2012-01-11  kingaa

	* [r589] src/euler.c: - bug fix: inappropriate choice of number of
	  steps in some circumstances

2012-01-10  kingaa

	* [r588] inst/ChangeLog: - update ChangeLog for version 0.40-1
	* [r587] .Rbuildignore: - don't ignore .rda files in inst/doc

2012-01-09  kingaa

	* [r586] DESCRIPTION, src/lpa.c: - add LPA model codes to src

2012-01-08  kingaa

	* [r585] inst/doc/manual.pdf: - updated manual
	* [r584] DESCRIPTION, R/plugins.R, R/pomp.R, R/trajectory-pomp.R,
	  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/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/gompertz-multi-mif.rda, inst/doc/gompertz-trajmatch.rda,
	  inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
	  inst/doc/manual.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, man/pomp-class.Rd, man/pomp.Rd,
	  src/euler.c, src/pomp_internal.h, src/rprocess.c,
	  src/trajectory.c, tests/sir.Rout.save: - include zeronames in
	  basic 'pomp' object. this is passed to 'rprocess' and used by the
	  codes in 'trajectory'.
	  - add a new section to the 'advanced topics' vignette to discuss
	  'zeronames' and accumulator variables.
	  - fix a bug in 'trajectory' for maps and 'discrete.time.sim' in
	  that step sizes were treated as variable (as for Euler steps)
	  rather than as fixed.
	* [r583] man/slice-design.Rd: - minor fix
	* [r582] inst/data-R/blowflies.R, inst/data-R/dacca.R,
	  inst/data-R/euler.sir.R, inst/data-R/gillespie.sir.R,
	  inst/data-R/gompertz.R, inst/data-R/ou2.R, inst/data-R/ricker.R,
	  inst/data-R/rw2.R, inst/data-R/verhulst.R: - use higher
	  compression
	* [r581] NAMESPACE:
	* [r580] R/parmat.R, man/parmat.Rd: - the 'parmat' function to
	  construct parameter matrices in one line
	* [r579] .Rbuildignore: - add an .Rbuildignore file

2012-01-07  kingaa

	* [r578] inst/doc/advanced_topics_in_pomp.Rnw, inst/examples/sir.R,
	  inst/examples/sir.c: - update the examples
	* [r577] DESCRIPTION, R/pomp.R, R/trajectory-pomp.R,
	  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, inst/data-R/dacca.R,
	  inst/data-R/euler.sir.R, inst/data-R/gillespie.sir.R,
	  inst/data-R/gompertz.R, inst/data-R/ou2.R, inst/data-R/ricker.R,
	  inst/data-R/rw2.R, inst/data-R/verhulst.R,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/gompertz-multi-mif.rda, inst/doc/gompertz-trajmatch.rda,
	  inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
	  inst/doc/manual.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, man/pomp-class.Rd, man/pomp.Rd,
	  src/trajectory.c: - add 'skelmap.delta.t' as a slot in the basic
	  'pomp' object

2012-01-05  kingaa

	* [r576] DESCRIPTION, data/LondonYorke.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/euler.sir.R,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  inst/doc/manual.pdf, man/trajectory-pomp.Rd: - update the data
	  files and vignettes
	  - the 'euler.sir' data()-loadable example now uses 'zeronames'
	  for the deterministic skeleton
	* [r575] inst/doc/manual.Rnw, inst/doc/manual.pdf: - put the manual
	  into the set of vignettes
	* [r574] tests/ou2-probe.Rout.save, tests/ricker-probe.Rout.save: -
	  update the unit tests
	* [r573] R/trajectory-pomp.R, src/euler.c, src/pomp_internal.h,
	  src/sir.c, src/trajectory.c, tests/sir.R, tests/sir.Rout.save: -
	  put calculation of Euler steps into a separate routine, now used
	  both by the Euler plugin and by the deterministic map iterator
	  - 'trajectory' can now make use of 'zeronames' a la the Euler
	  plugin
	  - 'trajectory' for maps can now handle a general timestep
	* [r572] inst/doc/index.html, inst/doc/manual.Rnw,
	  inst/doc/manual.pdf: - include the manual pdf among the vignettes

2011-12-24  kingaa

	* [r571] DESCRIPTION, R/pomp.R, man/pomp.Rd, tests/fhn.Rout.save,
	  tests/ricker-probe.Rout.save: - finish removing deprecated
	  'skeleton.map' and 'skeleton.vectorfield' interface
	* [r570] NAMESPACE, R/profile-design.R, R/slice-design.R,
	  R/sobol.R, man/profile-design.Rd, man/slice-design.Rd,
	  man/sobol.Rd, tests/fhn.R: - remove deprecated codes
	  'slice.design', 'sobol.design', and 'profile.design'

2011-12-14  kingaa

	* [r569] inst/NEWS: - update NEWS file
	  - 'bsmc' is actually still using 'sample.int' (the last log entry
	  notwithstanding)

2011-12-13  kingaa

	* [r568] DESCRIPTION, R/bsmc.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  man/bsmc.Rd, tests/ou2-bsmc.R, tests/ou2-bsmc.Rout.save: - fix
	  some inconsistencies with the arguments of 'bsmc'
	  - switch 'bsmc' to using 'systematic_resampling' instead of
	  'sample.int'

2011-11-22  kingaa

	* [r567] R/bsmc.R, inst/NEWS: - update NEWS file
	* [r566] DESCRIPTION, R/bsmc.R, inst/TODO: - fix bug in 'bsmc' that
	  arises when the state space is 1-D (add drop=FALSE flag to []
	  operation)

2011-11-12  kingaa

	* [r565] DESCRIPTION, inst/ChangeLog, inst/NEWS: - version 0.39-4

2011-11-10  kingaa

	* [r564] DESCRIPTION, R/sannbox.R, tests/ou2-probe.Rout.save: -
	  change SANN algorithm in sannbox to replace non-finite
	  objective-function values with a big number (as is done in
	  optim's SANN).
	  - update test file

2011-10-21  kingaa

	* [r563] DESCRIPTION, R/nlf-objfun.R, R/traj-match.R: - fix
	  infelicity in 'traj.match' and 'nlf' that arises when the 'data'
	  slot has no rownames (thanks to K. Hader) for pointing it out

2011-10-18  kingaa

	* [r562] tests/ou2-probe.R: - avoid deprecated mean(<data-frame>)
	* [r561] DESCRIPTION, R/pomp-methods.R, inst/NEWS, man/probe.Rd,
	  man/spect.Rd, man/traj-match.Rd: - minor corrections to the
	  documentation

2011-09-05  kingaa

	* [r560] inst/ChangeLog: - update ChangeLog
	* [r559] tests/ou2-icfit.Rout.save: - update file
	* [r558] DESCRIPTION, R/mif.R, inst/NEWS, man/mif.Rd,
	  tests/ou2-icfit.R, tests/ou2-icfit.Rout.save, tests/sir-icfit.R,
	  tests/sir-icfit.Rout.save: - 'mif' is modified to allow
	  estimation of IVPs only
	  - update the 'mif' help page to document this
	  - add codes to test this in 'tests/ou2-icfit'
	  - remove the 'sir-icfit' test codes for the moment

2011-09-03  kingaa

	* [r557] DESCRIPTION, inst/NEWS, src/initstate.c, tests/rw2.R,
	  tests/rw2.Rout.save: - add trap for user initializer that does
	  not return vectors of a uniform size

2011-09-02  kingaa

	* [r556] DESCRIPTION, inst/NEWS, man/mif.Rd, man/pfilter.Rd: -
	  improve the help files for 'pfilter' and 'mif' so as to explain
	  how to use non-scalar (vector or function) values for the 'Np'
	  argument.
	  - the 'mif' help file description of the 'ic.lag' argument also
	  improved

2011-08-31  kingaa

	* [r555] tests/sir-icfit.Rout.save:
	* [r554] NAMESPACE, R/profile-design.R, R/slice-design.R,
	  R/sobol.R, inst/NEWS, inst/TODO, man/profile-design.Rd,
	  man/slice-design.Rd, man/sobol.Rd, tests/ou2-mif.R,
	  tests/ou2-mif.Rout.save, tests/sir-icfit.R: - deprecate
	  'sobol.design' and 'slice.design' in favor of 'sobolDesign' and
	  'sliceDesign'
	* [r553] R/traj-match.R, tests/ou2-trajmatch.R,
	  tests/ou2-trajmatch.Rout.save: - fix bug in 'traj.match' to do
	  with parameters not being saved when the pomp object had an empty
	  'params' slot
	* [r552] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: -
	  try using PNG instead of JPEG to get around R-Forge's limitations
	* [r551] inst/ChangeLog: - update ChangeLog
	* [r550] DESCRIPTION, NAMESPACE, R/mif.R, R/profile-design.R,
	  inst/NEWS, man/profile-design.Rd: - replace 'profile.design' by
	  'profileDesign' to eliminate warnings during package check
	  ('profile.design' is mistaken for an undocumented S3 method). The
	  former is now deprecated.

2011-08-30  kingaa

	* [r549] R/pfilter.R, inst/NEWS, tests/filtfail.Rout.save,
	  tests/pfilter.R, tests/pfilter.Rout.save: - Bug fix: when
	  'pfilter' is called with a single parameter vector supplied in
	  the 'params' argument, these parameters are copied into the
	  'params' slot of the resulting 'pfilterd.pomp' object.

