[Pomp-commits] r310 - in pkg/pomp: . inst inst/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Aug 30 18:17:49 CEST 2010
Author: kingaa
Date: 2010-08-30 18:17:49 +0200 (Mon, 30 Aug 2010)
New Revision: 310
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/inst/ChangeLog
pkg/pomp/inst/doc/advanced_topics_in_pomp.pdf
pkg/pomp/inst/doc/intro_to_pomp.pdf
Log:
- update the vignettes
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2010-08-26 21:59:10 UTC (rev 309)
+++ pkg/pomp/DESCRIPTION 2010-08-30 16:17:49 UTC (rev 310)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.32-4
-Date: 2010-08-26
+Version: 0.32-5
+Date: 2010-08-30
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>
Modified: pkg/pomp/inst/ChangeLog
===================================================================
--- pkg/pomp/inst/ChangeLog 2010-08-26 21:59:10 UTC (rev 309)
+++ pkg/pomp/inst/ChangeLog 2010-08-30 16:17:49 UTC (rev 310)
@@ -1,1124 +1,5 @@
-2010-08-24 kingaa
+2010-08-26 kingaa
- * [r304] inst/ChangeLog: - update changelog
- * [r303] DESCRIPTION, data/dacca.rda, data/euler.sir.rda,
- data/gillespie.sir.rda, data/ou2.rda, data/ricker.rda,
- inst/ChangeLog, inst/data-R/ricker.R,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf, man/ricker.Rd, src/ricker.c,
- tests/ricker.R, tests/ricker.Rout.save: - include a
- Poisson-Ricker example
- - update the vignettes
- * [r302] R/trajectory-pomp.R: - modify the algorithm in the case of
- a discrete-time map so that the assumption that 'times' are
- consecutive is no longer implicitly made
- * [r301] R/euler.R, R/plugins.R, R/pomp-fun.R, R/pomp.R,
- man/plugins.Rd: - modify 'pomp.fun' so that the prototype is
- passed as an unevaluated call rather than as a character string
- (thus avoiding issues with escaped characters"
- - modify the plug-in 'discrete.time.sim' so that delta.t=1 is
- enforced
- * [r299] inst/doc/pomp.bib: - update bibliography
+ * [r309] ., DESCRIPTION, NAMESPACE, R, data, inst, man, src, tests:
+ - move everything in pkg/ to pkg/pomp
-2010-08-23 kingaa
-
- * [r297] R/basic-probes.R: - another minor bug fix
- * [r296] R/basic-probes.R: - bug fix in 'probe.acf'
- * [r295] DESCRIPTION:
- * [r293] inst/ChangeLog, inst/NEWS: - update NEWS and ChangeLog
-
-2010-08-19 kingaa
-
- * [r291] DESCRIPTION, NAMESPACE, R/bsmc.R, tests/ou2-probe-match.R,
- tests/ou2-probe-match.Rout.save: - add in tests for probe
- matching
-
-2010-08-04 kingaa
-
- * [r290] DESCRIPTION: - use Dan's full name
-
-2010-08-03 kingaa
-
- * [r289] DESCRIPTION, NAMESPACE, R/basic-probes.R, R/probe-match.R,
- R/probe.R, R/spect-match.R, R/spect.R, man/basic-probes.Rd,
- man/probe.Rd, man/probed-pomp-class.Rd,
- man/probed-pomp-methods.Rd, man/spect-pomp-class.Rd,
- man/spect.Rd: - add in the probe- and spectral-matching codes
- (thanks to Dan Reuman and Bruce Kendall)
- * [r288] R/nlf.R: - bug fix
-
-2010-07-19 kingaa
-
- * [r287] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: - update
- the vignette
- * [r286] DESCRIPTION, NAMESPACE, R/pomp-methods.R, inst/ChangeLog,
- inst/NEWS, man/pomp-methods.Rd, tests/rw2.R, tests/rw2.Rout.save,
- tests/sir.R, tests/sir.Rout.save: - added new 'window',
- 'timezero', and 'timezero<-' methods for 'pomp' objects
-
-2010-07-06 kingaa
-
- * [r285] R/pomp-methods.R: - error checking in 'data.array'
- * [r284] R/pfilter.R: - minor
- * [r283] R/pmcmc.R: - unname before 'coef<-' to avoid warning
-
-2010-07-02 kingaa
-
- * [r282] R/mif.R, R/pomp-methods.R, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf, inst/doc/pomp.bib,
- man/pomp-methods.Rd, man/simulate-pomp.Rd, tests/rw2.R,
- tests/rw2.Rout.save: - add warning in 'coef<-' where parameter
- values might unintentionally be mismatched
- - redefine some of the generics using standardGeneric()
- - change 'include.t0' argument in 'time<-()' to 't0' to match
