2008-07-20  kingaa

	* pomp/src/euler.c: fix bug with Euler simulator
	handle names in user-defined rprocess when given as an R function
	move {Get,Put}RNGState out of the Euler simulator (it must be put into native codes when these are used)

2008-07-20  kingaa

	* pomp/src/rmeasure.c: minor changes

2008-07-20  kingaa

	* pomp/tests/: logistic.R, sir.R: when dprocess is being tested, ensure that exactly one Euler step is taken at each step

2008-07-20  kingaa

	* pomp/: inst/examples/sir.c, src/sir.c: move GetRNGState and PutRNGState into the one-step Euler simulator

2008-07-18  kingaa

	* pomp/inst/examples/rw2.R: random walk example

2008-07-17  kingaa

	* pomp/src/eulermultinom.c: bug fix

2008-07-17  kingaa

	* pomp/man/pomp.Rd: typo

2008-07-17  kingaa

	* pomp/inst/examples/logistic.R: the Euler-Maruyama logistic SDE from the 'tests' directory.

2008-07-17  kingaa

	* pomp/src/: dprocess.c, pomp_internal.h, rmeasure.c, rprocess.c: fix error messages

2008-07-17  kingaa

	* pomp/tests/logistic.Rout.save: add the skeleton

2008-07-17  kingaa

	* pomp/: man/mif-class.Rd, man/ou2.Rd, man/pomp-class.Rd,
	  man/pomp.Rd, R/aaa.R, R/pomp.R, src/dmeasure.c, src/ou2.c,
	  src/pomp.h, src/pomp_internal.h, src/rmeasure.c, DESCRIPTION: remove 'obsnames' as an argument to 'pomp'
	remove the 'obsindex' slot from the pomp class
	remove 'int *obsindex' as an argument to the C-level prototypes for rmeasure and dmeasure functions
	change ou2.c accordingly
	when 'rmeasure' is specified as an R function returning names, these are now checked against the names of the data variables and sorted out accordingly

2008-07-17  kingaa

	* pomp/inst/doc/intro_to_pomp.Rnw: reformulated the process model
	should be more transparent

2008-07-17  kingaa

	* pomp/tests/logistic.R: add skeleton

2008-07-16  kingaa

	* pomp/tests/: logistic.R, logistic.Rout.save: one-variable example using Euler-Maruyama
	a continuous-time Verhulst-Pearl SDE with lognormal measurement error

2008-07-16  kingaa

	* pomp/inst/: ChangeLog, NEWS: remove changelog from CVS
	add NEWS file

2008-07-16  kingaa

	* pomp/: inst/include/pomp.h, src/dmeasure.c, src/euler.c,
	  src/lookup_table.c, src/pomp.h, src/rmeasure.c, src/skeleton.c: streamline lookup_table algorithm and interface

2008-07-16  kingaa

	* pomp/inst/examples/sir.R: add R-function version for comparison

2008-07-16  kingaa

	* pomp/: inst/examples/sir.c, src/sir.c,
	  inst/doc/intro_to_pomp.Rnw: cosmetic

2008-07-16  kingaa

	* pomp/src/: euler.h, lookup_table.h: reorganize header files

2008-07-15  kingaa

	* pomp/: DESCRIPTION, NAMESPACE, data/ou2.rda,
	  inst/doc/compiled_code_in_pomp.Rnw, inst/doc/intro_to_pomp.Rnw,
	  inst/examples/sir.R, inst/examples/sir.c, man/dmeasure-pomp.Rd,
	  man/dprocess-pomp.Rd, man/euler.Rd, man/eulermultinom.Rd,
	  man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd,
	  man/pomp-class.Rd, man/pomp-methods.Rd, man/pomp.Rd,
	  man/skeleton-pomp.Rd, R/aaa.R, R/compare.mif.R,
	  R/dmeasure-pomp.R, R/dprocess-pomp.R, R/euler.R,
	  R/init.state-pomp.R, R/mif.R, R/pomp-methods.R, R/pomp.R,
	  R/rmeasure-pomp.R, R/rprocess-pomp.R, R/simulate-pomp.R,
	  R/skeleton-pomp.R, src/dmeasure.c, src/dprocess.c, src/euler.c,
	  src/initstate.c, src/lookup_table.c, src/ou2.c, src/pomp_fun.c,
	  src/rmeasure.c, src/rprocess.c, src/sir.c, src/skeleton.c,
	  tests/ou2-kalman.R, tests/ou2-kalman.Rout.save, tests/ou2-mif.R,
	  tests/ou2-mif.Rout.save, tests/rw2.R, tests/rw2.Rout.save,
	  tests/sir.R, tests/sir.Rout.save: changed the structure of the 'pomp' object to support native routines as well as R functions.
	this involves creating a new class 'pomp.fun' to encode either an R function or a native routine.
	a new low-level function 'pomp_fun_handler' (file pomp_fun.c) to handle base-level pomp functions that may be R functions or native routines.
	future support for formulae is envisioned.
	a new slot 'PACKAGE' has also been added to 'pomp' to carry the name of the shared-object (DLL) holding native routines.

	added support for covariates (via lookup tables) directly into the 'pomp' class.
	this involves adding slots 'tcovar', 'covar', and 'covarnames'.

