2010-10-12  kingaa

	* [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