2011-08-29  kingaa

	* [r548] DESCRIPTION, inst/ChangeLog, inst/TODO:
	* [r547] data/LondonYorke.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: -
	  compress the data files

2011-08-24  kingaa

	* [r546] R/plot-pomp.R: - one can now change the ylabels in
	  plotting a pomp object
	* [r545] DESCRIPTION, NAMESPACE, R/plot-pomp.R, R/pomp-methods.R,
	  inst/NEWS, src/initstate.c, src/lookup_table.c,
	  src/pomp_internal.h, tests/gillespie.Rout.save,
	  tests/sir.Rout.save: - improve 'lookup_in_table', which can now
	  handle multiple index values
	  - as(po,'data.frame'), 'po' a 'pomp' object, now has columns for
	  (interpolated) covariates
	  - plot(po) behaves as before if 'po' is a 'pomp' object

2011-08-23  kingaa

	* [r544] DESCRIPTION, data/dacca.rda, inst/data-R/dacca.R: - fix
	  infelicity in 'dacca' object

2011-08-17  kingaa

	* [r543] DESCRIPTION, inst/doc/ricker-probe-plot.jpg: - minor
	  changes
	* [r542] inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf, inst/doc/pomp.bib,
	  inst/doc/ricker-probe-plot.jpg: - update reference in intro
	  vignette
	* [r541] inst/ChangeLog: - update ChangeLog
	* [r540] inst/NEWS: - update NEWS file
	* [r539] man/pomp-methods.Rd, src/dprocess.c: - remove unused
	  variable in 'dprocess.c'
	  - use \S3method markup in documentation of 'as.data.frame.pomp'
	* [r538] DESCRIPTION, inst/ChangeLog: - to upload to CRAN
	* [r537] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
	  inst/doc/pomp.bib, inst/doc/ricker-probe-plot.jpg: - update
	  reference in intro vignette

2011-08-15  kingaa

	* [r536] inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - update vignettes
	* [r535] inst/doc/Makefile, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ricker-probe-plot.jpg: -
	  keep the jpeg files

2011-08-14  kingaa

	* [r534] DESCRIPTION, src/pfilter.c, src/sir.c: - clean up some of
	  the C code to get rid of annoying warnings

2011-08-08  kingaa

	* [r533] DESCRIPTION, inst/ChangeLog, inst/TODO:
	* [r532] data/gillespie.sir.rda, inst/data-R/gillespie.sir.R,
	  inst/examples/gompertz.R, inst/examples/sir.R,
	  inst/examples/sir.c, man/gompertz.Rd: - include parameter
	  transformations in 'gillespie.sir'
	  - bring examples into line with codes in vignettes
	* [r531] data/verhulst.rda, inst/data-R/verhulst.R,
	  tests/verhulst.R, tests/verhulst.Rout.save: - re-code verhulst
	  example with more exemplary style.
	  - include a new unit-test in tests/verhulst.R

2011-08-02  kingaa

	* [r530] DESCRIPTION, R/mif-methods.R, R/pomp-methods.R,
	  inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
	  man/mif-methods.Rd, tests/gompertz.R, tests/gompertz.Rout.save: -
	  add 'transform' argument to 'conv.rec' method for 'mif' objects
	  - add new unit test 'tests/gompertz.R' which tests the
	  transformation facilities in 'coef', 'coef<-', and 'conv.rec'
	  - small changes to 'intro_to_pomp' vignette
	  - bug fix in 'pomp:::pomp.transform'

2011-07-28  kingaa

	* [r529] inst/ChangeLog:
	* [r528] DESCRIPTION, R/pomp-methods.R, R/pomp.R,
	  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/ChangeLog,
	  inst/NEWS, inst/data-R/dacca.R, inst/data-R/euler.sir.R,
	  inst/data-R/gompertz.R, inst/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/gompertz-multi-mif.rda, inst/doc/gompertz-trajmatch.rda,
	  inst/doc/intro_to_pomp.Rnw, 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,
	  man/dacca.Rd, man/pomp-class.Rd, man/pomp-methods.Rd,
	  man/pomp.Rd, src/sir.c, tests/ricker.Rout.save,
	  tests/rw2.Rout.save, tests/sir-icfit.Rout.save, tests/sir.R,
	  tests/sir.Rout.save: - add facility for parameter transformations
	  to pomp:
	  - 'pomp' takes two new optional arguments: 'parameter.transform',
	  'parameter.inv.transform'
	  - 'coef' and 'coef<-' methods take new optional argument
	  'transform' which applies the appropriate transform when TRUE
	  - all data()-loadable objects are changed accordingly:
	  'euler.sir', 'dacca', and 'gompertz' make use of this facility
	  - the section on parameter transformation in the 'intro_to_pomp'
	  vignette has been changed accordingly
	  - add a section on byte-compiled code to the advanced topics
	  vignette

2011-07-24  kingaa

	* [r527] inst/ChangeLog: - update ChangeLog
	* [r526] DESCRIPTION, src/SSA.f, tests/fhn.Rout.save,
	  tests/filtfail.Rout.save, tests/gillespie.Rout.save,
	  tests/logistic.Rout.save, tests/ou2-bsmc.Rout.save,
	  tests/ou2-forecast.Rout.save, tests/ou2-kalman.Rout.save,
	  tests/ou2-mif.Rout.save, tests/ou2-nlf.Rout.save,
	  tests/ou2-pmcmc.Rout.save, tests/ou2-probe.Rout.save,
	  tests/ou2-procmeas.Rout.save, tests/ou2-simulate.Rout.save,
	  tests/ou2-trajmatch.Rout.save, tests/pfilter.Rout.save,
	  tests/pomppomp.Rout.save, tests/ricker-probe.Rout.save,
	  tests/ricker-spect.Rout.save, tests/ricker.Rout.save,
	  tests/rw2.Rout.save, tests/sir-icfit.Rout.save,
	  tests/sir.Rout.save, tests/skeleton.Rout.save,
	  tests/synlik.Rout.save: - modify src/SSA.f to get rid of warning
	  messages seen in gfortran-4.6
	  - update tests/*.Rout.save files

2011-07-11  kingaa

	* [r525] DESCRIPTION, inst/ChangeLog,
	  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: - add 'pdftex' option to
	  \usepackage{graphicx} in vignettes

2011-07-07  kingaa

	* [r524] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - version 0.38-5
	* [r523] DESCRIPTION:
	* [r522] inst/doc/intro_to_pomp.Rnw: - fix typo in intro vignette
	  (thanks to Andreas Handel)

2011-07-05  kingaa

	* [r521] inst/NEWS: - update NEWS file
	* [r520] DESCRIPTION, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
	  - update ChangeLog

2011-06-30  kingaa

	* [r519] R/pfilter.R: - an error is generated in 'pfilter' if
	  'dmeasure' returns any non-finite value (not just NA, as before)
	* [r518] DESCRIPTION, R/spect.R: - fix 'spect' so that the
	  frequencies reflect the timescale of observation

2011-06-29  kingaa

	* [r517] DESCRIPTION, R/aaa.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:

2011-06-09  kingaa

	* [r516] inst/ChangeLog, man/eulermultinom.Rd: - tweak to
	  'eulermultinom' man page

2011-06-08  kingaa

	* [r515] DESCRIPTION, inst/ChangeLog, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf: - remove the deterministic skeleton
	  from the SIR-model pomp objects.

2011-06-07  kingaa

	* [r514] man/dacca.Rd, man/eulermultinom.Rd: - fix 'dacca.Rd' to
	  eliminate codoc warning
	  - provide ascii-only eqns for 'eulermultinom' help

2011-06-06  kingaa

	* [r513] man/gompertz.Rd: - fix Gompertz model documentation
	* [r512] DESCRIPTION, inst/NEWS: - update NEWS file
	* [r511] man/bsplines.Rd, man/dacca.Rd, man/eulermultinom.Rd,
	  man/gompertz.Rd, man/nlf.Rd, man/plugins.Rd, man/pomp-methods.Rd,
	  man/pomp.Rd, man/ricker.Rd: - documentation improvements

2011-06-05  kingaa

	* [r510] DESCRIPTION, R/pomp.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, src/pfilter.c, src/tsir.c: - remove
	  unused variables in C codes (per build warning)
	  - fix errors in 'intro to pomp' vignette
	  - minor change to some warnings in 'pomp'

2011-06-03  kingaa

	* [r509] DESCRIPTION, inst/NEWS,
	  inst/doc/advanced_topics_in_pomp.Rnw, man/pfilter.Rd,
	  man/plugins.Rd, man/pomp.Rd, man/simulate-pomp.Rd: - many minor
	  improvements to the help pages

2011-06-02  kingaa

	* [r508] DESCRIPTION, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, inst/doc/nlf-block-boot.rda,
	  inst/doc/nlf-lag-tests.rda: - improvements/corrections to the
	  intro vignette

2011-06-01  kingaa

	* [r507] inst/NEWS: - update NEWS file
	* [r506] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
	  inst/doc/nlf-multi-short.rda: - abbreviate one results file
	* [r505] 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: - added binary results files for
	  nlf portion of intro vignette

2011-05-31  kingaa

	* [r504] inst/ChangeLog, inst/NEWS,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
	* [r503] DESCRIPTION, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, inst/doc/pomp.bib: - add section on
	  NLF to intro vignette (by S. Ellner)

2011-05-27  kingaa

	* [r502] R/nlf.R: - fix newly introduced bug
	* [r501] DESCRIPTION, R/nlf.R, tests/ou2-nlf.R,
	  tests/ou2-nlf.Rout.save: - fix bug in 'nlf': nconverge was
	  essentially ignored