- 'time()'
- - improve documentation of 'simulate' method slightly
- - add Bhadra article to pomp.bib
-
-2010-06-30 kingaa
-
- * [r281] DESCRIPTION, R/traj-match.R, R/trajmatch.R,
- man/mif-class.Rd, man/traj-match.Rd, man/trajmatch.Rd: - minor
- rearrangements of files
- - fix typo
- * [r279] inst/doc/pomp.bib: - fix Andrieu et al. entry
- * [r278] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf: - vignettes and Changelog up to date
- * [r275] DESCRIPTION, NAMESPACE, R/compare.pmcmc.R,
- R/pmcmc-methods.R, R/pmcmc.R, R/simulate-pomp.R, inst/NEWS,
- inst/doc/pomp.bib, man/pmcmc-class.Rd, man/pmcmc-methods.Rd,
- man/pmcmc.Rd, tests/ou2-pmcmc.R: - add PMCMC method from Andrieu
- et al. (2010)
- - add error check on 'nsim' in 'simulate' method for 'pomp'
-
-2010-06-23 kingaa
-
- * [r272] inst/ChangeLog, inst/NEWS, inst/doc/pomp.bib: - add NEWS
- entry on the Liu & West implementation
- - update reference database
- * [r271] DESCRIPTION, NAMESPACE: - update the NAMESPACE and
- DESCRIPTION files
- * [r270] R/bsmc.R, man/bsmc.Rd, tests/ou2-bsmc.R,
- tests/ou2-bsmc.Rout.save: - add functionality for the Bayesian
- sequential Monte Carlo algorithm of Liu & West, implemented as
- 'bsmc'.
-
-2010-06-22 kingaa
-
- * [r269] R/bsplines.R: - simplify
-
-2010-06-14 kingaa
-
- * [r268] DESCRIPTION, data/dacca.rda, data/euler.sir.rda,
- data/gillespie.sir.rda, data/ou2.rda, data/rw2.rda,
- data/verhulst.rda, inst/ChangeLog, inst/NEWS,
- inst/data-R/dacca.R, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf, man/dacca.Rd, src/cholmodel.c: The
- cholera transmission model from King, A. A., Ionides, E. L.,
- Pascual, M., and Bouma, M. J. (2008) Inapparent infections and
- cholera dynamics, Nature 454:877--880 together with data from the
- Dacca district of historic Bengal are now included.
- Data provided courtesy of Menno J. Bouma.
-
-2010-05-31 kingaa
-
- * [r267] DESCRIPTION, NAMESPACE, R/nlf.R, R/trajectory-pomp.R: -
- move deSolve, subplex from Depends to Import
- * [r266] DESCRIPTION, NAMESPACE, R/aaa.R, R/dmeasure-pomp.R,
- R/dprocess-pomp.R, R/init.state-pomp.R, R/mif-class.R,
- R/mif-methods.R, R/mif.R, R/particles-mif.R, R/pfilter.R,
- R/pomp-fun.R, R/pomp-methods.R, R/pomp.R, R/rmeasure-pomp.R,
- R/rprocess-pomp.R, R/skeleton-pomp.R, R/trajectory-pomp.R: - use
- the Collate option in package DESCRIPTION
-
-2010-05-26 kingaa
-
- * [r264] DESCRIPTION, inst/ChangeLog, inst/doc/ecology.bst,
- inst/doc/fullnat.bst, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf, src/dmeasure.c, src/pomp_fun.c,
- src/rmeasure.c: - slight improvements to dmeasure & rmeasure
- methods
- - change bibliography style in vignettes
-
-2010-05-23 kingaa
-
- * [r263] man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd: - trying
- to get Carles' name right
- * [r257] DESCRIPTION:
-
-2010-05-22 kingaa
-
- * [r256] DESCRIPTION:
-
-2010-05-21 kingaa
-
- * [r255] inst/ChangeLog:
- * [r254] inst/NEWS: - documenting changes
- * [r253] inst/CHANGES_0.29-1.txt: - word wrap
- * [r252] inst/CHANGES_0.29-1.txt: - describe the changes in version
- 0.29-1
-
-2010-05-20 kingaa
-
- * [r251] inst/ChangeLog:
- * [r250] R/aaa.R, R/pomp.R, data/euler.sir.rda,
- data/gillespie.sir.rda, data/ou2.rda, data/rw2.rda,
- data/verhulst.rda, inst/ChangeLog, inst/data-R/euler.sir.R,
- inst/data-R/gillespie.sir.R, inst/data-R/ou2.R,
- inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
- inst/doc/ou2-first-mif.rda, inst/doc/ou2-trajmatch.rda,
- inst/examples/sir.R, inst/examples/sir.c, inst/include/pomp.h,
- man/pomp-class.Rd, man/pomp.Rd, src/dmeasure.c, src/ou2.c,
- src/pomp.h, src/rmeasure.c, src/sir.c, tests/sir.R,
- tests/sir.Rout.save: - add 'obsnames' slot to the 'pomp' class
- - change 'dmeasure' and 'rmeasure' functions to make use of
- 'obsnames' in the case of user-supplied native routines
