[Pomp-commits] r641 - in pkg: . data inst inst/data-R inst/doc src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 4 14:20:13 CEST 2012
Author: kingaa
Date: 2012-04-04 14:20:13 +0200 (Wed, 04 Apr 2012)
New Revision: 641
Added:
pkg/tests/bbs.R
pkg/tests/bbs.Rout.save
Modified:
pkg/.Rbuildignore
pkg/DESCRIPTION
pkg/data/bbs.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/sir.R
pkg/inst/doc/Makefile
pkg/inst/doc/manual.pdf
pkg/src/lpa.c
Log:
- bug fix
- reconfigure vignette Makefile to do compression
- do not re-build vignettes
Modified: pkg/.Rbuildignore
===================================================================
--- pkg/.Rbuildignore 2012-04-01 19:42:33 UTC (rev 640)
+++ pkg/.Rbuildignore 2012-04-04 12:20:13 UTC (rev 641)
@@ -1,3 +1,5 @@
+inst/doc/Makefile
+inst/doc/(.+?)\.rda$
inst/doc/(.+?)\.bst$
inst/doc/(.+?)\.R$
inst/doc/(.+?)\.png$
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-04-01 19:42:33 UTC (rev 640)
+++ pkg/DESCRIPTION 2012-04-04 12:20:13 UTC (rev 641)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.41-1
-Date: 2012-04-01
+Version: 0.41-2
+Date: 2012-04-04
Revision: $Rev$
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>
@@ -12,6 +12,7 @@
License: GPL(>= 2)
LazyLoad: true
LazyData: false
+BuildVignettes: no
Collate: aaa.R version.R eulermultinom.R plugins.R
parmat.R slice-design.R profile-design.R sobol.R bsplines.R sannbox.R
pomp-fun.R pomp.R pomp-methods.R rmeasure-pomp.R rprocess-pomp.R init-state-pomp.R
Modified: pkg/data/bbs.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 2012-04-01 19:42:33 UTC (rev 640)
+++ pkg/inst/NEWS 2012-04-04 12:20:13 UTC (rev 641)
@@ -1,4 +1,7 @@
NEWS
+0.41-2
+ o Fix bug in 'bbs' example.
+
0.41-1
o New arguments in 'mif', 'nlf', 'bsmc', 'pmcmc', 'probe-match', and 'traj-match' allow the estimation to be done on a transformed parameter space.
When 'transform=TRUE' in these commands ('transform.params=TRUE' for 'nlf'), estimation is performed on the transformed parameter space.
Modified: pkg/inst/data-R/sir.R
===================================================================
--- pkg/inst/data-R/sir.R 2012-04-01 19:42:33 UTC (rev 640)
+++ pkg/inst/data-R/sir.R 2012-04-04 12:20:13 UTC (rev 641)
@@ -148,18 +148,13 @@
statenames=c("S","I","R","cases","W"),
paramnames=c(
"gamma","mu","iota",
- "beta1","beta.sd","pop","rho",
- "nbasis","degree","period"
+ "log.beta1","beta.sd","pop","rho",
+ "nbasis","degree","period",
+ "S.0","I.0","R.0"
),
zeronames=c("cases"),
comp.names=c("S","I","R"),
ic.names=c("S.0","I.0","R.0"),
- log.transformed=c(
- "gamma","mu","iota","sigma",
- "beta1","beta.sd",
- "S.0","I.0","R.0"
- ),
- logit.transformed="rho",
parameter.transform="_sir_par_trans",
parameter.inv.transform="_sir_par_untrans",
initializer=function(params, t0, comp.names, ic.names, ...) {
@@ -175,7 +170,7 @@
coef(po) <- c(
gamma=1/3,mu=0.0,iota=0.0,
nbasis=1,degree=0,period=1,
- beta1=1.4,
+ log.beta1=0.33,
beta.sd=0,
pop=1400,
rho=0.9,sigma=3.6,
@@ -184,3 +179,4 @@
bbs <- po
save(bbs,file="bbs.rda",compress="xz")
+
Modified: pkg/inst/doc/Makefile
===================================================================
--- pkg/inst/doc/Makefile 2012-04-01 19:42:33 UTC (rev 640)
+++ pkg/inst/doc/Makefile 2012-04-04 12:20:13 UTC (rev 641)
@@ -8,9 +8,9 @@
default: vignettes compress clean
-compress: export R_QPDF=qpdf
-compress: export R_GSCMD=gs
-compress: export GS_QUALITY=ebook
+compress: R_QPDF=qpdf
+compress: R_GSCMD=gs
+compress: GS_QUALITY=ebook
compress: advanced_topics_in_pomp.pdf intro_to_pomp.pdf manual.pdf
for i in $^; do \
Modified: pkg/inst/doc/manual.pdf
===================================================================
--- pkg/inst/doc/manual.pdf 2012-04-01 19:42:33 UTC (rev 640)
+++ pkg/inst/doc/manual.pdf 2012-04-04 12:20:13 UTC (rev 641)
@@ -1,2269 +1,2834 @@
%PDF-1.5
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[TRUNCATED]
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