2011-05-22  kingaa

	* [r500] DESCRIPTION, inst/ChangeLog:
	* [r499] R/pomp.R, inst/NEWS, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf: - fix bug in pomp-pomp to do with
	  userdata slot not being preserved
	  - improve the intro to pomp vignette (much more explanation of
	  the SIR model)

2011-05-20  kingaa

	* [r498] inst/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/advanced_topics_in_pomp.pdf: - fix some typos in the
	  Advanced Topics vignette
	* [r497] data/ou2.rda, inst/data-R/ou2.R: - minor tweak to ou2 pomp
	* [r496] inst/ChangeLog:
	* [r495] man/pomp-package.Rd: - update the package?pomp help page.
	* [r494] DESCRIPTION: - correct the date
	* [r493] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: -
	  cosmetic fix
	* [r492] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - update changelog and vignettes
	* [r491] inst/doc/Makefile, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf: - plot probe figure as jpeg to reduce
	  size of PDF
	* [r490] DESCRIPTION, R/mif.R, R/pfilter.R, R/pmcmc.R,
	  data/blowflies.rda, data/dacca.rda, data/euler.sir.rda,
	  data/gillespie.sir.rda, data/gompertz.rda, data/ricker.rda,
	  data/rw2.rda, data/verhulst.rda, inst/ChangeLog, inst/NEWS,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/gompertz-multi-mif.rda, inst/doc/gompertz-trajmatch.rda,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ricker-mif.rda,
	  inst/doc/ricker-probe-match.rda, man/pfilter.Rd, src/pfilter.c,
	  tests/ou2-forecast.R, tests/ou2-forecast.Rout.save,
	  tests/ou2-mif.R, tests/ou2-mif.Rout.save, tests/ou2-procmeas.R,
	  tests/ou2-procmeas.Rout.save, tests/ou2-trajmatch.Rout.save,
	  tests/pfilter.R, tests/pfilter.Rout.save, tests/sir-icfit.R,
	  tests/sir-icfit.Rout.save, tests/synlik.R,
	  tests/synlik.Rout.save: - pfilter has been redesigned to allow
	  variable numbers of particles
	  - pmcmc and mif have been modified to accommodate this
	  - the 'saved.states' and 'saved.params' slots in 'pfilterd.pomp'
	  objects are now lists of rank-2 arrays (they were each a rank-3
	  array)

2011-05-19  kingaa

	* [r489] tests/ou2-procmeas.R, tests/ou2-procmeas.Rout.save: - new
	  test for dmeasure and dprocess in ou2
	* [r488] data/ou2.rda, inst/data-R/ou2.R, man/ou2.Rd, src/ou2.c,
	  tests/ou2-probe.Rout.save: - rework the OU2 model slightly
	* [r487] tests/sir.Rout.save: - update sir test
	* [r486] DESCRIPTION, data/blowflies.rda, data/dacca.rda,
	  data/gompertz.rda, data/ou2.rda, data/ricker.rda, data/rw2.rda,
	  data/verhulst.rda, inst/NEWS, inst/doc/gompertz-multi-mif.rda,
	  inst/doc/gompertz-trajmatch.rda, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ricker-mif.rda,
	  inst/doc/ricker-probe-match.rda, tests/sir-icfit.Rout.save,
	  tests/sir.R: - minor improvements to 'intro to pomp' vignette
	  - update data objects
	  - update tests
	* [r485] data/euler.sir.rda, data/gillespie.sir.rda,
	  inst/examples/sir.c, src/sir.c: - change the measurement model
	  for the SIR example
	* [r484] inst/data-R/ou2.R, inst/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/advanced_topics_in_pomp.pdf: - improve the 'advanced
	  topics' vignette
	  - update the data()-loadable ou2 object
	* [r483] inst/examples/ou2.c, src/ou2.c: - modifications to the C
	  codes for the OU2 example
	* [r482] R/plugins.R: - change 'discrete.time.sim' so that
	  'delta.t' is not a required argument of 'step.fun'
	* [r481] man/pomp-package.Rd, man/pomp.Rd: - improve the
	  documentation a bit

2011-05-17  kingaa

	* [r480] man/pomp.Rd: - put in links to pomp methods

2011-05-16  kingaa

	* [r479] DESCRIPTION, R/sannbox.R, R/sobol.R, R/spect-match.R,
	  R/spect.R: - replace some instances of 'sapply' with 'vapply'

2011-05-13  kingaa

	* [r478] DESCRIPTION, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
	  - update DESCRIPTION and ChangeLog
	* [r477] data/blowflies.rda, data/dacca.rda, data/euler.sir.rda,
	  data/gillespie.sir.rda, data/ou2.rda, data/rw2.rda,
	  data/verhulst.rda, inst/NEWS,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/gompertz-multi-mif.rda, inst/doc/gompertz-trajmatch.rda,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ricker-mif.rda,
	  inst/doc/ricker-probe-match.rda, man/pomp.Rd: - update vignettes
	  - update data()-loadable objects
	  - minor tweak to pomp man page
	  - tweak to NEWS file

2011-05-12  kingaa

	* [r476] DESCRIPTION: - fix author line
	* [r475] DESCRIPTION, inst/ChangeLog, inst/NEWS: - update ChangeLog
	  and NEWS

2011-05-11  kingaa

	* [r474] tests/sir-icfit.R, tests/sir-icfit.Rout.save: - add a test
	  for the new 'pfilter'-based initial-condition-estimation method
	* [r473] tests/ou2-forecast.R, tests/ou2-forecast.Rout.save: -
	  update this test to use new 'save.params' option
	* [r472] tests/logistic.Rout.save: - minor change
	* [r471] tests/fhn.Rout.save: - minor change
	* [r470] R/mif.R, R/pfilter.R, R/pmcmc.R, inst/NEWS,
	  man/pfilter.Rd: - add new argument 'save.params' to 'pfilter' to
	  allow saving the parameter portion of the particles
	  - change the 'pfilterd.pomp' slot name 'last.states' to
	  'saved.states', which connects with the option name
	  - add a new slot 'saved.params' to the 'pfilterd.pomp' object
	  - update 'pmcmc' and 'mif' in accordance with the above changes
	  - modify 'pfilter' so that
	  'coef(pfilter(obj,params=theta))==theta' as in 'mif', 'simulate',
	  etc.
	* [r469] DESCRIPTION, R/pfilter.R, inst/ChangeLog, inst/NEWS,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  src/pfilter.c: - eliminate unnecessary copying of identical
	  parameter particles

2011-05-10  kingaa

	* [r468] DESCRIPTION:

2011-05-09  kingaa

	* [r467] inst/ChangeLog, inst/NEWS,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/index.html,
	  inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: - add a
	  diagram to intro vignette
	  - add 'index.html' file for vignettes
	  - fix NEWS file format
	* [r464] inst/NEWS: - update
	* [r463] NAMESPACE, R/pomp.R, 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/ChangeLog, inst/NEWS, inst/data-R/euler.sir.R,
	  inst/data-R/gompertz.R, inst/data-R/ou2.R, inst/data-R/ricker.R,
	  inst/data-R/verhulst.R, inst/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/gompertz-trajmatch.rda, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, inst/examples/gompertz.R,
	  inst/examples/gompertz.c, inst/examples/logistic.R,
	  inst/examples/sir.R, inst/include/pomp.h, man/pomp-class.Rd,
	  man/pomp.Rd, src/pomp.h, src/skeleton.c, tests/fhn.R,
	  tests/fhn.Rout.save, tests/logistic.R, tests/logistic.Rout.save,
	  tests/ou2-simulate.Rout.save, tests/pomppomp.R,
	  tests/pomppomp.Rout.save, tests/ricker.Rout.save, tests/rw2.R,
	  tests/rw2.Rout.save, tests/sir.R, tests/sir.Rout.save,
	  tests/skeleton.Rout.save: - the 'pomp' arguments 'skeleton.map'
	  and 'skeleton.vectorfield' are now deprecated in favor of
	  'skeleton' and 'skeleton.type'
	  - 'pomp' is now a generic function with methods for data of type
	  'numeric', 'matrix', 'data.frame', and 'pomp'. the latter method
	  allows for copying of 'pomp' objects with modification.
	* [r462] R/pomp-methods.R: - remove printing of call slot
	* [r461] src/gompertz.c: - better commenting and some cleanup
	* [r460] R/pomp-fun.R: - fix bug in error-checking
	  - allow pass-through of 'pomp.fun' objects
	* [r459] DESCRIPTION, R/simulate-pomp.R, R/trajectory-pomp.R: -
	  remove the warnings that were added in 0.34-1 regarding changed
	  default behavior of 'simulate' and 'trajectory'

2011-05-05  kingaa

	* [r458] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf:
	* [r457] DESCRIPTION, data/blowflies.rda, data/dacca.rda,
	  inst/ChangeLog, inst/data-R/blowflies.R,
	  inst/data-R/blowflies.csv, inst/data-R/dacca.R,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  man/blowflies.Rd, man/dacca.Rd, src/tsir.c: - add blowflies
	  example
	  - fix bug in tsir code
	  - rearrange 'dacca' example