- - modify prototypes of user-supplied native routines for
- measurement models in keeping with this
- - modify source code for SIR and OU2 models
- * [r249] src/pomp_internal.h: - initialize arrays with NA
-
-2010-05-19 kingaa
-
- * [r248] inst/ChangeLog:
- * [r247] DESCRIPTION, inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf, inst/examples/euler_sir.R,
- inst/examples/logistic.R, inst/examples/rw2.R,
- inst/examples/sir.R, inst/examples/sir.c, src/sir.c: - improve
- the vignettes
- - improve the examples
-
-2010-05-18 kingaa
-
- * [r246] NAMESPACE, R/plugins.R, data/euler.sir.rda,
- data/gillespie.sir.rda, data/ou2.rda, data/rw2.rda,
- data/verhulst.rda, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
- inst/doc/ou2-first-mif.rda, inst/doc/ou2-trajmatch.rda,
- man/plugins.Rd: - add the rprocess plugin 'discrete.time.sim',
- which is essentially identical to 'euler.sim'
-
-2010-05-17 kingaa
-
- * [r245] inst/examples/euler_sir.R: - slight change to euler_sir
- example
- * [r243] DESCRIPTION, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf: - cosmetology
- * [r242] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: -
- minor edits to intro vignette
- * [r241] man/LondonYorke.Rd: - cosmetology
- * [r240] man/trajectory-pomp.Rd: - index by the new generic
- 'trajectory'
- * [r239] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
- inst/doc/ou2-trajmatch.rda, inst/doc/pomp.bib: - add section on
- trajectory matching to the intro vignette
-
-2010-05-16 kingaa
-
- * [r237] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: -
- some minor additions to the intro vignette
-
-2010-05-11 kingaa
-
- * [r236] man/eulermultinom.Rd, man/plugins.Rd, man/pomp.Rd: -
- update documentation
- * [r235] DESCRIPTION: - added Helen Wearing as an author for her
- work with the stochastic simulation algorithms
-
-2010-05-10 kingaa
-
- * [r234] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf: - updated vignettes
- * [r233] man/euler.Rd: - the old plugins are deprecated: move their
- man pages to 'internal'
- * [r232] inst/doc/ou2-first-mif.rda: - binary file with saved
- results
- * [r231] man/euler.sir.Rd, man/sir.Rd: - tidying up
- * [r230] R/euler.R: - preserve backward compatibility
- * [r229] inst/ChangeLog:
- * [r228] data/euler.sir.rda, inst/ChangeLog,
- inst/data-R/euler.sir.R, inst/doc/Makefile,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/ecology.bst,
- inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
- inst/doc/pomp.bib: - improve the "intro_to_pomp" vignette
- * [r227] tests/gillespie.R, tests/gillespie.Rout.save: - tests for
- new gillespie simulator
- * [r226] DESCRIPTION: - new version
- * [r225] NAMESPACE: - new functions exported
- * [r224] inst/include/pomp.h, man/euler.sir.Rd, man/ou2.Rd,
- man/pomp-package.Rd, man/pomp.Rd, man/verhulst.Rd,
- tests/logistic.R, tests/logistic.Rout.save, tests/ou2-kalman.R,
- tests/ou2-kalman.Rout.save, tests/ou2-mif.R,
- tests/ou2-mif.Rout.save, tests/ou2-nlf.R,
- tests/ou2-nlf.Rout.save, tests/ou2-trajmatch.R,
- tests/ou2-trajmatch.Rout.save, tests/pfilter.Rout.save,
- tests/sir.R, tests/sir.Rout.save: - tests and man pages
- corresponding to last changes
- * [r223] R/euler.R, data/euler.sir.rda, data/gillespie.sir.rda,
- data/ou2.rda, data/rw2.rda, data/verhulst.rda, inst/NEWS,
- inst/data-R/euler.sir.R, inst/data-R/gillespie.sir.R,
- inst/data-R/ou2.R, inst/data-R/rw2.R, inst/data-R/verhulst.R,
- inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf, inst/examples/euler_sir.R,
- inst/examples/euler_sir.c, inst/examples/logistic.R,
- inst/examples/rw2.R, inst/examples/sir.c, src/SSA.f,
- src/SSA_wrapper.c, src/euler.c, src/euler_sir.c,
- src/euler_sir_density.c, src/pomp.h, src/sir.c: - encoding models
- is now much easier through the use of "plugin" modules.
