ save(true.fit,file=binary.file,compress=TRUE)
}
@
From \verb+true.fit$params+ and \verb+true.fit$se+ we get the estimates ($\pm$ 1 standard error)
@@ -1359,7 +1360,7 @@
load(binary.file)
} else {
<<nlf-boot>>
- save(pars,file=binary.file)
+ save(pars,file=binary.file,compress=TRUE)
}
@
<<>>=
@@ -1413,7 +1414,7 @@
load(binary.file)
} else {
<<nlf-block-boot>>
- save(pars,file=binary.file)
+ save(pars,file=binary.file,compress=TRUE)
}
@
Modified: pkg/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/manual.pdf
===================================================================
--- pkg/inst/doc/manual.pdf 2012-01-05 20:06:21 UTC (rev 576)
+++ pkg/inst/doc/manual.pdf 2012-01-07 16:05:13 UTC (rev 577)
@@ -213,15 +213,16 @@
>>
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[TRUNCATED]
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svnlook diff /svnroot/pomp -r 577
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