2011-05-04  kingaa

	* [r456] R/aaa.R, R/mif-methods.R, R/pfilter-methods.R,
	  R/pfilter.R, man/mif-methods.Rd, man/pfilter-methods.Rd,
	  man/pfilter.Rd: - 'pred.mean', 'pred.var', and 'filter.mean'
	  methods are now defined for 'pfilterd.pomp' objects (and not just
	  'mif' objects)
	* [r455] R/trajectory-pomp.R: - 'trajectory' now gives a more
	  informative error when no skeleton is present
	* [r454] DESCRIPTION, 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/ChangeLog,
	  inst/NEWS, inst/data-R/dacca.R, inst/data-R/euler.sir.R,
	  inst/data-R/gillespie.sir.R, inst/data-R/gompertz.R,
	  inst/data-R/ou2.R, inst/data-R/ricker.R, inst/data-R/rw2.R,
	  inst/data-R/verhulst.R, src/blowfly.c, src/probe_acf.c: - fix bug
	  in error message in 'probe_acf.c'
	  - update data()-loadable examples

2011-05-03  kingaa

	* [r453] inst/doc/intro_to_pomp.pdf:
	* [r452] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: -
	  minor improvement to 'compare.mif' figure
	* [r451] tests/filtfail.R, tests/filtfail.Rout.save,
	  tests/sir-icfit.R, tests/sir-icfit.Rout.save: - two new tests:
	  'sir-icfit' and 'filtfail'
	* [r450] DESCRIPTION, R/pfilter.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, src/pfilter.c, src/resample.c,
	  tests/ou2-probe.Rout.save, tests/ricker-probe.Rout.save,
	  tests/ricker.Rout.save: - move resampling and random-walking
	  inside 'pfilter.internal' into C (pfilter.c)
	  - move resampling codes from 'resample.c' to 'pfilter.c'
	  - update test .save files
	  - minor corrections in 'intro_to_pomp' vignette
	* [r449] R/bsplines.R, man/bsplines.Rd: - add 'names' argument

2011-04-27  kingaa

	* [r448] inst/ChangeLog, inst/NEWS: - version 0.36-5
	  - update NEWS file and Changelog

2011-04-24  kingaa

	* [r447] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf:
	* [r446] DESCRIPTION, R/pfilter.R, inst/ChangeLog, src/resample.c:
	  - fix bug in 'pfilter' introduced in version 0.32-6 (rev 315):
	  upon filtering failure, state variables were left un-updated.
	  Thanks to Karim Khader for noticing circumstances that led to the
	  notice of this bug.
	  - minor rearrangement of the codes in resample.c

2011-04-20  kingaa

	* [r445] DESCRIPTION, 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/gompertz.R, inst/doc/gompertz-multi-mif.rda,
	  inst/doc/gompertz-trajmatch.rda, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ou2-multi-mif.rda,
	  inst/doc/ou2-trajmatch.rda, src/gompertz.c: - improvements to the
	  "intro" vignette
	  - fix problem with gompertz measurement model
	* [r444] DESCRIPTION, R/pomp-methods.R, 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/ChangeLog, inst/data-R/gompertz.R,
	  inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/gompertz-multi-mif.rda, inst/doc/gompertz-trajmatch.rda,
	  inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
	  inst/doc/pomp.bib, man/gompertz.Rd, src/gompertz.c: - fix bug in
	  'states' method when 'states' slot is empty
	  - add Gompertz model
	  - edit 'intro_to_pomp' vignette to focus on Gompertz model

2011-04-19  kingaa

	* [r443] tests/synlik.Rout.save: - add tests/synlik.Rout.save file
	* [r442] DESCRIPTION, R/probe.R, man/probed-pomp-methods.Rd,
	  tests/synlik.R: - add 'logLik' method for probed.pomp objects

2011-04-15  kingaa

	* [r441] man/probe.Rd: - synchronize with changes in probe.R

2011-04-13  kingaa

	* [r440] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - updated vignettes and changelog

2011-04-12  kingaa

	* [r439] DESCRIPTION, R/plugins.R, R/probe-match.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, man/plugins.Rd: - add 'sannbox'
	  constrained simulated annealing method for probe matching
	  - re-implement the 'discrete.time.sim' plugin

2011-02-22  kingaa

	* [r437] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
	  inst/doc/ou2-multi-mif.rda: - tinker with mif example in intro
	  vignette
	* [r436] R/pomp.R: - do a check in 'pomp' to make sure tcovar
	  embraces times; warn else

2011-02-19  kingaa

	* [r435] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: -
	  improvements to the intro vignette

2011-02-18  kingaa

	* [r434] inst/ChangeLog, inst/doc/ou2-first-mif.rda,
	  inst/doc/ou2-multi-mif.rda: - multiple mif runs from different
	  starting places
	* [r433] src/blowfly.c: - allow for variable delta.t

2011-02-16  kingaa

	* [r432] DESCRIPTION, R/version.R, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ou2-trajmatch.rda,
	  inst/doc/ricker-mif.rda, inst/doc/ricker-probe-match.rda: -
	  additions to the intro vignette
	  - add "version()" to report/check pomp version

2010-11-30  kingaa

	* [r431] DESCRIPTION, R/aaa.R: - revert last change

2010-11-29  kingaa

	* [r430] DESCRIPTION, R/aaa.R: - turn banner back on

2010-11-24  kingaa

	* [r429] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - update changelog and vignettes
	* [r428] R/pomp.R: - set storage.mode of 'covar' and 'tcovar' to
	  'double'
	* [r427] DESCRIPTION, NAMESPACE, R/aaa.R, R/probe-match.R,
	  R/traj-match.R, inst/NEWS, man/probe.Rd: - make 'probe.match'
	  into a method
	  - tinker with generics
	* [r426] inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ou2-first-mif.rda,
	  inst/doc/ou2-trajmatch.rda: - update vignettes

2010-11-23  kingaa

	* [r425] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf, src/dmeasure.c: - cosmetics
	  - update ChangeLog & vignettes
	* [r424] man/trajectory-pomp.Rd, tests/fhn.Rout.save,
	  tests/ou2-trajmatch.R, tests/ou2-trajmatch.Rout.save: - update
	  the tests
	  - fix the example in 'trajectory'
	  - the deterministic skeleton for 'euler.sir' now includes a state
	  variable for the approximate number of cases (not cumulative
	  cases as before)
	* [r423] DESCRIPTION, NAMESPACE, R/aaa.R, R/dmeasure-pomp.R,
	  R/pomp-fun.R, R/pomp.R, R/rmeasure-pomp.R, R/skeleton-pomp.R,
	  R/traj-match.R, R/trajectory-pomp.R, data/dacca.rda,
	  data/gillespie.sir.rda, data/ou2.rda, data/ricker.rda,
	  data/rw2.rda, data/verhulst.rda, inst/ChangeLog, inst/NEWS,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  man/traj-match.Rd, man/trajectory-pomp.Rd, src/dmeasure.c,
	  src/pomp_fun.c, src/pomp_internal.h, src/rmeasure.c,
	  src/simulate.c, src/skeleton.c, src/trajectory.c: - when PACKAGE
	  is undefined in 'pomp' or 'pomp.fun', the default is now ""
	  (rather than 'character(0)')
	  - rewrite 'simulate' and 'trajectory' to minimize extraction from
	  'pomp.fun' objects (and consequent lookup of dynamically-loaded
	  symbols).
	  - rewrite 'skeleton', 'rmeasure', and 'dmeasure' in keeping with
	  above
	  - rewrite 'traj.match' internals
	  - add 'sannbox' box-constrained simulated annealing algorithm to
	  'traj.match' suite of optimizers
	  - 'traj.match' generates an error when 'est' is not supplied and
	  'eval.only=FALSE'
	  - for continuous-time POMPs, 'trajectory' computation is now done
	  by a single call to 'deSolve::ode' (vs. one call for each
	  parameter set as before)
	  - new .Call-able function 'get_pomp_fun' to extract from
	  'pomp.fun' objects
	  - iteration of discrete-time deterministic skeleton maps is now
	  done in C for speed (new file 'trajectory.c')
	* [r422] R/dprocess-pomp.R: - fix bug
	* [r421] R/sannbox.R: - add a simulated annealing algorithm with
	  box constraints

2010-11-17  kingaa

	* [r420] src/dmeasure.c, src/rmeasure.c, src/skeleton.c: - remove
	  some redundant/unnecessary lines

2010-11-16  kingaa

	* [r419] R/skeleton-pomp.R: - remove one layer of try/catch
	* [r418] src/skeleton.c: - minor tweaks

2010-11-14  kingaa

	* [r417] DESCRIPTION, NAMESPACE, R/aaa.R, R/bsmc.R,
	  R/dmeasure-pomp.R, R/dprocess-pomp.R, R/init-state-pomp.R,
	  R/mif.R, R/rmeasure-pomp.R, R/rprocess-pomp.R, inst/ChangeLog,
	  man/dmeasure-pomp.Rd, man/dprocess-pomp.Rd,
	  man/init.state-pomp.Rd, man/pomp-methods.Rd,
	  man/rmeasure-pomp.Rd, man/rprocess-pomp.Rd, man/skeleton-pomp.Rd,
	  man/traj-match.Rd, man/trajectory-pomp.Rd: - make declarations of
	  generics uniform

2010-11-09  kingaa

	* [r416] DESCRIPTION, R/traj-match.R,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
	  - revert version dependence to R>=2.10.1
	  - fix bug in 'traj.match'
	* [r415] DESCRIPTION, R/traj-match.R,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  tests/ou2-trajmatch.R, tests/ou2-trajmatch.Rout.save: - fix bug
	  in 'traj.match'