- - old plugins are now deprecated.
- - several example pomps are now loadable via the data() command.
- - new gillespie simulator (most of the work due to Helen Wearing)
- * [r222] R/trajmatch.R: - purely cosmetic
- * [r221] R/euler.R, man/euler.Rd: - old euler plugins
- * [r220] R/euler.R, R/plugins.R, man/euler.Rd, man/plugins.Rd: -
- rename these files
-
-2010-05-06 kingaa
-
- * [r219] DESCRIPTION, R/aaa.R, R/pfilter.R, R/pomp-fun.R,
- R/pomp-methods.R, R/pomp.R, data/euler.sir.rda, data/ou2.rda,
- data/rw2.rda, data/verhulst.rda, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
- man/pfilter.Rd, man/pomp-class.Rd, man/pomp-fun.Rd,
- tests/rw2.Rout.save, tests/sir.Rout.save: - add a new slot,
- 'call', to the pomp class
- - improve the way that pomps are printed and 'show'n
- - streamline pomp construction using pomp.fun
- - save Np and tol in the list returned by 'pfilter'
-
-2010-04-29 kingaa
-
- * [r218] tests/pfilter.R, tests/pfilter.Rout.save: - tests for
- 'pfilter'
- * [r217] inst/ChangeLog: - version 0.28-4
- * [r216] DESCRIPTION, R/pfilter.R, R/trajmatch.R,
- data/euler.sir.rda, data/ou2.rda, data/rw2.rda,
- data/verhulst.rda, inst/ChangeLog, inst/data-R/ou2.R,
- man/trajmatch.Rd, src/skeleton.c, tests/examples.R,
- tests/logistic.Rout.save, tests/ou2-forecast.Rout.save,
- tests/ou2-kalman.Rout.save, tests/ou2-nlf.Rout.save,
- tests/ou2-simulate.Rout.save, tests/ou2-trajmatch.Rout.save,
- tests/rw2.Rout.save, tests/sir.Rout.save: - change the
- trajectory-matching algorithm so that it depends on 'trajectory':
- it is no longer to set the process noise to zero manually in
- order to use this method
- - clean up error handling in 'pfilter'
- - update .Rout.save files in 'tests'
- - make 'skeleton' sensitive to variable names
- * [r215] R/compare.mif.R, R/mif.R, R/nlf-funcs.R, R/nlf-guts.R,
- R/nlf.R, R/pfilter-mif.R, R/pfilter.R, R/plot-pomp.R,
- R/pomp-methods.R, R/pomp.R, R/slice.R, R/trajectory-pomp.R,
- man/pfilter.Rd: - replace ':' construct with 'seq' and 'seq_len'
- throughout
- - add 'seed' argument to 'pfilter'
- * [r214] R/nlf-funcs.R, R/nlf-lql.R, R/nlf-objfun.R, R/nlf.R,
- man/dmeasure-pomp.Rd, man/dprocess-pomp.Rd,
- man/init.state-pomp.Rd, man/mif-class.Rd, man/nlf.Rd,
- man/particles-mif.Rd, man/pomp-class.Rd, man/rmeasure-pomp.Rd,
- man/rprocess-pomp.Rd, man/skeleton-pomp.Rd: - nlf now takes an
- optional argument 'transform' which transforms the data before
- fitting
- - the low-level interface documentation now has keyword
- 'internal' which keeps it out of the manual
-
-2010-04-07 kingaa
-
- * [r213] DESCRIPTION, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- - version 0.28-3
- * [r212] man/LondonYorke.Rd: - improve documentation slightly
-
-2010-04-06 kingaa
-
- * [r211] man/pomp-package.Rd: - include version message
-
-2010-03-15 kingaa
-
- * [r210] inst/data-R/make.R: - not needed
- * [r209] inst/data-R/dacca-census.q, inst/data-R/dacca-cholera.q,
- inst/data-R/dacca-mle.q, inst/data-R/dacca.R: - dacca data-object
- not yet ready for prime time
- * [r208] DESCRIPTION, inst/data-R, inst/data-src,
- tests/ou2-forecast.Rout.save, tests/sir.Rout.save: - rename
- data-src data-R
- - update the test .Rout.save files
- * [r207] inst/data-src, inst/data-src/dacca-census.q,
- inst/data-src/dacca-cholera.q, inst/data-src/dacca-mle.q,
- inst/data-src/dacca.R, inst/data-src/euler.sir.R,
- inst/data-src/make.R, inst/data-src/ou2.R, inst/data-src/rw2.R,
- inst/data-src/verhulst.R: - add source code for the
- data()-loadable examples
-
-2010-03-13 kingaa
-
- * [r206] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf: - version 0.28-1
- * [r205] DESCRIPTION: - go back to LazyData: false to avoid some
- ugly problems
- * [r204] R/pomp.R, data/euler.sir.R, data/euler.sir.rda,
- data/ou2.R, data/ou2.rda, data/rw2.R, data/rw2.rda,