	'rmeasure', 'dmeasure', 'skeleton', and 'init.state' now perform lookup when covariates exist and pass this information to the user-defined function.
	'rprocess' and 'dprocess' receive the full lookup table ('tcovar' plus 'covar').

	'rmeasure', 'dmeasure', and 'skeleton' are now specified by a function (or native routine) that does the computation for ONE state vector and ONE parameter vector.
	this is analogous to the way that 'init.state' has operated from the beginning.
	it greatly simplifies model specification from the user's point of view.
	the low-level interface methods are unchanged.
	as a result, there is no longer a need for 'pomp.skeleton', which no longer exists.

	the SIR, OU, and random-walk examples have been modified to accommodate these changes.
	all tests pass.

	the interface to the 'euler.simulate' and 'euler.density' facilities have changed to make them consistent with the new pomp class.

2008-07-15  kingaa

	* pomp/: inst/include/euler.h, inst/include/lookup_table.h,
	  inst/include/pomp.h, src/bspline.c, src/dsobol.c,
	  src/eulermultinom.c, src/pomp.h, src/pomp_internal.h,
	  src/resample.c: reorganize header files

2008-05-23  kingaa

	* pomp/R/: dmeasure-pomp.R, dprocess-pomp.R, rmeasure-pomp.R,
	  rprocess-pomp.R: change error handling

2008-05-23  kingaa

	* pomp/R/: dmeasure-pomp.R, dprocess-pomp.R, rmeasure-pomp.R,
	  rprocess-pomp.R: change error handling

2008-05-21  kingaa

	* pomp/src/: ou2.c, pomp.h: better macros

2008-05-21  kingaa

	* pomp/man/pomp-methods.Rd: attempt at documenting coerce methods

2008-05-21  kingaa

	* pomp/: R/euler.R, inst/include/euler.h, man/euler.Rd,
	  src/euler.c, src/euler.h, src/sir.c, inst/examples/sir.c,
	  inst/examples/sir.R: add support for column-names in covariate table

2008-05-21  kingaa

	* pomp/R/pomp.R: inline the default initializer

2008-05-21  kingaa

	* pomp/R/: pomp-methods.R, print-pomp.R: move print and show methods for pomp to pomp-methods.R

2008-05-21  kingaa

	* pomp/man/pomp-methods.Rd: attempt at documenting coerce methods

2008-05-21  kingaa

	* pomp/src/: ou2.c, pomp.h: better macros

2008-05-21  kingaa

	* pomp/R/pomp.R: inline the default initializer

2008-05-21  kingaa

	* pomp/R/: pomp-methods.R, print-pomp.R: move print and show methods for pomp to pomp-methods.R

2008-05-21  kingaa

	* pomp/: inst/examples/sir.R, inst/examples/sir.c, R/euler.R,
	  inst/include/euler.h, man/euler.Rd, src/euler.c, src/euler.h,
	  src/sir.c: add support for column-names in covariate table

2008-05-21  kingaa

	* pomp/man/: pomp-class.Rd, pomp-methods.Rd, pomp.Rd: add pomp-methods.Rd

2008-05-21  kingaa

	* pomp/: man/pomp-class.Rd, man/pomp-methods.Rd, man/pomp.Rd,
	  R/aaa.R: add pomp-methods.Rd

2008-05-20  kingaa

	* pomp/tests/ou2-kalman.Rout.save: file ou2-kalman.Rout.save was added on branch release_0-19 on 2008-05-20 16:30:45 +0000

2008-05-20  kingaa

	* pomp/tests/ou2-mif.Rout.save: file ou2-mif.Rout.save was added on branch release_0-19 on 2008-05-20 16:30:45 +0000

2008-05-20  kingaa

	* pomp/tests/ou2-simulate.Rout.save: file ou2-simulate.Rout.save was added on branch release_0-19 on 2008-05-20 16:30:46 +0000

2008-05-20  kingaa

	* pomp/tests/rw2.Rout.save: file rw2.Rout.save was added on branch release_0-19 on 2008-05-20 16:30:46 +0000