2010-11-08  kingaa

	* [r414] DESCRIPTION, R/traj-match.R, data/euler.sir.rda,
	  inst/data-R/euler.sir.R, man/traj-match.Rd, src/sir.c,
	  tests/sir.R, tests/sir.Rout.save: - 'traj.match' is now
	  implemented as a generic with methods for 'pomp' and
	  'traj.matched.pomp' objects
	  - the 'euler.sir' example has a different skeleton, one for which
	  'cases' gives the approximate weekly number of new cases
	* [r413] DESCRIPTION, NAMESPACE, R/probe-match.R, R/spect-match.R,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  man/pfilter.Rd, man/pmcmc-class.Rd, man/pmcmc.Rd, man/probe.Rd,
	  man/probed-pomp-class.Rd, man/spect-pomp-class.Rd, man/spect.Rd,
	  man/traj-match.Rd, tests/ricker-probe.R,
	  tests/ricker-probe.Rout.save, tests/ricker-spect.R,
	  tests/ricker-spect.Rout.save: - arrange for all classes to be
	  exported
	  - rearrange documentation for classes; now it's together with the
	  constructors
	  - fix bug in 'spect.match' with eval.only=TRUE
	  - add slot in 'probe.matched.pomp' to make it parallel with
	  'spect.matched.pomp'

2010-11-07  kingaa

	* [r412] R/traj-match.R, inst/ChangeLog,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ou2-first-mif.rda,
	  inst/doc/ou2-trajmatch.rda: - streamline 'traj.match' slightly
	* [r411] R/nlf-objfun.R, R/spect.R, inst/doc/intro_to_pomp.Rnw,
	  man/basic-probes.Rd, man/spect.Rd: - replace 'data.array' with
	  'obs' as the preferred method
	* [r410] R/traj-match.R, R/trajectory-pomp.R, inst/ChangeLog,
	  src/sir.c: - fix traj-match objective function
	  - minor tweak to trajectory generic
	  - make the variables 'cases' in SIR trajectories integer-valued
	* [r409] src/probe_acf.c, src/synth_lik.c: - get rid of some unused
	  varibles

2010-11-05  kingaa

	* [r407] DESCRIPTION, R/mif-class.R, R/mif.R, R/particles-mif.R,
	  R/pfilter-mif.R, R/pfilter.R, R/pmcmc.R, 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/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  inst/doc/ou2-first-mif.rda, inst/doc/ou2-trajmatch.rda,
	  man/bsmc.Rd, man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd,
	  man/pfilter.Rd, man/pmcmc-class.Rd, man/pmcmc-methods.Rd,
	  man/pmcmc.Rd, man/probe.Rd, man/probed-pomp-methods.Rd,
	  man/spect.Rd, man/traj-match.Rd, man/trajectory-pomp.Rd,
	  tests/ou2-forecast.R, tests/ou2-forecast.Rout.save,
	  tests/ou2-mif.R, tests/ou2-mif.Rout.save, tests/ou2-pmcmc.R,
	  tests/ou2-pmcmc.Rout.save: - create new class 'pfilterd.pomp' to
	  hold results of 'pfilter'
	  - the classes 'mif' and 'pmcmc' now inherit from 'pfilterd.pomp'
	  - changed the internal representation of 'mif' object (expanded
	  'alg.pars' list to separate slots)
	  - the arguments to the generic 'dprior' have changed
	  - rearrange internal structure of 'mif' algorithm
	  - rearrange internal structure of 'pmcmc' algorithm
	  - add 'mif' and 'pmcmc' methods for 'pfilterd.pomp' objects
	  - remove 'pfilter' method for 'mif' objects: the 'pfilter' method
	  for 'pfilterd.pomp' objects does the job now
	  - change output of 'pfilter' when 'save.states=TRUE': now states
	  at final time are stored in slot 'last.states'
	  - it is now allowed to call 'pfilter' with 'save.states=TRUE' on
	  a 'mif' object.
	  - the internal man pages for various of the classes have yet to
	  be updated
	* [r405] DESCRIPTION, NAMESPACE, R/aaa.R, R/probe-match.R,
	  R/spect-match.R, R/traj-match.R, man/traj-match.Rd,
	  tests/ou2-trajmatch.R, tests/ou2-trajmatch.Rout.save: - if
	  eval.only=TRUE in traj.match, spect.match, or probe.match, the
	  returned convergence field is now NA and the message says "no
	  optimization performed"
	  - traj.match now returns an object of class traj.matched.pomp, a
	  new class that inherits from 'pomp'
	  - the 'states' slot in the 'traj.matched.pomp' object is now
	  filled with the trajectory
	  - more optimization methods are now provided in 'traj.match'
	  - the only class now exported is 'pomp'.

2010-10-25  kingaa

	* [r404] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - version 0.35-1
	* [r403] DESCRIPTION, NAMESPACE, R/spect-match.R, R/spect.R,
	  inst/NEWS, man/mif.Rd, man/probe.Rd, tests/ou2-mif.R,
	  tests/ou2-mif.Rout.save, tests/ricker.R, tests/ricker.Rout.save:
	  - remove 'seed' slot from 'spect.pomp' objects
	  - tinker with tests
	  - 'tests/ricker.R' now contains a MIF vs PM contest
	  - temporarily remove 'mif.profile.design' from the visible
	  interface

2010-10-24  kingaa

	* [r402] DESCRIPTION, inst/ChangeLog: - update changelog
	* [r401] src/pomp_mat.h, src/probe_marginal.c, src/probe_nlar.c,
	  src/synth_lik.c, tests/ou2-probe.Rout.save,
	  tests/ricker-probe.Rout.save: - get rid of all pivoting in
	  synthetic likelihood calculation
	  - make the inline routines in 'pomp_mat.h' a bit more flexible

2010-10-23  kingaa

	* [r400] DESCRIPTION:
	* [r399] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf: - update changelog and vignettes
	* [r398] src/synth_lik.c: - make headers complete
	* [r397] tests/ou2-mif.Rout.save, tests/ou2-probe.Rout.save,
	  tests/ricker-probe.Rout.save: - update the tests
	* [r396] R/probe-match.R: - go back to using synthetic likelihood
	  as the objective function
	  - deal with missing 'nsim'
	* [r395] src/probe.c: - prevent protection stack overflow with nsim
	  large
	* [r394] src/pomp_mat.h, src/synth_lik.c: - fix bug to do with
	  pivoting in 'synth_lik.c'

2010-10-21  kingaa

	* [r393] R/probe-match.R: - bug fix

2010-10-20  kingaa

	* [r392] NAMESPACE, R/mif.R, R/probe-match.R, R/probe.R,
	  man/mif.Rd, man/probed-pomp-class.Rd, tests/ou2-mif.R: - remove
	  'seed' slot from 'probed.pomp'-class objects
	  - add alternative 'neg.synth.loglik' objective function for
	  'probe-match'
	  - add new 'mif.profile.design' function for setting up 'mif'
	  profiling computations
	* [r391] inst/NEWS: - update NEWS file
	* [r390] DESCRIPTION, src/blowfly.c: - add C codes for blowfly
	  example

2010-10-19  kingaa

	* [r389] R/probe.R, man/probed-pomp-class.Rd,
	  tests/ou2-probe.Rout.save, tests/ricker-probe.Rout.save: - add
	  'synth.loglik' slot to the 'probed.pomp' object
	* [r388] tests/ou2-probe.R, tests/ricker-probe.R: - tests to go
	  along with new 'probe.ccf' options
	* [r387] DESCRIPTION, NAMESPACE, R/basic-probes.R,
	  man/basic-probes.Rd, src/probe_acf.c, src/synth_lik.c: - add
	  'synth_loglik.c': synthetic likelihood computation a la Wood
	  (2010)
	  - add 'correlation' option

2010-10-18  kingaa

	* [r386] src/probe_acf.c, src/probe_ccf.c: - move probe_ccf codes
	  to probe_acf.c
	* [r385] DESCRIPTION, R/basic-probes.R, man/basic-probes.Rd,
	  src/probe_acf.c, src/probe_ccf.c, tests/ou2-probe.R,
	  tests/ou2-probe.Rout.save, tests/ricker-probe.R,
	  tests/ricker-probe.Rout.save: - change interface to 'probe.acf':
	  now any positive lags can be specified
	  - rearrange 'probe_acf.c' and 'probe_ccf.c' cosmetically
	* [r384] src/pomp_mat.h, src/probe_marginal.c, src/probe_nlar.c: -
	  rework pomp_mat.h to make the LAPACK interface a bit more
	  flexible

2010-10-13  kingaa

	* [r383] R/pomp-methods.R: - bug fix
	* [r382] inst/NEWS: - update NEWS file

2010-10-12  kingaa

	* [r381] man/probe.Rd: - tinker with 'probe' example
	* [r380] inst/ChangeLog:
	* [r379] R/probe.R, R/simulate-pomp.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  man/probed-pomp-methods.Rd, tests/ou2-probe.R,
	  tests/ou2-probe.Rout.save, tests/ricker-probe.R,
	  tests/ricker-probe.Rout.save: - add method to coerce
	  'probed.pomp' objects to data.frames
	  - in 'simulate-pomp', it is only sometimes necessary to coerce to
	  'pomp'