- data/verhulst.R, data/verhulst.rda, man/mif.Rd,
- src/euler_sir_density.c, src/eulermultinom.c,
- tests/ou2-forecast.R, tests/sir.R: - move default initializer to
- pomp namespace
- - go back to binary format data-loadable examples to avoid the
- ugly problem of tag-along environments
- - speed up for degenerate cases in reulermultinom
- - put euler-density function for SIR model into source (though it
- is not used at present)
-
-2010-02-11 kingaa
-
- * [r203] R/mif.R: - fix of bug that occurs when mif's 'start'
- argument is specified with parameters in a different order than
- they occur in the 'params' slot of the pomp object
-
-2010-01-28 kingaa
-
- * [r202] man/LondonYorke.Rd: - add reference for London & Yorke
- * [r201] data/LondonYorke.rda, man/LondonYorke.Rd: - add the data
- set of London & Yorke
-
-2010-01-27 kingaa
-
- * [r200] R/bsplines.R, man/bsplines.Rd, src/bspline.c: - some
- improvements in the B-spline codes
-
-2010-01-25 kingaa
-
- * [r198] inst/ChangeLog: - version 0.27-2
- * [r197] DESCRIPTION, NAMESPACE, R/bsplines.R, data/euler.sir.R,
- inst/ChangeLog, inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
- inst/examples/euler_sir.R, inst/examples/euler_sir.c,
- inst/include/pomp.h, src/bspline.c, src/euler_sir.c, src/pomp.h,
- tests/sir.R, tests/sir.Rout.save: - add a new interface at the C
- level for evaluation of periodic B-splines bases.
- - rewrite the periodically-forced SIR model to use this facility.
- - rewrite the R level 'periodic.bspline.basis' function using the
- new C codes.
-
-2010-01-19 kingaa
-
- * [r196] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf: - update the vignettes for version
- 0.27-1
- * [r195] DESCRIPTION, inst/ChangeLog: - version 0.27-1
- * [r194] DESCRIPTION, R/mif.R, R/pfilter-mif.R, R/pfilter.R,
- inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf, man/mif.Rd, man/pfilter.Rd,
- tests/ou2-mif.R, tests/ou2-mif.Rout.save: - remove the 'warn'
- argument from pfilter and functions that call it.
- now 'verbose=TRUE' gives the same behavior.
- also, change the default of 'verbose' to 'getOption("verbose")'.
- - minor improvements to the documentation
-
-2010-01-06 kingaa
-
- * [r193] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- - bug fix in Advanced Topics vignette
-
-2009-12-31 kingaa
-
- * [r192] inst/ChangeLog: - version 0.26-5
- * [r191] DESCRIPTION, data/euler.sir.R, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
- inst/examples/euler_sir.R, inst/examples/euler_sir.c,
- src/euler_sir.c, tests/sir.R, tests/sir.Rout.save: - make some
- simplifications to the advanced (SIR) example:
- it was confusing to have the dprocess specified when it is never
- used.
- better to leave this out until such time as we have a method that
- uses dprocess.
-
-2009-12-30 kingaa
-
- * [r190] DESCRIPTION, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- - version 0.26-4
- * [r189] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
- man/euler.Rd, man/mif.Rd, man/pomp-package.Rd, man/pomp.Rd: -
- some improvements to the documentation
-
-2009-12-28 kingaa
-
- * [r188] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf: - version 0.6-3
- * [r187] DESCRIPTION, inst/examples/euler_sir.R: - tests/examples.R
- has been improved for greater portability per suggestion of Brian
- Ripley
-
-2009-12-10 kingaa
-
- * [r186] man/pfilter.Rd: - fix argument order
-
-2009-12-09 kingaa
-
- * [r185] inst/ChangeLog:
- * [r184] inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: - fix
- some bugs and infelicities in the vignette
- * [r183] inst/ChangeLog:
- * [r182] DESCRIPTION: - version 0.26-2
- * [r181] R/mif.R, R/pfilter-mif.R, R/pfilter.R, man/pfilter.Rd,
- tests/ou2-forecast.R, tests/ou2-forecast.Rout.save: - in pfilter,
- add ability to save individual particles' state vectors. this
- feature is useful for forecasting.
