2013-01-09  kingaa

	* [r806] R/mif-class.R, R/mif.R, R/pfilter.R, R/pmcmc.R, inst/NEWS,
	  man/mif-class.Rd, man/mif.Rd, man/pfilter.Rd, tests/ou2-mif2.R,
	  tests/ou2-mif2.Rout.save: - integrate MIF2
	* [r805] R/example.R: - improved 'pompExample'
	* [r804] tests/bbs-trajmatch.R, tests/bbs-trajmatch.Rout.save,
	  tests/bbs.R, tests/bbs.Rout.save, tests/blowflies.R,
	  tests/blowflies.Rout.save, tests/dacca.R, tests/dacca.Rout.save,
	  tests/dimchecks.R, tests/dimchecks.Rout.save, tests/gillespie.R,
	  tests/gillespie.Rout.save, tests/gompertz.R,
	  tests/gompertz.Rout.save, tests/ou2-bsmc.R,
	  tests/ou2-bsmc.Rout.save, tests/ou2-forecast.R,
	  tests/ou2-forecast.Rout.save, tests/ou2-icfit.R,
	  tests/ou2-icfit.Rout.save, tests/ou2-kalman.R,
	  tests/ou2-kalman.Rout.save, tests/ou2-mif-fp.R,
	  tests/ou2-mif-fp.Rout.save, tests/ou2-mif.R,
	  tests/ou2-mif.Rout.save, tests/ou2-nlf.R,
	  tests/ou2-nlf.Rout.save, tests/ou2-pmcmc.R,
	  tests/ou2-pmcmc.Rout.save, tests/ou2-probe.R,
	  tests/ou2-probe.Rout.save, tests/ou2-procmeas.R,
	  tests/ou2-procmeas.Rout.save, tests/ou2-simulate.R,
	  tests/ou2-simulate.Rout.save, tests/ou2-trajmatch.R,
	  tests/ou2-trajmatch.Rout.save, tests/partrans.R,
	  tests/partrans.Rout.save, tests/pfilter.R,
	  tests/pfilter.Rout.save, tests/pomppomp.R,
	  tests/pomppomp.Rout.save, tests/ricker-bsmc.R,
	  tests/ricker-bsmc.Rout.save, tests/ricker-probe.R,
	  tests/ricker-probe.Rout.save, tests/ricker-spect.R,
	  tests/ricker-spect.Rout.save, tests/ricker.R,
	  tests/ricker.Rout.save, tests/rw2.R, tests/rw2.Rout.save,
	  tests/sir.R, tests/sir.Rout.save, tests/skeleton.R,
	  tests/skeleton.Rout.save, tests/steps.R, tests/steps.Rout.save,
	  tests/synlik.R, tests/synlik.Rout.save, tests/verhulst.R,
	  tests/verhulst.Rout.save: - improved 'pompExample'
	* [r803] man/blowflies.Rd, man/dacca.Rd, man/example.Rd,
	  man/gompertz.Rd, man/init.state-pomp.Rd, man/ou2.Rd,
	  man/parmat.Rd, man/probe.Rd, man/ricker.Rd, man/rw2.Rd,
	  man/simulate-pomp.Rd, man/sir.Rd, man/spect.Rd,
	  man/traj-match.Rd, man/trajectory-pomp.Rd, man/verhulst.Rd: -
	  improved 'pompExample'
	* [r802] man/pomp.Rd: - minor fix
	* [r801] .Rbuildignore, DESCRIPTION, data/bbs.rda,
	  data/blowflies.rda, data/dacca.rda, data/euler.sir.rda,
	  data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda,
	  data/ricker.rda, data/rw2.rda, data/verhulst.rda, inst/NEWS,
	  inst/examples/bbs.R, inst/examples/euler.sir.R,