2008-05-20  kingaa

	* pomp/R/: compare.mif.R, plot-pomp.R: ask=TRUE ==> ask=dev.interactive(orNone=TRUE)

2008-05-20  kingaa

	* pomp/R/compare.mif.R: file compare.mif.R was added on branch release_0-19 on 2008-05-20 16:20:10 +0000

2008-05-19  kingaa

	* pomp/inst/doc/: compiled_code_in_pomp.Rnw, intro_to_pomp.Rnw: remove Sys.time calls

2008-05-18  kingaa

	* pomp/: DESCRIPTION, NAMESPACE,
	  inst/doc/compiled_code_in_pomp.Rnw, inst/doc/intro_to_pomp.Rnw,
	  inst/examples/sir.R, man/pomp.Rd, tests/ou2-kalman.R,
	  tests/ou2-mif.R, tests/ou2-simulate.R, tests/ou2-trajmatch.R,
	  tests/rw2.R: use 'pomp' as package name (not 'pomp.devel')

2008-05-18  kingaa

	* pomp/tests/: ou2-kalman.R: use init.state

2008-05-18  kingaa

	* pomp/: DESCRIPTION, NAMESPACE,
	  inst/doc/compiled_code_in_pomp.Rnw, inst/doc/intro_to_pomp.Rnw,
	  inst/examples/sir.R, man/cqlf.Rd, R/NLF.R, R/NLF.mvn.guts.R,
	  R/NLF.objfun.R, R/col.rep.R, R/compare.mif.R, R/cqlf.R,
	  R/mif-methods.R, R/trajmatch.R, man/NLF.Rd, man/NLF.guts.Rd,
	  man/NLF.objfun.Rd, man/mif-methods.Rd, man/pomp.Rd,
	  man/trajmatch.Rd, src/cqlf.cc, src/gamma.f, src/multinom.f,
	  src/pertcode.f, src/poisson.f, src/randpack.f, src/SSA.f,
	  tests/ou2-kalman.R, tests/ou2-mif.R, tests/ou2-simulate.R,
	  tests/ou2-trajmatch.R, tests/rw2.R: all NCEAS development files

2008-05-18  kingaa

	* pomp/man/: pomp.Rd, rmeasure-pomp.Rd: fix typos

2008-05-18  kingaa

	* pomp/: data/ou2.rda, inst/doc/compiled_code_in_pomp.pdf,
	  inst/doc/compiled_code_in_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
	  inst/doc/intro_to_pomp.Rnw: add the vignette PDFs and 'ou2.rda' to the repository
	fix seeds in the vignette Sweave docs

2008-05-18  kingaa

	* pomp/: R/init.state-pomp.R, src/initstate.c, NAMESPACE: streamline init.state: put low-level functionality into C

2008-05-18  kingaa

	* pomp/man/: dmeasure-pomp.Rd, dprocess-pomp.Rd, rmeasure-pomp.Rd,
	  rprocess-pomp.Rd: add some links

2008-05-18  kingaa

	* pomp/: R/init.state-pomp.R, src/initstate.c: streamlined

2008-05-18  kingaa

	* pomp/src/initstate.c: file initstate.c was added on branch release_0-18 on 2008-05-18 19:12:17 +0000

2008-05-18  kingaa

	* pomp/: NAMESPACE, R/init.state-pomp.R, src/initstate.c: streamline init.state

2008-05-18  kingaa

	* pomp/man/: dmeasure-pomp.Rd, dprocess-pomp.Rd, rmeasure-pomp.Rd,
	  rprocess-pomp.Rd: add links

2008-05-17  kingaa

	* pomp/inst/doc/: compiled_code_in_pomp.Rnw, intro_to_pomp.Rnw: set seeds

2008-05-17  kingaa

	* pomp/inst/doc/: compiled_code_in_pomp.Rnw, intro_to_pomp.Rnw: set seeds

2008-05-17  kingaa

	* pomp/inst/doc/compiled_code_in_pomp.pdf: file compiled_code_in_pomp.pdf was added on branch devel_0-3 on 2008-05-17 16:42:23 +0000

2008-05-17  kingaa

	* pomp/inst/doc/intro_to_pomp.pdf: file intro_to_pomp.pdf was added on branch devel_0-3 on 2008-05-17 16:42:23 +0000

2008-05-17  kingaa

	* pomp/inst/doc/intro_to_pomp.Rnw: bug fix

2008-05-17  kingaa

	* pomp/: NAMESPACE, R/dmeasure-pomp.R, R/dprocess-pomp.R,
	  R/rmeasure-pomp.R, R/rprocess-pomp.R, R/simulate-pomp.R,
	  src/dmeasure.c, src/dprocess.c, src/rmeasure.c, src/rprocess.c: put four basic functions into C