- * [r180] tests/ou2-mif.Rout.save: - correct test results
- * [r179] R/mif.R, tests/ou2-mif.R: - bug fix in 'mif' relating to
- non-standard particles functions
-
-2009-11-16 kingaa
-
- * [r178] data/euler.sir.R, data/ou2.R, data/rw2.R, data/verhulst.R:
- - cosmetology
-
-2009-11-15 kingaa
-
- * [r177] DESCRIPTION, data/euler.sir.R, data/euler.sir.rda,
- data/ou2.R, data/ou2.rda, data/rw2.R, data/rw2.rda,
- data/verhulst.R, data/verhulst.rda, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- - now use lazy-loading for datasets
-
-2009-11-12 kingaa
-
- * [r176] DESCRIPTION, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- - version 0.26-7
- * [r175] R/nlf.R, tests/ou2-nlf.R, tests/ou2-nlf.Rout.save: - bug
- fix in NLF code (for eval.only=TRUE)
-
-2009-10-12 kingaa
-
- * [r174] tests/ou2-mif.Rout.save: - update ou2-mif.Rout.save
- * [r173] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf: - version 0.25-6
- * [r172] DESCRIPTION, R/mif.R, tests/ou2-mif.R: - add error trap to
- prevent non-finite parameters from being estimated
-
-2009-10-07 kingaa
-
- * [r171] DESCRIPTION, NAMESPACE, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- - version 0.25-5
- * [r170] R/slice.R, man/slice.Rd, man/sobol.Rd: - add a new
- function: profile.design, to aid in construction of likelihood
- profiles
-
-2009-09-30 kingaa
-
- * [r169] DESCRIPTION: - fix Carles' name
-
-2009-09-21 kingaa
-
- * [r163] inst/ChangeLog:
- * [r162] DESCRIPTION, NAMESPACE, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf: - version 0.25-4
- * [r161] src/euler.c: - fix bug that crops up when dt=0
- * [r160] R/slice.R, man/slice.Rd: - add a new function
- "slice.design" for help with sliced likelihoods
- * [r159] R/aaa.R, R/pomp-methods.R, man/pomp-methods.Rd,
- tests/rw2.R, tests/rw2.Rout.save, tests/sir.R,
- tests/sir.Rout.save: - add a new "time<-" method for
- manipulating/subsetting time series
-
-2009-07-08 kingaa
-
- * [r158] man/trajmatch.Rd: make the documentation a bit more
- explicit
-
-2009-07-07 kingaa
-
- * [r157] data/verhulst.rda, man/verhulst.Rd: add stochastic
- Verhulst-Pearl (logistic) model to the set of examples
- * [r156] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf:
- * [r155] DESCRIPTION, NAMESPACE, R/trajmatch.R, data/euler.sir.rda,
- data/ou2.rda, data/rw2.rda, man/trajmatch.Rd,
- tests/ou2-mif.Rout.save, tests/ou2-trajmatch.R,
- tests/ou2-trajmatch.Rout.save: add trajectory-matching method
-
-2009-06-24 kingaa
-
- * [r154] tests/rw2.R, tests/rw2.Rout.save: fix tests of 'rw2'
- * [r153] DESCRIPTION, R/mif.R, R/pomp-methods.R, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
- man/mif.Rd, tests/logistic.Rout.save, tests/ou2-kalman.Rout.save,
- tests/ou2-mif.R, tests/ou2-mif.Rout.save, tests/ou2-nlf.R,
- tests/ou2-nlf.Rout.save, tests/ou2-simulate.Rout.save,
- tests/rw2.R, tests/rw2.Rout.save, tests/sir.R,
- tests/sir.Rout.save: better testing
- some more error checking in 'mif'
-
-2009-06-23 kingaa
-
- * [r152] DESCRIPTION, R/mif.R, data/euler.sir.rda, data/ou2.rda,
- data/rw2.rda, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
- man/mif.Rd, tests/ou2-mif.R, tests/ou2-mif.Rout.save: alg.pars
- has been removed as an argument to 'mif'
-
-2009-06-19 kingaa
-
- * [r151] DESCRIPTION, inst/ChangeLog,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- version 0.24-7
- * [r150] src/initstate.c: check for duplication of names between
- states and parameters
- manage the pointer protection stack more sensibly
-
-2009-06-17 kingaa
-
- * [r149] src/lookup_table.c: minor changes to C code (remove unused
- variable)
- * [r148] DESCRIPTION, NAMESPACE, R/mvnorm.R, R/nlf-guts.R: make use
- of mvtnorm::dmvnorm now instead of our own version