2010-10-11  kingaa

	* [r378] tests/ricker-probe.Rout.save: - update
	  'tests/ricker-probe.Rout.save'
	* [r377] R/simulate-pomp.R, tests/ricker-probe.R,
	  tests/ricker-spect.R, tests/ricker-spect.Rout.save: - fix bug in
	  'simulate' as applied to objects inheriting from 'pomp'
	  - add 'tests/ricker-spect.Rout.save'

2010-10-10  kingaa

	* [r376] DESCRIPTION, inst/ChangeLog: - version 0.34-2
	* [r375] inst/doc/advanced_topics_in_pomp.Rnw,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  src/rprocess.c, src/simulate.c: - accelerate 'rprocess' and
	  'simulate' by using 'memcpy' where appropriate
	  - change the order of topics in 'advanced_topics_in_pomp'
	  vignette

2010-10-07  kingaa

	* [r374] R/pfilter.R: - update pfilter.R to make use of the
	  'offset' argument to 'rprocess'
	* [r373] DESCRIPTION:
	* [r372] NAMESPACE, R/pomp-methods.R, R/rprocess-pomp.R,
	  R/simulate-pomp.R, inst/ChangeLog, inst/NEWS,
	  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,
	  man/pomp-methods.Rd, man/rprocess-pomp.Rd, src/pomp_internal.h,
	  src/rprocess.c, src/simulate.c, tests/fhn.R, tests/fhn.Rout.save,
	  tests/gillespie.Rout.save, tests/logistic.Rout.save,
	  tests/ou2-bsmc.Rout.save, tests/ou2-forecast.Rout.save,
	  tests/ou2-kalman.Rout.save, tests/ou2-mif.Rout.save,
	  tests/ou2-nlf.Rout.save, tests/ou2-pmcmc.Rout.save,
	  tests/ou2-probe.Rout.save, tests/ou2-simulate.Rout.save,
	  tests/ou2-trajmatch.Rout.save, tests/pfilter.Rout.save,
	  tests/ricker-probe.Rout.save, tests/ricker.Rout.save,
	  tests/rw2.Rout.save, tests/sir.Rout.save,
	  tests/skeleton.Rout.save: - add 'offset' argument to 'rprocess'
	  - implement 'simulate' in C for speed
	  - add 'obs' method as synonym for 'data.array'
	  - add FitzHugh-Nagumo model tests
	* [r371] R/aaa.R: - remove banner

2010-10-06  kingaa

	* [r370] inst/ChangeLog, inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf:
	* [r369] src/probe_ccf.c, src/probe_marginal.c, src/probe_nlar.c: -
	  remove unused variables

2010-10-05  kingaa

	* [r368] inst/CITATION: - update citation
	* [r367] R/simulate-pomp.R: - minor changes
	* [r366] inst/examples/ou2.c: - put in source code for ou2 example
	  as promised in vignette
	* [r365] data/ou2.rda, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  inst/doc/ou2-first-mif.rda, inst/doc/ou2-trajmatch.rda,
	  src/ou2.c, tests/gillespie.Rout.save, tests/logistic.Rout.save,
	  tests/ou2-bsmc.Rout.save, tests/ou2-forecast.Rout.save,
	  tests/ou2-kalman.Rout.save, tests/ou2-mif.Rout.save,
	  tests/ou2-nlf.Rout.save, tests/ou2-pmcmc.Rout.save,
	  tests/ou2-probe.Rout.save, tests/ou2-simulate.Rout.save,
	  tests/ou2-trajmatch.Rout.save, tests/pfilter.Rout.save,
	  tests/ricker-probe.Rout.save, tests/ricker.Rout.save,
	  tests/rw2.Rout.save, tests/sir.Rout.save,
	  tests/skeleton.Rout.save: - fix a bug in 'ou2'
	* [r364] R/aaa.R: - fiddle with the banner
	* [r363] inst/ChangeLog:
	* [r362] tests/ou2-pmcmc.Rout.save, tests/skeleton.R,
	  tests/skeleton.Rout.save: - add in results from ou2-pmcmc test
	  - add another set of tests in 'skeleton.R'
	* [r361] DESCRIPTION, R/aaa.R, R/nlf-lql.R, R/nlf-objfun.R,
	  R/nlf.R, R/pomp-methods.R, R/simulate-pomp.R, R/spect.R,
	  R/traj-match.R, R/trajectory-pomp.R, data/euler.sir.rda,
	  data/gillespie.sir.rda, data/ou2.rda, data/ricker.rda,
	  data/rw2.rda, data/verhulst.rda, inst/ChangeLog, inst/NEWS,
	  inst/data-R/ou2.R, 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/pomp-class.Rd, man/simulate-pomp.Rd, man/trajectory-pomp.Rd,
	  man/verhulst.Rd, src/probe.c, tests/gillespie.R,
	  tests/gillespie.Rout.save, tests/logistic.R,
	  tests/logistic.Rout.save, tests/ou2-forecast.R,
	  tests/ou2-forecast.Rout.save, tests/ou2-nlf.Rout.save,
	  tests/ou2-probe.Rout.save, tests/ou2-simulate.Rout.save,
	  tests/ou2-trajmatch.Rout.save, tests/ricker-probe.Rout.save,
	  tests/ricker.R, tests/ricker.Rout.save, tests/rw2.Rout.save,
	  tests/sir.Rout.save: - The default behaviors of 'simulate' and
	  'trajectory' with respect to the argument 'times' has changed.
	  There is a new argument, 't0', which specifies the time at which
	  the initial conditions obtain. The default for 't0' is
	  'timezero(object)'. The default for 'times' is now
	  'time(object,t0=FALSE)' (it was 'time(object,t0=TRUE)'). This
	  change eliminates an infelicity in which 'simulate' and
	  'trajectory' returned undesired values at the initial time. To
	  aid users in modifying their codes, a warning is now displayed
	  whenever a potentially affected call is made.
	  - A banner is now displayed on package attachment. This will be
	  used to report important changes.

2010-10-04  kingaa

	* [r360] R/trajectory-pomp.R: - put guts of trajectory calculation
	  into the named function 'trajectory.internal'
	* [r359] man/euler.Rd: - remove documentation for removed plugins
	* [r358] DESCRIPTION, NAMESPACE, R/euler.R: - remove the functions
	  'euler.simulate', 'onestep.simulate', and 'onestep.density',
	  deprecated since version 0.29-1
	* [r357] DESCRIPTION, R/aaa.R: - add a banner message on
	  attachment.
	* [r356] R/simulate-pomp.R: - 'simulate.internal' is now the named
	  function for the guts of 'simulate'

2010-10-01  kingaa

	* [r355] DESCRIPTION, NAMESPACE, R/compare-mif.R,
	  R/compare-pmcmc.R, R/compare.mif.R, R/compare.pmcmc.R,
	  R/init-state-pomp.R, R/init.state-pomp.R, R/mif.R, R/nlf-guts.R,
	  R/pmcmc.R, R/pomp-methods.R, R/probe-match.R, R/probe.R,
	  R/spect-match.R, R/spect.R, data/dacca.rda, data/euler.sir.rda,
	  data/gillespie.sir.rda, data/ou2.rda, data/rw2.rda,
	  data/verhulst.rda, inst/NEWS, man/basic-probes.Rd,
	  man/pomp-methods.Rd, man/probe.Rd, man/spect.Rd,
	  tests/ou2-probe.R, tests/ou2-probe.Rout.save,
	  tests/ricker-probe.R, tests/ricker-probe.Rout.save,
	  tests/ricker-spect.R, tests/ricker.R, tests/ricker.Rout.save: -
	  fix the behavior of 'coef<-' to make it match simple vector
	  replacement by name. This is not a backward-compatible change but
	  should be stable since it so much simpler, more flexible, and
	  more intuitive.
	  - drop unneeded 'as.vector' in 'nlf'
	  - add 'params' argument to 'probe' and 'spect'. This allows the
	  user to override the default 'params=coef(object)'.
	  - add tests for 'spect' in 'tests/ricker-spect.R'
	  - drop the slow 'probe.cor' and 'probe.cov' in favor of
	  'probe.acf' and 'probe.ccf' which are written in C.
	  - change the names of some source files

2010-09-30  kingaa

	* [r354] R/nlf-guts.R, R/nlf-lql.R, R/nlf.R: - cosmetology
	* [r353] man/basic-probes.Rd: - update the man page to include
	  'probe.ccf'

2010-09-29  kingaa

	* [r352] DESCRIPTION, NAMESPACE, R/basic-probes.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  inst/doc/ou2-first-mif.rda, inst/doc/ou2-trajmatch.rda,
	  src/probe_ccf.c, tests/ou2-probe.R: - add in a new probe,
	  'probe.ccf', which computes the CCF of two variables at various
	  lags
	* [r351] R/basic-probes.R, src/mat.c, src/pomp_internal.h,
	  src/pomp_mat.h, src/probe_marginal.c, src/probe_nlar.c: - remove
	  'mat.c' in favor of inline functions for regression, defined in
	  the new header 'pomp_mat.h'
	* [r350] src/euler.c, src/mat.c, src/pfilter.c, src/probe.c,
	  src/probe_acf.c, src/probe_marginal.c, src/probe_nlar.c: - remove
	  the last usages of dynamic allocation from 'mat.c'
	  - changes in the compiled codes to eliminate pedantic compiler
	  warnings
	* [r349] tests/ou2-probe.R, tests/ou2-probe.Rout.save: - an exact
	  check for the correctness of probe.acf is added
	* [r348] man/pomp-methods.Rd: - keep up with changes
	* [r347] tests/ou2-probe-match.R, tests/ou2-probe-match.Rout.save,
	  tests/ou2-probe.R, tests/ou2-probe.Rout.save: - change name of
	  file
	  - add in a test of probe.acf and probe.nlar
	* [r346] src/bspline.c: - use R_alloc instead of Calloc/Free
	* [r345] src/euler.c, src/rmeasure.c: - use R_alloc instead of
	  Calloc/Free
	* [r344] NAMESPACE, R/pomp-methods.R: - export the new S3
	  as.data.frame method for pomps
	* [r343] man/basic-probes.Rd, tests/ricker-probe.Rout.save: -
	  update documentation with an entry for 'probe.nlar'