	  inst/examples/gillespie.sir.R, inst/examples/sir.R,
	  man/blowflies.Rd, man/dacca.Rd, man/example.Rd, man/gompertz.Rd,
	  man/init.state-pomp.Rd, man/ou2.Rd, man/parmat.Rd, man/probe.Rd,
	  man/ricker.Rd, man/rw2.Rd, man/simulate-pomp.Rd, man/sir.Rd,
	  man/spect.Rd, man/traj-match.Rd, man/trajectory-pomp.Rd,
	  man/verhulst.Rd, tests/bbs-trajmatch.R,
	  tests/bbs-trajmatch.Rout.save, tests/bbs.R, tests/bbs.Rout.save,
	  tests/blowflies.R, tests/blowflies.Rout.save, tests/dacca.R,
	  tests/dacca.Rout.save, tests/dimchecks.R,
	  tests/dimchecks.Rout.save, tests/fhn.Rout.save,
	  tests/filtfail.Rout.save, tests/gillespie.R,
	  tests/gillespie.Rout.save, tests/gompertz.R,
	  tests/gompertz.Rout.save, tests/logistic.Rout.save,
	  tests/ou2-bsmc.R, tests/ou2-bsmc.Rout.save, tests/ou2-forecast.R,
	  tests/ou2-forecast.Rout.save, tests/ou2-icfit.R,
	  tests/ou2-icfit.Rout.save, tests/ou2-kalman.R,
	  tests/ou2-kalman.Rout.save, tests/ou2-mif-fp.R,
	  tests/ou2-mif-fp.Rout.save, tests/ou2-mif.R,
	  tests/ou2-mif.Rout.save, tests/ou2-nlf.R,
	  tests/ou2-nlf.Rout.save, tests/ou2-pmcmc.R,
	  tests/ou2-pmcmc.Rout.save, tests/ou2-probe.R,
	  tests/ou2-probe.Rout.save, tests/ou2-procmeas.R,
	  tests/ou2-procmeas.Rout.save, tests/ou2-simulate.R,
	  tests/ou2-simulate.Rout.save, tests/ou2-trajmatch.R,
	  tests/ou2-trajmatch.Rout.save, tests/partrans.R,
	  tests/partrans.Rout.save, tests/pfilter.R,
	  tests/pfilter.Rout.save, tests/pomppomp.R,
	  tests/pomppomp.Rout.save, tests/ricker-bsmc.R,
	  tests/ricker-bsmc.Rout.save, tests/ricker-probe.R,
	  tests/ricker-probe.Rout.save, tests/ricker-spect.R,
	  tests/ricker-spect.Rout.save, tests/ricker.R,
	  tests/ricker.Rout.save, tests/rw2.R, tests/rw2.Rout.save,
	  tests/sir.R, tests/sir.Rout.save, tests/skeleton.R,
	  tests/skeleton.Rout.save, tests/steps.R, tests/steps.Rout.save,
	  tests/synlik.R, tests/synlik.Rout.save, tests/verhulst.R,
	  tests/verhulst.Rout.save: - get rid of all data()-loadable pomp
	  objects, replacing them with the new 'pompExample' facility
	* [r800] DESCRIPTION, NAMESPACE, R/example.R, inst/data-R,
	  inst/examples/blowflies.R, inst/examples/dacca.R,
	  inst/examples/ewmeas.csv, inst/examples/gompertz.R,
	  inst/examples/ou2.R, inst/examples/ricker.R, inst/examples/rw2.R,
	  inst/examples/sir.R, inst/examples/verhulst.R: - remove
	  data()-loadable pomp objects in favor of the new 'pompExample'
	  mechanism.