2008-05-16  kingaa

	* pomp/: R/mif.R, R/pfilter.R, R/pomp-methods.R, man/pomp-class.Rd,
	  man/simulate-pomp.Rd, R/pomp.R: improved 'time' method

2008-05-15  kingaa

	* pomp/man/: euler.Rd, mif.Rd, pomp-class.Rd, pomp.Rd: improved documentation

2008-05-14  kingaa

	* pomp/inst/doc/: Makefile, intro_to_pomp.Rnw, random_walk.Rnw: change name of vignette from "random_walk" to the more descriptive "intro_to_pomp"

2008-05-14  kingaa

	* pomp/: inst/doc/compiled_code_in_pomp.Rnw, man/mif.Rd,
	  man/pomp-package.Rd: remove reference to pomp.devel

2008-05-13  kingaa

	* pomp/: R/pomp-methods.R, man/pomp-class.Rd: better 'coef<-' method for pomp objects

2008-05-13  kingaa

	* pomp/src/sir.c: SIR example

2008-05-13  kingaa

	* pomp/man/euler.Rd: add euler_density
	add sir example

2008-05-13  kingaa

	* pomp/: man/eulermultinom.Rd, src/eulermultinom.c: improved interface

2008-05-13  kingaa

	* pomp/tests/ou2-simulate.R: fix seed

2008-05-13  kingaa

	* pomp/man/mif-methods.Rd: no plot method (yet)

2008-05-13  kingaa

	* pomp/: R/euler.R, inst/include/euler.h, src/euler.c, src/euler.h: improve euler model interface
	add support for euler densities

2008-05-13  kingaa

	* pomp/inst/include/: interp.h, lookup_table.h: lookup_table.h replaces interp.h

2008-05-13  kingaa

	* pomp/src/: lookup_table.c, lookup_table.h: replace 'interp.c' and 'interp.h'

2008-05-13  kingaa

	* pomp/R/eulermultinom.R: use .Call interface

2008-05-13  kingaa

	* pomp/inst/examples/: sir.R, sir.c: improved example

2008-05-13  kingaa

	* pomp/inst/doc/compiled_code_in_pomp.Rnw: description of .C and .Call interface

2008-05-13  kingaa

	* pomp/R/: bsplines.R, dmeasure-pomp.R, dprocess-pomp.R,
	  init.state-pomp.R, mif.R, particles-mif.R, pfilter.R, pomp.R,
	  rmeasure-pomp.R, rprocess-pomp.R, sobol.R: better error handling

2008-05-13  kingaa

	* pomp/src/: interp.c, interp.h: replaced by lookup_table

2008-05-07  kingaa

	* pomp/man/simulate-mif.Rd: no longer needed

2008-05-07  kingaa

	* pomp/R/plot-pomp.R: support for >10 variables

2008-05-04  kingaa

	* pomp/man/pfilter.Rd: documentation fix

2008-05-04  kingaa

	* pomp/: DESCRIPTION, R/aaa.R, inst/doc/random_walk.Rnw,
	  inst/examples/sir.R, man/mif-class.Rd, man/mif-methods.Rd,
	  man/mif.Rd, man/pfilter.Rd, man/pomp-class.Rd,
	  man/pomp-package.Rd, man/simulate-pomp.Rd, R/mif-methods.R,
	  R/mif.R, R/pfilter-mif.R, R/pfilter.R, R/pomp-methods.R,
	  R/simulate-mif.R, R/simulate-pomp.R, tests/ou2-mif.R,
	  tests/ou2-simulate.R: added 'params' and 'states' slots to the 'pomp' object
	many changes to methods as a result

2008-05-02  kingaa

	* pomp/: DESCRIPTION, inst/examples/sir.R, man/pfilter.Rd,
	  tests/ou2-kalman.R: bug fixes

2008-05-02  kingaa

	* pomp/DESCRIPTION: bug fix

2008-05-02  kingaa

	* pomp/inst/examples/sir.R: bug fix

2008-05-02  kingaa

	* pomp/: man/dmeasure-pomp.Rd, man/dprocess-pomp.Rd,
	  man/init.state-pomp.Rd, man/mif-class.Rd, man/mif.Rd,
	  man/pfilter.Rd, man/pomp-class.Rd, man/pomp-package.Rd,
	  man/pomp.Rd, R/aaa.R, man/rmeasure-pomp.Rd, man/rprocess-pomp.Rd,
	  man/simulate-pomp.Rd, R/init.state-pomp.R, R/mif.R,
	  R/particles-mif.R, R/pfilter-mif.R, R/pfilter.R, R/pomp.R,
	  R/simulate-mif.R, R/simulate-pomp.R: major revision

	pomp object now contains a slot 'initializer'
	this holds a function which initializes the unobserved (state) process when given parameters

