[Pomp-commits] r576 - in pkg: . data inst inst/data-R inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jan 5 21:06:23 CET 2012
Author: kingaa
Date: 2012-01-05 21:06:21 +0100 (Thu, 05 Jan 2012)
New Revision: 576
Modified:
pkg/DESCRIPTION
pkg/data/LondonYorke.rda
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/euler.sir.R
pkg/inst/doc/advanced_topics_in_pomp.pdf
pkg/inst/doc/intro_to_pomp.pdf
pkg/inst/doc/manual.pdf
pkg/man/trajectory-pomp.Rd
Log:
- update the data files and vignettes
- the 'euler.sir' data()-loadable example now uses 'zeronames' for the deterministic skeleton
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-01-05 19:34:16 UTC (rev 575)
+++ pkg/DESCRIPTION 2012-01-05 20:06:21 UTC (rev 576)
@@ -2,7 +2,7 @@
Type: Package
Title: Statistical inference for partially observed Markov processes
Version: 0.40-1
-Date: 2011-12-24
+Date: 2012-01-06
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/data/LondonYorke.rda
===================================================================
(Binary files differ)
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 19:34:16 UTC (rev 575)
+++ pkg/inst/NEWS 2012-01-05 20:06:21 UTC (rev 576)
@@ -1,4 +1,13 @@
NEWS
+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.
+
+ 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'.
+
+ o Include the user manual PDF among the vignettes.
+
0.39-5
o Bug fix in 'bsmc' that arises when the state space is 1-D.
Thanks to Arnab Bhattacharya for finding the bug.
Modified: pkg/inst/data-R/euler.sir.R
===================================================================
--- pkg/inst/data-R/euler.sir.R 2012-01-05 19:34:16 UTC (rev 575)
+++ pkg/inst/data-R/euler.sir.R 2012-01-05 20:06:21 UTC (rev 576)
@@ -47,10 +47,7 @@
x0 <- numeric(length(snames))
names(x0) <- snames
x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
- ## since 'cases' is in 'zeronames' above, the IC for this variable
- ## will only matter in trajectory computations
- ## In trajectory computations, however, 'cases' will be roughly the weekly number of new cases
- x0["cases"] <- x0["I"]*exp(params["gamma"])/52
+ x0["cases"] <- 0
x0
}
)
Modified: pkg/inst/doc/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)
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 19:34:16 UTC (rev 575)
+++ pkg/inst/doc/manual.pdf 2012-01-05 20:06:21 UTC (rev 576)
@@ -10033,8 +10033,8 @@
>> endobj
1549 0 obj <<
/Author()/Title()/Subject()/Creator(LaTeX with hyperref package)/Producer(pdfTeX-1.40.10)/Keywords()
-/CreationDate (D:20120105141829-05'00')
-/ModDate (D:20120105141829-05'00')
+/CreationDate (D:20120105144954-05'00')
+/ModDate (D:20120105144954-05'00')
/Trapped /False
/PTEX.Fullbanner (This is pdfTeX, Version 3.1415926-1.40.10-2.2 (TeX Live 2009/Debian) kpathsea version 5.0.0)
>> endobj
@@ -11594,7 +11594,7 @@
<< /Size 1550
/Root 1548 0 R
/Info 1549 0 R
-/ID [<E0D5A9855B19A23A0296996F3E23587F> <E0D5A9855B19A23A0296996F3E23587F>] >>
+/ID [<46953D8E93BA6B63486BF5E73BB1A4AF> <46953D8E93BA6B63486BF5E73BB1A4AF>] >>
startxref
452556
%%EOF
Modified: pkg/man/trajectory-pomp.Rd
===================================================================
--- pkg/man/trajectory-pomp.Rd 2012-01-05 19:34:16 UTC (rev 575)
+++ pkg/man/trajectory-pomp.Rd 2012-01-05 20:06:21 UTC (rev 576)
@@ -39,7 +39,9 @@
When the skeleton is a vectorfield, \code{trajectory} integrates it using \code{\link[deSolve]{ode}}.
- Unresolved issue: What is the behavior if \code{type="map"} and \code{times} are non-integral?
+ When the skeleton is a map, \code{trajectory} iterates it.
+ By default, time is advanced 1 unit per iteration.
+ The user can change this behavior by specifying the desired timestep using the argument \code{skelmap.delta.t} in the construction of the \code{pomp} object.
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
\examples{
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