2013-01-08  kingaa

	* [r797] data/bbs.rda, data/blowflies.rda, data/dacca.rda,
	  data/euler.sir.rda, data/gillespie.sir.rda, data/gompertz.rda,
	  data/ou2.rda, data/ricker.rda, data/rw2.rda, data/verhulst.rda: -
	  update data directory
	* [r794] DESCRIPTION, R/mif.R, tests/bbs.Rout.save,
	  tests/gompertz.Rout.save, tests/ou2-bsmc.Rout.save,
	  tests/ou2-mif.Rout.save: - update tests
	* [r793] DESCRIPTION, R/pfilter.R, R/pomp-class.R, R/pomp.R: - some
	  changes preparatory to merging in mif2

2012-09-14  kingaa

	* [r780] src/pomp_fun.c: - more informative error message when
	  pomp_fun handler fails

2012-08-22  kingaa

	* [r778] DESCRIPTION, inst/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/bsmc-ricker-flat-prior.rda,
	  inst/doc/bsmc-ricker-normal-prior.rda,
	  inst/doc/complex-sir-def.rda, inst/doc/fullnat.bst,
	  inst/doc/gompertz-multi-mif.rda,
	  inst/doc/gompertz-pfilter-guess.rda,
	  inst/doc/gompertz-trajmatch.rda, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/nlf-block-boot.rda, inst/doc/nlf-boot.rda,
	  inst/doc/nlf-fit-from-truth.rda, inst/doc/nlf-fits.rda,
	  inst/doc/nlf-lag-tests.rda, inst/doc/nlf-multi-short.rda,
	  inst/doc/plugin-C-code.rda, inst/doc/plugin-R-code.rda,
	  inst/doc/pomp.bib, inst/doc/ricker-comparison.rda,
	  inst/doc/ricker-first-probe.rda, inst/doc/ricker-mif.rda,
	  inst/doc/ricker-probe-match.rda, inst/doc/ricker-probe.rda,
	  inst/doc/sim-sim.rda, inst/doc/sir-pomp-def.rda,
	  inst/doc/vectorized-C-code.rda, inst/doc/vectorized-R-code.rda: -
	  remove vignette codes

2012-08-08  kingaa

	* [r765] DESCRIPTION, inst/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/bsmc-ricker-normal-prior.rda,
	  inst/doc/complex-sir-def.rda,
	  inst/doc/gompertz-pfilter-guess.rda, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, inst/doc/plugin-C-code.rda,
	  inst/doc/plugin-R-code.rda, inst/doc/ricker-comparison.rda,
	  inst/doc/ricker-first-probe.rda, inst/doc/ricker-probe.rda,
	  inst/doc/sim-sim.rda, inst/doc/sir-pomp-def.rda,
	  inst/doc/vectorized-C-code.rda, inst/doc/vectorized-R-code.rda: -
	  store more intermediate results in the building of the vignettes
	  to make vignette-checking quicker

2012-08-03  kingaa

	* [r757] tests/fhn.R, tests/fhn.Rout.save, tests/ricker-spect.R,
	  tests/ricker-spect.Rout.save, tests/ricker.R,
	  tests/ricker.Rout.save, tests/rw2.R, tests/rw2.Rout.save,
	  tests/sir.R, tests/sir.Rout.save: - more modifications to test
	  files
	* [r756] DESCRIPTION, inst/NEWS, tests/ou2-probe.R,
	  tests/ou2-probe.Rout.save, tests/ricker-bsmc.R,
	  tests/ricker-bsmc.Rout.save, tests/ricker-probe.R,
	  tests/ricker-probe.Rout.save: - clean up tests

2012-07-31  kingaa

	* [r753] DESCRIPTION, R/authors.R, inst/NEWS,
	  man/pfilter-methods.Rd: - add authors list
	  - add documentation of 'cond.logLik' and 'eff.sample.size'

2012-07-13  kingaa

	* [r752] DESCRIPTION, NAMESPACE, R/aaa.R, R/mif.R,
	  R/pfilter-methods.R, tests/gompertz.R, tests/gompertz.Rout.save,
	  tests/ou2-mif.Rout.save: - add 'eff.sample.size' and
	  'cond.logLik' methods for 'pfilterd.pomp' objects
	  - make 'non-finite parameters' warning message more informative
	* [r751] DESCRIPTION, src/dmeasure.c: - fix bug in 'dmeasure' when
	  log=T. bug found by R. Reiner.