- * [r147] R/nlf-guts.R: duplicate codes removed
- * [r146] R/mvnorm.R: updated
-
-2009-06-03 kingaa
-
- * [r145] DESCRIPTION, inst/ChangeLog: version 0.24-5
- * [r144] data/euler.sir.rda, inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf: improvements to vignettes
-
-2009-06-02 kingaa
-
- * [r143] inst/ChangeLog: version 0.24-4
- * [r142] data/euler.sir.rda, data/ou2.rda, inst/doc/Makefile,
- inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/compiled_code_in_pomp.Rnw,
- inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf: more changes to documentation
- reconfigure vignettes somewhat
- * [r141] DESCRIPTION:
- * [r140] man/init.state-pomp.Rd, man/pomp.Rd, man/simulate-pomp.Rd,
- man/trajectory-pomp.Rd: add some nice examples
- * [r139] R/nlf.R:
- * [r138] man/bsplines.Rd, man/dmeasure-pomp.Rd,
- man/dprocess-pomp.Rd, man/euler.Rd, man/euler.sir.Rd,
- man/eulermultinom.Rd, man/init.state-pomp.Rd, man/mif-class.Rd,
- man/mif-methods.Rd, man/mif.Rd, man/nlf.Rd, man/ou2.Rd,
- man/particles-mif.Rd, man/pfilter.Rd, man/pomp-class.Rd,
- man/pomp-methods.Rd, man/pomp-package.Rd, man/pomp.Rd,
- man/rmeasure-pomp.Rd, man/rprocess-pomp.Rd, man/simulate-pomp.Rd,
- man/skeleton-pomp.Rd, man/sobol.Rd, man/trajectory-pomp.Rd:
- further improvements to documentation
-
-2009-06-01 kingaa
-
- * [r137] man/euler.Rd, man/pomp.Rd: further clarify documentation
-
-2009-05-28 kingaa
-
- * [r136] inst/ChangeLog, inst/doc/compiled_code_in_pomp.Rnw,
- inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf: remove prompt and continue characters
- from vignette documents
- * [r135] data/euler.sir.rda, data/ou2.rda, data/rw2.rda,
- inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf: version 0.24-3
- * [r134] DESCRIPTION, R/bsplines.R, man/bsplines.Rd, src/bspline.c:
- fix up the bspline.basis function
-
-2009-05-26 kingaa
-
- * [r133] DESCRIPTION, man/pomp-package.Rd, man/pomp.Rd: clarify
- some documentation
-
-2009-05-21 kingaa
-
- * [r132] man/pomp-package.Rd, man/pomp.Rd: clarify the
- documentation on pomp object construction
-
-2009-05-14 kingaa
-
- * [r131] inst/include/pomp.h: fix documentation
- * [r130] man/nlf.Rd: fix documentation
- * [r129] src/pomp.h: fix documentation
- * [r128] src/euler.c: clean up the C codes in 'euler.c'
-
-2009-05-13 kingaa
-
- * [r127] inst/ChangeLog, inst/doc/compiled_code_in_pomp.Rnw,
- inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf: version 0.24-1
- * [r126] inst/ChangeLog:
- * [r125] DESCRIPTION, R/simulate-pomp.R, data/euler.sir.rda,
- data/ou2.rda, data/rw2.rda, inst/examples/logistic.R,
- man/simulate-pomp.Rd, tests/logistic.R, tests/logistic.Rout.save,
- tests/ou2-nlf.R, tests/ou2-nlf.Rout.save, tests/ou2-simulate.R,
- tests/ou2-simulate.Rout.save: now when 'simulate' is called with
- nsim=1 (the default), a single 'pomp' object is returned rather
- than (per the old behavior) a list containing one 'pomp' object.
-
-2009-05-12 kingaa
-
- * [r124] DESCRIPTION: fix bug in documentation
- * [r123] man/pfilter.Rd: fix bug in documentation
-
-2009-05-07 kingaa
-
- * [r122] DESCRIPTION, inst/ChangeLog,
- inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- version 0.23-6
- * [r121] inst/doc/compiled_code_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf, inst/include/pomp.h,
- src/eulermultinom.c, src/pomp.h, tests/sir.R,
- tests/sir.Rout.save: streamline "reulermultinom" by moving
- GetRNGstate() and PutRNGstate() outside of a level of looping. If
- you want to use 'reulermultinom' at the C level, you must take
- care that it is wrapped inside of the RNGstate functions. An
- approx. 10-fold increase in speed for the euler.simulate function
- is realized by this simple change.
