[Pomp-commits] r312 - pkg/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Aug 30 18:23:09 CEST 2010
Author: kingaa
Date: 2010-08-30 18:23:09 +0200 (Mon, 30 Aug 2010)
New Revision: 312
Modified:
pkg/inst/ChangeLog
Log:
- update ChangeLog
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2010-08-30 16:21:37 UTC (rev 311)
+++ pkg/inst/ChangeLog 2010-08-30 16:23:09 UTC (rev 312)
@@ -1,5 +1,1159 @@
+2010-08-30 kingaa
+
+ * [r311] DESCRIPTION, NAMESPACE, R, data, inst, man,
+ pomp/DESCRIPTION, pomp/NAMESPACE, pomp/R, pomp/data, pomp/inst,
+ pomp/man, pomp/src, pomp/tests, src, tests: - put everything in
+ pkg/pomp back into pkg
+ * [r310] pomp/DESCRIPTION, pomp/inst/ChangeLog,
+ pomp/inst/doc/advanced_topics_in_pomp.pdf,
+ pomp/inst/doc/intro_to_pomp.pdf: - update the vignettes
+
2010-08-26 kingaa
- * [r309] ., DESCRIPTION, NAMESPACE, R, data, inst, man, src, tests:
- - move everything in pkg/ to pkg/pomp
+ * [r309] DESCRIPTION, NAMESPACE, R, data, inst, man, pomp,
+ pomp/DESCRIPTION, pomp/NAMESPACE, pomp/R, pomp/data, pomp/inst,
+ pomp/man, pomp/src, pomp/tests, src, tests: - move everything in
+ pkg/ to pkg/pomp
+ * [r308] inst/examples/sir.R, inst/examples/sir.c: - simplify the
+ SIR example using compiled code
+ * [r307] DESCRIPTION, src/R_init_pomp.c: - register C-callable
+ routines
+2010-08-25 kingaa
+
+ * [r306] DESCRIPTION, R/probe.R, tests/ou2-probe-match.R,
+ tests/ou2-probe-match.Rout.save: - bug fix in 'probe'
+
+2010-08-24 kingaa
+
+ * [r305] data/euler.sir.rda, data/gillespie.sir.rda, data/ou2.rda,
+ data/ricker.rda, inst/ChangeLog, inst/data-R/euler.sir.R,
+ inst/data-R/gillespie.sir.R, inst/data-R/ou2.R,
+ inst/data-R/ricker.R, inst/doc/advanced_topics_in_pomp.Rnw,
+ inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
+ inst/examples/sir.R, inst/examples/sir.c, src/cholmodel.c,
+ src/ou2.c, src/ricker.c, src/sir.c: - change names of C routines
+ to keep namespace open (prepend C symbols in the package with
+ "_")
+ * [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
+
+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
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 312
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