2012-07-10  kingaa

	* [r750] DESCRIPTION, R/builder.R, inst/include/pomp.h, src/pomp.h,
	  src/pomp_internal.h, src/sir.c: - fix bug with pompBuilder on mac

2012-07-02  kingaa

	* [r744] DESCRIPTION: - require only R version >= 2.14.1

2012-07-01  kingaa

	* [r743] DESCRIPTION, inst/ChangeLog: - update changelog & date
	* [r742] R/pomp-methods.R, R/pomp.R: - force storage.type to double
	  for params slot

2012-06-29  kingaa

	* [r741] inst/ChangeLog, tests/sir.Rout.save: - update changelog
	  and unit test
	* [r740] DESCRIPTION, R/pomp.R, inst/NEWS, man/pomp.Rd,
	  tests/sir.R: - add 'params' argument to 'pomp' constructor
	* [r739] R/traj-match.R, man/traj-match.Rd, tests/bbs-trajmatch.R,
	  tests/bbs-trajmatch.Rout.save: - extra arguments (...) to
	  'traj.match.objfun' are now passed on to the ODE integrator in
	  case the skeleton is a vectorfield

2012-06-18  kingaa

	* [r732] inst/include/pomp.h: - update installed version of
	  'pomp.h'
	* [r731] DESCRIPTION, inst/NEWS, src/pomp.h: - update NEWS file
	  - minor changes to 'pomp.h'

2012-06-12  kingaa

	* [r729] inst/doc/pomp.bib: - update bibliography database

2012-06-01  kingaa

	* [r727] DESCRIPTION, demo/sir.R, inst/include/pomp.h,
	  src/lookup_table.c, src/pomp.h: - remove superfluous warnings
	  from 'lookup_table'
	  - fix 'sir' demo to work with covariate table
	  - add some inline functions to 'pomp.h'
	* [r726] DESCRIPTION, R/builder.R, demo/gompertz.R, man/builder.Rd:
	  - fix incorrect error messages in 'pompBuilder'
	  - allow 'pompBuilder' to deal with covariates

2012-05-29  kingaa

	* [r725] DESCRIPTION, R/builder.R, R/pomp.R, demo/gompertz.R,
	  demo/sir.R, man/builder.Rd, man/pomp.Rd: - add support for
	  parameter transformations to 'pompBuilder'
	  - more error-trapping in 'pomp'
	  - update demos to use compiled parameter transformations
	  - fix minor omission in 'pomp' man page

2012-05-14  kingaa

	* [r722] DESCRIPTION: - update DESCRIPTION
	* [r721] inst/ChangeLog, inst/NEWS,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
	  - update changelog NEWS file and vignettes

2012-05-12  kingaa

	* [r716] DESCRIPTION, R/dmeasure-pomp.R, R/dprocess-pomp.R,
	  R/pomp-methods.R, R/rmeasure-pomp.R, R/rprocess-pomp.R,
	  R/skeleton-pomp.R, R/trajectory-pomp.R: - use fewer anonymous
	  functions

2012-05-10  kingaa

	* [r715] DESCRIPTION, tests/sir.R, tests/sir.Rout.save: - add unit
	  test for new trajectory codes

2012-05-09  kingaa

	* [r714] inst/ChangeLog:

2012-05-08  kingaa

	* [r713] DESCRIPTION, R/trajectory-pomp.R, src/trajectory.c: - use
	  R_PreserveObject and R_ReleaseObject rather than the 'savelist'
	  trick
	* [r711] DESCRIPTION:

2012-05-07  kingaa

	* [r707] inst/ChangeLog, inst/NEWS: - update NEWS and ChangeLog

2012-05-06  kingaa

	* [r706] inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - update vignettes