2010-09-28  kingaa

	* [r339] NAMESPACE, R/basic-probes.R, src/probe_nlar.c,
	  tests/ricker-probe.R: - add new 'probe.nlar': this probe performs
	  a polynomial autoregression on a univariate series and returns
	  the coefficients. Recommended by Wood (2010).
	* [r338] src/probe_marginal.c: - change names returned by
	  'probe.marginal'
	* [r337] R/probe.R: - fix up labels when many probes are used
	* [r334] man/sobol.Rd: - fix documentation error
	* [r333] DESCRIPTION, NAMESPACE, R/profile-design.R,
	  R/slice-design.R, R/slice.R, R/sobol.R, inst/NEWS,
	  man/profile-design.Rd, man/slice-design.Rd, man/slice.Rd,
	  man/sobol.Rd: - rearrange the slice and profile design functions
	  to make them easier to use
	* [r330] src/pomp_internal.h: - use R_STATIC macro

2010-09-26  kingaa

	* [r329] tests/ricker-probe.Rout.save: - improve tests for probes
	* [r328] tests/ricker-probe.R: - improve tests for probes
	* [r327] src/probe_marginal.c: - bug fix

2010-09-25  kingaa

	* [r326] DESCRIPTION, R/probe-match.R, R/probe.R, src/probe.c,
	  tests/ricker-probe.R: - fix bug with unnamed probes

2010-09-24  kingaa

	* [r325] inst/ChangeLog: - update ChangeLog
	* [r324] DESCRIPTION, NAMESPACE, R/basic-probes.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  inst/doc/pomp.bib, man/basic-probes.Rd, src/Makevars, src/mat.c,
	  src/pomp_internal.h, src/probe_acf.c, src/probe_marginal.c,
	  tests/ou2-probe-match.R, tests/ou2-probe-match.Rout.save,
	  tests/ricker-probe.R, tests/ricker-probe.Rout.save: -
	  probe.marginal and probe.median are introduced, based on the
	  recommendation of Wood (2010)
	  - probe.acf and probe.marginal are now coded in C for speed
	  - probe.acf is slightly changed to use the natural definition of
	  ACF
	  - these ideas follow the recommendations of Simon Wood (2010)
	  - a test file, using the Ricker example, is included
	* [r323] NAMESPACE: - update NAMESPACe
	* [r322] R/probe-match.R, R/probe.R, src/probe.c: - put the most
	  computationally-intensive bits of the probe calculations into C
	* [r321] R/pomp-methods.R, man/pomp-methods.Rd: - add S3 method
	  as.data.frame.pomp
	* [r320] DESCRIPTION, src/pfilter.c: - bug fix

2010-09-23  kingaa

	* [r319] R/probe.R: - empirical p-values are computed incorrectly.
	  fix this.

2010-09-21  kingaa

	* [r317] inst/doc/advanced_topics_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf, inst/doc/ou2-first-mif.rda,
	  inst/doc/ou2-trajmatch.rda: - update the vignettes

2010-09-20  kingaa

	* [r316] inst/ChangeLog: - update changelog
	* [r315] DESCRIPTION, NAMESPACE, R/pfilter.R, inst/ChangeLog,
	  inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  src/pfilter.c, tests/ricker.Rout.save: - move most time-consuming
	  computations in pfilter into C
	  - thus: new file src/pfilter.c

2010-08-31  kingaa

	* [r314] man/pomp.Rd: - minor clarification

2010-08-30  kingaa

	* [r313] pomp:
	* [r312] inst/ChangeLog: - update ChangeLog
	* [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, 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
	  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
	  required arguments to pomp. The 'alg.pars' argument will be
	  removed in a future release. Use of this argument now results in
	  a warning message.
	  

2009-04-13  kingaa

	* [r92] DESCRIPTION, data/ou2.rda, inst/ChangeLog,
	  inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf,
	  tests/ou2-mif.Rout.save:
	* [r91] inst/ChangeLog:
	* [r90] R/mif.R, man/mif.Rd, tests/ou2-mif.R: rewrite mif methods
	  to use 'mif.internal'.
	  this obviates the need for a user-visible '.ndone' argument.
	  add some reporting when verbose=TRUE.
	  the 'particles' function can now be altered after the mif object
	  is created.
	  some new tests have been added to tests/ou2-mif.R
	* [r89] R/pfilter.R: a bit less reporting when verbose=TRUE

2009-04-11  kingaa

	* [r88] tests/ou2-mif.R, tests/ou2-mif.Rout.save: tests added for
	  'mif' and 'pfilter'
	* [r87] R/mif.R: modified in accordance with changes made in
	  revision 86.
	* [r86] R/pfilter-mif.R, R/pfilter.R, man/pfilter.Rd: put the guts
	  of the particle filter into 'pfilter.internal'.
	  this can be used by 'mif' directly and by methods for 'pfilter'.
	  this obviates the need for the argument .rw.sd in the
	  user-visible methods.

2009-04-10  kingaa

	* [r85] inst/ChangeLog:
	* [r84] DESCRIPTION:
	* [r83] DESCRIPTION, R/mif.R, R/pfilter.R, man/mif.Rd,
	  man/pfilter.Rd: The handling of the argument 'pars' and 'ivps' in
	  mif has been changed to eliminate redundancy and a possible
	  source of errors. Now 'pars' and 'ivps' are checked to make sure
	  that all names are in 'names(start)' and 'names(rw.sd)' and that
	  they are mutually disjoint. Further, all the entries in
	  'rw.sd[pars]' and 'rw.sd[ivps]' must be positive or an error is
	  generated. If 'rw.sd' has positive values in slots not in the
	  union of 'ivps' and 'pars', these are ignored and a warning is
	  generated. The 'random.walk.sd' slot of the resulting 'mif'
	  object contains only nonzero entries corresponding to the union
	  of 'pars' and 'ivps'.
	  
	  If 'pars' is not specified in the arguments, then it is taken to
	  be
	  'names(rw.sd)[!(names(rw.sd)%in%ivps)]'
	  
	  Thus it is no longer necessary to specify 'pars' explicitly,
	  provided one takes care that all and only nonzero entries in
	  'rw.sd' correspond to parameters that one wishes to estimate. One
	  can be a bit more careless with 'rw.sd' if one uses 'pars'. In
	  any case, entries in 'rw.sd' that are zero are ignored.
	  
	  The computation of prediction means and variances and filtering
	  means in 'pfilter' is handled differently. When used as a
	  toplevel function (i.e., when the .rw.sd parameter used
	  internally by 'mif' is unset), then the prediction means and
	  variances and the filtering means are only computed for the state
	  variables. This eliminates an annoying and unnecessary behavior
	  that arose when parameters were set to nonfinite values.
	  
	  When .rw.sd is set (as when 'mif' calls 'pfilter'), the
	  prediction means and variances are computed only for all state
	  variables, but for only those parameters which are undergoing the
	  MIF random walk. Filtering means are computed for all state
	  variables and parameters, since they are needed for the fixed-lag
	  smoothing on the initial-value parameters.
	* [r82] man/mif-class.Rd, man/mif-methods.Rd: fix some
	  documentation infelicities and bugs

2009-03-16  kingaa

	* [r81] inst/CITATION: fix Carles accent

2009-03-13  kingaa

	* [r80] man/pomp-methods.Rd: improve documentation for coef<-
	  method for pomp object

2009-03-11  kingaa

	* [r79] DESCRIPTION, inst/ChangeLog:
	* [r78] man/eulermultinom.Rd, src/eulermultinom.c: replace "euler
	  infelicity" Rprintf statements with warnings
	* [r77] inst/CITATION: add CITATION file

2009-02-03  kingaa

	* [r76] inst/ChangeLog:
	* [r75] DESCRIPTION, R/mif.R, man/mif.Rd, man/pomp-methods.Rd,
	  man/trajectory-pomp.Rd, src/euler_sir.c, src/sir.c: changes to
	  documentation and default arguments so as to bring these into
	  agreement. (discrepancies revealed by Kurt Hornik's extensive
	  codoc testing).