2008-05-02  kingaa

	* pomp/inst/doc/random_walk.Rnw: streamline and bugfix

2008-05-02  kingaa

	* pomp/: R/bsplines.R, man/bsplines.Rd: remove restriction on periodic B-splines that they be evaluated only within their fundamental domain

2008-05-02  kingaa

	* pomp/: inst/examples/sir.R, inst/examples/sir.c,
	  inst/include/euler.h, R/euler.R, R/eulermultinom.R,
	  inst/include/interp.h, man/euler.Rd, man/eulermultinom.Rd,
	  src/euler.c, src/euler.h, src/interp.c, src/interp.h: support for Euler-multinomial models

2008-05-02  kingaa

	* pomp/: man/sobol.Rd, R/sobol.R: Sobol' low discrepancy sequences

2007-12-04  kingaa

	* pomp/: R/pomp.R, man/pomp.Rd: t0 can be as large as times[1], but no larger

2007-12-04  kingaa

	* pomp/: R/bsplines.R, R/simulate-pomp.R, man/simulate-pomp.Rd: bug fix

2007-11-13  kingaa

	* pomp/R/pfilter.R: more informative error when some prediction variances are non-finite

2007-10-09  kingaa

	* pomp/R/bsplines.R: fix buglet in warning message

2007-07-23  kingaa

	* pomp/man/: mif.Rd, pomp-package.Rd: fix reference to vignette

2007-07-23  kingaa

	* pomp/inst/doc/random_walk.Rnw: fix the seed for the generation of ou2

2007-07-23  kingaa

	* pomp/man/ou2.Rd: revert to version 1.1

2007-07-23  kingaa

	* pomp/R/zzz.R: not needed

2007-07-23  kingaa

	* pomp/DESCRIPTION: changed vignette handling
	fixed code-documentation mismatch
	explicit mention of C functions in NAMESPACE

2007-07-23  kingaa

	* pomp/: R/bsplines.R, R/pfilter.R, NAMESPACE: C functions are now explicitly declared in NAMESPACE

2007-07-23  kingaa

	* pomp/data/ou2.rda: file ou2.rda was added on branch devel_0-3 on 2008-05-17 16:42:23 +0000

2007-07-23  kingaa

	* pomp/data/ou2.rda: file ou2.rda was added on branch release_0-18 on 2008-05-17 15:54:20 +0000

2007-07-23  kingaa

	* pomp/: data/ou2.rda, inst/doc/Makefile, inst/doc/random_walk.Rnw,
	  inst/doc/random_walk_example.Rnw, man/ou2.Rd: revamp the way the vignettes are handled
	automatically generated
	build of target 'dist' is now independent of 'check'

2007-07-22  kingaa

	* pomp/man/pfilter.Rd: fix code-doc mismatch in arguments of pfilter.mif

2007-07-22  kingaa

	* pomp/DESCRIPTION: replace SaveImage with LazyLoad

2007-07-22  kingaa

	* pomp/src/ou2.c: correct improper use of SET_ELEMENT

2007-07-22  kingaa

	* pomp/R/plot-pomp.R: xy.labels is now set

2007-07-22  kingaa

	* pomp/R/pfilter.R: add ... argument to pfilter.pomp

2007-07-22  kingaa

	* pomp/R/pfilter-mif.R: pass arguments down to pfilter.pomp explicitly (rather than through ...)

2007-07-22  kingaa

	* pomp/man/pfilter.Rd: correct the code-documentation mistmatches
	.rw.sd is now documented

2007-07-20  aking

	* pomp/src/bspline.c: use const where appropriate

2007-07-20  aking

	* pomp/man/: mif-class.Rd, mif-methods.Rd, mif.Rd,
	  particles-mif.Rd, pfilter.Rd, pomp-class.Rd, pomp-package.Rd,
	  pomp.Rd: improve documentation

2007-07-20  aking

	* pomp/man/: mif-class.Rd, mif-methods.Rd, pfilter.Rd: add references

2007-07-19  aking

	* pomp/: DESCRIPTION, NAMESPACE, R/aaa.R, man/mif-methods.Rd: nlme is not required

2007-07-18  aking

	* pomp/: DESCRIPTION, GPL, NAMESPACE: release version of pomp