2012-05-03  kingaa

	* [r705] R/trajectory-pomp.R: - really fix bug in 'trajectory' that
	  occurs when 'zeronames' has length > 1
	* [r704] src/R_init_pomp.c: - forgot to export
	  'get_pomp_userdata_int' and 'get_pomp_userdata_double'
	* [r703] DESCRIPTION, R/builder.R, R/trajectory-pomp.R, demo/sir.R:
	  - fix bug in 'trajectory' for vectorfield case that shows up when
	  'zeronames' has length > 1
	  - re-work 'sir' demo so that it uses 'pompBuilder'

2012-05-02  kingaa

	* [r702] inst/ChangeLog:
	* [r701] R/trajectory-pomp.R, src/pomp_internal.h, src/skeleton.c,
	  src/trajectory.c: - work on the guts of the 'skeleton' and
	  'trajectory' for speed up in vectorfield case
	* [r700] tests/demos.R: - remove automatic running of demos (since
	  this fails under windows)
	* [r699] R/builder.R: - add declarations for
	  'get_pomp_userdata_int' and 'get_pomp_userdata_double'
	* [r698] src/rmeasure.c: - remove unused variables
	* [r697] DESCRIPTION, inst/ChangeLog:
	* [r696] demo/gompertz.R, demo/sir.R, src/dmeasure.c, src/euler.c,
	  src/pomp_internal.h, src/rmeasure.c, src/skeleton.c,
	  src/trajectory.c, tests/demos.R, tests/examples.R: - changes to
	  eliminate pedantic warnings
	  - put covariate table interpolation into vectorfield trajectory
	  computation
	* [r695] inst/ChangeLog:
	* [r694] DESCRIPTION, R/trajectory-pomp.R, src/trajectory.c: - more
	  work on the guts of 'trajectory' for the vectorfield case

2012-05-01  kingaa

	* [r693] src/trajectory.c: - make sure to set up 'userdata' access
	  to user functions
	* [r692] inst/ChangeLog:
	* [r691] R/simulate-pomp.R, R/trajectory-pomp.R, tests/ricker.R,
	  tests/ricker.Rout.save: - make 'sim' and 'traj' into factors when
	  'simulate' or 'trajectory' are called with 'as.data.frame=TRUE'

2012-04-30  kingaa

	* [r690] inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf:
	* [r689] inst/ChangeLog:
	* [r688] DESCRIPTION, R/builder.R, inst/ChangeLog, man/builder.Rd,
	  src/trajectory.c: - rework the guts of 'iterate_map' for much
	  faster trajectory calculation

2012-04-29  kingaa

	* [r687] src/dmeasure.c, src/skeleton.c: - more work on the guts

2012-04-28  kingaa

	* [r686] DESCRIPTION, src/euler.c, src/rmeasure.c: - more changes
	  to the guts

2012-04-27  kingaa

	* [r685] DESCRIPTION, R/pomp-fun.R, R/pomp.R, data/bbs.rda,
	  data/blowflies.rda, data/dacca.rda, data/euler.sir.rda,
	  data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda,
	  data/ricker.rda, data/rw2.rda, data/verhulst.rda,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/bsmc-ricker-flat-prior.rda,
	  inst/doc/gompertz-multi-mif.rda, inst/doc/gompertz-trajmatch.rda,
	  inst/doc/intro_to_pomp.pdf, inst/doc/nlf-block-boot.rda,
	  inst/doc/nlf-boot.rda, inst/doc/nlf-fit-from-truth.rda,
	  inst/doc/nlf-fits.rda, inst/doc/nlf-lag-tests.rda,
	  inst/doc/nlf-multi-short.rda, inst/doc/ricker-mif.rda,
	  inst/doc/ricker-probe-match.rda, src/dmeasure.c, src/euler.c,
	  src/lookup_table.c, src/partrans.c, src/pomp_fun.c,
	  src/pomp_internal.h, src/rmeasure.c, src/skeleton.c: - changes to
	  the guts of 'rmeasure', 'dmeasure', 'partrans', and the Euler
	  rprocess plugins