-
-2009-05-05 kingaa
-
- * [r120] inst/include/pomp.h: fix the pomp.h header comments
-
-2009-05-01 kingaa
-
- * [r119] R/init.state-pomp.R: when params is missing, use params <-
- coef(object)
-
-2009-04-29 kingaa
-
- * [r118] src/pomp.h: fix comments
- * [r117] inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf:
- * [r116] DESCRIPTION, inst/include/pomp.h, man/euler.Rd,
- src/euler.c, src/lookup_table.c, src/pomp.h, src/pomp_internal.h:
- rearrange the headers
- rename the prototypes for native routines used in Euler and
- onestep plugins
- * [r115] src/bspline.c, src/dsobol.c:
-
-2009-04-28 kingaa
-
- * [r114] inst/ChangeLog: version 0.23-4
- * [r113] data/rw2.rda, man/rw2.Rd, tests/rw2.R,
- tests/rw2.Rout.save: add a new data()-accessible pomp object,
- coding a very simple 2D random walk
- * [r112] DESCRIPTION, NAMESPACE, R/euler.R, data/euler.sir.rda,
- data/ou2.rda, inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf,
- inst/doc/intro_to_pomp.pdf, inst/examples/euler_sir.R,
- inst/examples/logistic.R, inst/examples/rw2.R, man/euler.Rd,
- src/euler.c, tests/logistic.R, tests/logistic.Rout.save,
- tests/sir.R, tests/sir.Rout.save: add onestep plugin to
- facilitate the construction of models for which explicit formulae
- are available for one-step transitions.
- * [r111] inst/CITATION: fix citation info
- * [r110] src/dprocess.c, src/rprocess.c: explicitly cast 'times' to
- double to avoid potential problems when R casts a sequence to
- integer storage type
- * [r109] man/pomp-package.Rd:
-
-2009-04-27 kingaa
-
- * [r108] inst/ChangeLog, inst/doc/Makefile,
- inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
-
-2009-04-26 kingaa
-
- * [r107] DESCRIPTION, inst/ChangeLog: version 0.23-3
- * [r106] data/euler.sir.rda, data/ou2.rda: use R-2.8.1 to generate
- the data/*.rda files
- * [r105] data/euler.sir.R, data/euler.sir.rda, data/ou2.R,
- data/ou2.rda: 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.
-
-2009-04-24 kingaa
-
- * [r104] R/trajectory-pomp.R, data/euler.sir.R, man/euler.sir.Rd,
- tests/sir.R, tests/sir.Rout.save: put 'euler.sir' in as an
- example pomp object obtainable via 'data(euler.sir)'
- make 'trajectory' a bit more user-friendly
- * [r103] man/euler.Rd: remove the examples in the 'euler' and
- 'SSA.simulate' man pages: refer the user to the 'examples'
- directory instead
- * [r102] DESCRIPTION, data/ou2.R, data/ou2.rda,
- inst/doc/compiled_code_in_pomp.Rnw, tests/ou2-kalman.Rout.save,
- tests/ou2-mif.Rout.save: replace the binary data 'ou2.rda' with R
- code in 'ou2.R'
-
-2009-04-21 kingaa
-
- * [r101] R/pomp.R: better error handling
- * [r100] R/pomp.R: time variable is not needed in the covar table
-
-2009-04-17 kingaa
-
- * [r99] inst/ChangeLog:
- * [r98] DESCRIPTION, data/ou2.rda, inst/ChangeLog,
- inst/doc/compiled_code_in_pomp.Rnw,
- inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
- inst/examples/euler_sir.R, inst/examples/euler_sir.c,
- inst/include/pomp.h, man/euler.Rd, src/euler.c, src/euler_sir.c,
- src/ou2.c, src/pomp.h, src/rmeasure.c, tests/sir.R,
- tests/sir.Rout.save: The 'euler' and 'rmeasure' evaluation codes
- now call GetRNGstate() and PutRNGstate() when the user-supplied
- function they will evaluate is a native routine. This means that
- potentially many fewer calls to these expensive functions can be
- made in, e.g., particle filtering or simulation of a large number
- of replicates and consequently significant performance gains.
-
-2009-04-16 kingaa
-
- * [r97] R/mif-methods.R, R/mif.R: use rowMeans and colMeans in
- place of apply where appropriate
- * [r96] man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd: update
- references for 'mif'
- * [r95] man/mif.Rd: fix order of arguments in documentation for
- 'mif'
-
-2009-04-14 kingaa
-
- * [r94] inst/ChangeLog:
- * [r93] DESCRIPTION, R/mif.R, data/ou2.rda, inst/ChangeLog,
- inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf, man/mif.Rd, tests/ou2-mif.R,
- tests/ou2-mif.Rout.save, tests/sir.Rout.save: The parameter
- 'alg.pars' is now deprecated. The four algorithm parameters Np,
- ic.lag, var.factor, cooling.factor are now specified directly as
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 310
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