2009-02-01  kingaa

	* [r74] inst/NEWS, man/nlf.Rd:

2009-01-31  kingaa

	* [r73] DESCRIPTION:
	* [r72] inst/ChangeLog:
	* [r71] man/nlf.Rd: documentation fix

2009-01-28  kingaa

	* [r70] R/plot-pomp.R: remove default for the (unused) 'y' argument
	* [r69] man/nlf.Rd: fix typos

2009-01-27  kingaa

	* [r68] inst/ChangeLog:
	* [r67] DESCRIPTION, R/trajectory-pomp.R: 'odesolve' has been
	  replaced by 'deSolve'
	* [r66] inst/examples/euler_sir.R, inst/examples/euler_sir.c,
	  inst/examples/sir.R, inst/examples/sir.c: moved 'sir.*' examples
	  to 'euler_sir.*'
	* [r65] DESCRIPTION, R/plot-pomp.R, inst/ChangeLog,
	  inst/examples/sir.R, man/pomp-methods.Rd: add package 'subplex'
	  as dependency
	  run examples that compile native code only if
	  Sys.info()['sysname']=='Linux'. This replaces the previous test
	  that .Platform$OS.type=='unix', which resulted in errors under
	  some versions of MacOSX.
	* [r64] inst/ChangeLog:

2009-01-26  kingaa

	* [r62] inst/ChangeLog:

2009-01-25  kingaa

	* [r61] DESCRIPTION: minor documentation corrections
	* [r60] man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd:

2009-01-17  kingaa

	* [r59] inst/ChangeLog:
	* [r58] tests/ou2-nlf.Rout.save:
	* [r57] tests/ou2-mif.Rout.save, tests/ou2-nlf.Rout:
	* [r56] tests/ou2-nlf.R, tests/ou2-nlf.Rout.save:

2009-01-16  kingaa

	* [r55] DESCRIPTION: add functionality for parameter estimation via
	  nonlinear forecasting, method due to Stephen P. Ellner and Bruce
	  E. Kendall
	* [r54] NAMESPACE, R/mvnorm.R, R/nlf-funcs.R, R/nlf-guts.R,
	  R/nlf-lql.R, R/nlf-objfun.R, R/nlf.R, data/ou2.rda,
	  inst/ChangeLog, inst/doc/compiled_code_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf, man/nlf.Rd, tests/ou2-nlf.R,
	  tests/ou2-nlf.Rout: add functionality for parameter estimation
	  via nonlinear forecasting, method due to Stephen P. Ellner and
	  Bruce E. Kendall
	* [r53] R/pfilter.R, man/pfilter.Rd: add 'verbose' option to
	  'pfilter'

2008-08-25  kingaa

	* [r52] data/ou2.rda, inst/ChangeLog,
	  inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
	* [r51] R/mif.R, man/mif.Rd, tests/ou2-mif.Rout.save: error trap in
	  'mif': 'rw.sd' must have names
	* [r50] DESCRIPTION, inst/NEWS, man/euler.Rd: better documentation
	  in 'euler.Rd'

2008-08-19  kingaa

	* [r49] inst/NEWS:

2008-08-15  kingaa

	* [r48] data/ou2.rda, inst/ChangeLog,
	  inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
	* [r47] tests/ou2-mif.Rout.save: fix bug in Euler step
	* [r46] tests/sir.R, tests/sir.Rout.save: improve test of SIR model
	* [r45] tests/logistic.Rout.save:
	* [r44] DESCRIPTION, src/euler.c: fix bug in Euler step

2008-08-14  kingaa

	* [r43] DESCRIPTION: make description more descriptive
	* [r42] inst/examples/sir.R: put trajectory computation into SIR
	  example

2008-08-13  kingaa

	* [r41] data/ou2.rda, inst/doc/compiled_code_in_pomp.pdf,
	  inst/doc/intro_to_pomp.pdf:
	* [r40] inst/ChangeLog:
	* [r39] inst/examples/sir.c: cosmetic
	* [r38] DESCRIPTION, NAMESPACE, R/aaa.R, R/pomp.R,
	  R/trajectory-pomp.R, data/ou2.rda, inst/examples/logistic.R,
	  inst/examples/sir.R, inst/examples/sir.c, man/mif-class.Rd,
	  man/pomp-class.Rd, man/pomp.Rd, man/skeleton-pomp.Rd,
	  man/trajectory-pomp.Rd, src/skeleton.c, tests/logistic.R,
	  tests/logistic.Rout.save, tests/sir.R, tests/sir.Rout.save: add
	  support for computing trajectories of the deterministic skeleton
	  the skeleton must now be specified when the pomp is created: if
	  the pomp is a discrete-time system, 'skeleton.map' is used to
	  specify its deterministic skeleton; if it is a continuous-time
	  system, 'skeleton.vectorfield' is used.
	  the new method 'trajectory' will, in the first case, iterate the
	  map to produce an itinerary and in the second case, it will call
	  'lsoda' from the now-required 'odesolve' package to compute the
	  trajectory.
	  some changes to the basic 'pomp' structure have been made to
	  facilitate all this.
	  specifically, a new slot, 'skeleton-type', distinguishes between
	  discrete-time and continuous-time systems

2008-08-01  kingaa

	* [r37] inst/ChangeLog:
	* [r36] inst/ChangeLog:
	* [r35] inst/examples/logistic.R: make dprocess depend on 'log'

2008-07-31  kingaa

	* [r34] inst/NEWS:
	* [r33] DESCRIPTION:
	* [r32] R/mif.R: improved error handling in mif
	* [r31] man/pomp.Rd: fix inaccuracy in documentation of rmeasure
	  and dmeasure arguments

2008-07-29  kingaa

	* [r29] inst/NEWS:
	* [r28] DESCRIPTION:
	* [r27] R/mif.R: bug fix in convergence record storage
	* [r26] R/mif.R: cosmetic

2008-07-26  kingaa

	* [r25] DESCRIPTION, inst/ChangeLog, inst/NEWS,
	  inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
	  inst/doc/intro_to_pomp.pdf, src/ou2.c: bug fix in
	  "intro_to_pomp.Rnw"

2008-07-25  kingaa

	* [r24] R/pfilter-mif.R:
	* [r23] inst/NEWS:
	* [r22] inst/NEWS:
	* [r21] data/ou2.rda, inst/ChangeLog,
	  inst/doc/compiled_code_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
	* [r20] tests/ou2-mif.Rout.save: no need to set rw.sd for
	  parameters that aren't estimated
	* [r19] inst/examples/logistic.R, inst/examples/rw2.R,
	  inst/examples/sir.R, tests/examples.R: add a test of the examples
	  in 'inst/examples' to the 'tests' directory
	  modify the sir.R example so that it attempts to build a
	  shared-object library only if .Platform$OS.type=='unix'
	* [r18] inst/doc/intro_to_pomp.Rnw, tests/ou2-mif.R: no need to
	  include zeros in 'rw.sd'
	* [r17] man/mif.Rd: improve documentation regarding arguments to
	  mif
	* [r16] R/aaa.R: remove a whole lot of stuff that somehow got in
	  from pomp.devel
	* [r15] inst/examples/sir.R: fix up R-function version
	* [r14] R/aaa.R: improve error handling: fix language and use
	  sQuote, dQuote where appropriate
	* [r13] DESCRIPTION:
	* [r12] R/compare.mif.R, R/dmeasure-pomp.R, R/dprocess-pomp.R,
	  R/euler.R, R/init.state-pomp.R, R/mif-methods.R, R/mif.R,
	  R/particles-mif.R, R/pfilter.R, R/plot-pomp.R, R/pomp-methods.R,
	  R/pomp.R, R/rmeasure-pomp.R, R/rprocess-pomp.R,
	  R/simulate-pomp.R, R/skeleton-pomp.R, R/sobol.R: improve error
	  handling: fix language and use sQuote, dQuote where appropriate
	* [r11] R/mif.R: trap as error parameters (including ivps) which
	  are to be estimated but which have zero rw.sd

2008-07-22  kingaa

	* [r10] inst/NEWS:
	* [r9] inst/ChangeLog:
	* [r8] inst/ChangeLog, inst/O_CHANGES:

2008-07-20  kingaa

	* [r7] DESCRIPTION, NAMESPACE, R/aaa.R, R/bsplines.R,
	  R/compare.mif.R, R/dmeasure-pomp.R, R/dprocess-pomp.R, R/euler.R,
	  R/eulermultinom.R, R/init.state-pomp.R, R/mif-methods.R, R/mif.R,
	  R/particles-mif.R, R/pfilter-mif.R, R/pfilter.R, R/plot-pomp.R,
	  R/pomp-methods.R, R/pomp.R, R/rmeasure-pomp.R, R/rprocess-pomp.R,
	  R/simulate-pomp.R, R/skeleton-pomp.R, R/sobol.R, inst,
	  inst/ChangeLog, inst/GPL, inst/LICENSE, inst/NEWS, inst/doc,
	  inst/doc/Makefile, 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, inst/examples,
	  inst/examples/logistic.R, inst/examples/rw2.R,
	  inst/examples/sir.R, inst/examples/sir.c, inst/include,
	  inst/include/pomp.h, man/bsplines.Rd, man/dmeasure-pomp.Rd,
	  man/dprocess-pomp.Rd, man/euler.Rd, man/eulermultinom.Rd,
	  man/init.state-pomp.Rd, man/mif-class.Rd, man/mif-methods.Rd,
	  man/mif.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, src,
	  src/bspline.c, src/dmeasure.c, src/dprocess.c, src/dsobol.c,
	  src/euler.c, src/eulermultinom.c, src/initstate.c,
	  src/lookup_table.c, src/ou2.c, src/pomp.h, src/pomp_fun.c,
	  src/pomp_internal.h, src/resample.c, src/rmeasure.c,
	  src/rprocess.c, src/sir.c, src/skeleton.c, src/sobol.f, tests,
	  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-simulate.R,
	  tests/ou2-simulate.Rout.save, tests/rw2.R, tests/rw2.Rout.save,
	  tests/sir.R, tests/sir.Rout.save: initial revision
	* [r6] data/ou2.rda:
	* [r5] data:

2007-06-25  stefan7th

	* [r1] ., R, man: Email in Readme changed