2012-04-26  kingaa

	* [r684] R/builder.R, demo/gompertz.R, inst/ChangeLog: - zeronames
	  argument in 'pompBuilder' is optional
	* [r683] DESCRIPTION, NAMESPACE, R/builder.R, data/bbs.rda,
	  data/blowflies.rda, data/dacca.rda, data/euler.sir.rda,
	  data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda,
	  data/ricker.rda, data/rw2.rda, data/verhulst.rda,
	  demo/gompertz.R, demo/logistic.R, inst/ChangeLog, inst/NEWS,
	  inst/data-R/sir.R, 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/gompertz.c,
	  inst/include/pomp.h, man/builder.Rd, src/R_init_pomp.c,
	  src/SSA_wrapper.c, src/dmeasure.c, src/euler.c, src/partrans.c,
	  src/pomp.h, src/pomp_internal.h, src/rmeasure.c, src/sir.c,
	  src/skeleton.c, src/userdata.c, tests/bbs.Rout.save,
	  tests/pfilter.Rout.save, tests/skeleton.R,
	  tests/skeleton.Rout.save: - add new facility for accessing
	  'userdata' from within user-defined native routines:
	  get_pomp_userdata{,_int,_double}
	  - change some data()-loadable examples to make use of this
	  - make 'pompBuilder' visible
	  - modify 'gompertz' demo to make use of 'pompBuilder'

2012-04-25  kingaa

	* [r682] inst/doc/advanced_topics_in_pomp.Rnw: - minor tweak to
	  pompBuilder example
	* [r681] NAMESPACE, R/trajectory-pomp.R, src/trajectory.c: - put in
	  a routine to reset external variables after deSolve call
	* [r680] src/bspline.c: - fix error message

2012-04-24  kingaa

	* [r679] DESCRIPTION, R/builder.R, inst/ChangeLog, inst/NEWS,
	  inst/TODO, inst/doc/Makefile,
	  inst/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/advanced_topics_in_pomp.pdf: - put 'pompBuilder'
	  demonstration into 'advanced topics' vignette
	* [r678] R/aaa.R, R/nlf-funcs.R, R/plot-pomp.R, R/pomp.R,
	  R/probe-match.R, R/probe.R, R/spect.R: - use 'paste0' where
	  appropriate. define 'paste0' for use with R <= 2.15.0

2012-04-23  kingaa

	* [r677] DESCRIPTION: - change Depends to 2.14.2
	* [r676] DESCRIPTION, R/builder.R, data/bbs.rda,
	  data/blowflies.rda, data/dacca.rda, data/euler.sir.rda,
	  data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda,
	  data/ricker.rda, data/rw2.rda, data/verhulst.rda, inst/NEWS,
	  inst/data-R/blowflies.R, src/blowfly.c, tests/blowflies.R,
	  tests/blowflies.Rout.save, tests/sir.Rout.save: - remove the
	  delay 'tau' from the blowflies example
	  - make the 'pompBuilder' work under 2.14.2
	  - update the data()-loadable examples

2012-04-21  kingaa

	* [r675] inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - update vignettes
	* [r674] DESCRIPTION, inst/ChangeLog, inst/NEWS: - bump version
	  number since R 2.15.0 is now needed
	* [r673] inst/NEWS, tests/pfilter.Rout.save: - update unit tests
	  and NEWS

2012-04-19  kingaa

	* [r670] DESCRIPTION, data/bbs.rda, data/blowflies.rda,
	  data/dacca.rda, data/euler.sir.rda, data/gillespie.sir.rda,
	  data/gompertz.rda, data/ou2.rda, data/ricker.rda, data/rw2.rda,
	  data/verhulst.rda, inst/data-R/blowflies.R, src/blowfly.c: - fix
	  segfault bug in blowfly example when tau is NA (thanks to Greg
	  Minshall for finding the bug)

2012-04-17  kingaa

	* [r664] ., .Rbuildignore, .Rinstignore, DESCRIPTION, NAMESPACE, R,
	  data, demo, inst, man, src, tests: - move everything down one
	  level

