2012-07-01 kingaa * [r742] R/pomp-methods.R, R/pomp.R: - force storage.type to double for params slot 2012-06-29 kingaa * [r741] inst/ChangeLog, tests/sir.Rout.save: - update changelog and unit test * [r740] DESCRIPTION, R/pomp.R, inst/NEWS, man/pomp.Rd, tests/sir.R: - add 'params' argument to 'pomp' constructor * [r739] R/traj-match.R, man/traj-match.Rd, tests/bbs-trajmatch.R, tests/bbs-trajmatch.Rout.save: - extra arguments (...) to 'traj.match.objfun' are now passed on to the ODE integrator in case the skeleton is a vectorfield 2012-06-18 kingaa * [r732] inst/include/pomp.h: - update installed version of 'pomp.h' * [r731] DESCRIPTION, inst/NEWS, src/pomp.h: - update NEWS file - minor changes to 'pomp.h' 2012-06-12 kingaa * [r729] inst/doc/pomp.bib: - update bibliography database 2012-06-01 kingaa * [r727] DESCRIPTION, demo/sir.R, inst/include/pomp.h, src/lookup_table.c, src/pomp.h: - remove superfluous warnings from 'lookup_table' - fix 'sir' demo to work with covariate table - add some inline functions to 'pomp.h' * [r726] DESCRIPTION, R/builder.R, demo/gompertz.R, man/builder.Rd: - fix incorrect error messages in 'pompBuilder' - allow 'pompBuilder' to deal with covariates 2012-05-29 kingaa * [r725] DESCRIPTION, R/builder.R, R/pomp.R, demo/gompertz.R, demo/sir.R, man/builder.Rd, man/pomp.Rd: - add support for parameter transformations to 'pompBuilder' - more error-trapping in 'pomp' - update demos to use compiled parameter transformations - fix minor omission in 'pomp' man page 2012-05-14 kingaa * [r722] DESCRIPTION: - update DESCRIPTION * [r721] inst/ChangeLog, inst/NEWS, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: - update changelog NEWS file and vignettes 2012-05-12 kingaa * [r716] DESCRIPTION, R/dmeasure-pomp.R, R/dprocess-pomp.R, R/pomp-methods.R, R/rmeasure-pomp.R, R/rprocess-pomp.R, R/skeleton-pomp.R, R/trajectory-pomp.R: - use fewer anonymous functions 2012-05-10 kingaa * [r715] DESCRIPTION, tests/sir.R, tests/sir.Rout.save: - add unit test for new trajectory codes 2012-05-09 kingaa * [r714] inst/ChangeLog: 2012-05-08 kingaa * [r713] DESCRIPTION, R/trajectory-pomp.R, src/trajectory.c: - use R_PreserveObject and R_ReleaseObject rather than the 'savelist' trick * [r711] DESCRIPTION: 2012-05-07 kingaa * [r707] inst/ChangeLog, inst/NEWS: - update NEWS and ChangeLog 2012-05-06 kingaa * [r706] inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: - update vignettes 2012-05-03 kingaa * [r705] R/trajectory-pomp.R: - really fix bug in 'trajectory' that occurs when 'zeronames' has length > 1 * [r704] src/R_init_pomp.c: - forgot to export 'get_pomp_userdata_int' and 'get_pomp_userdata_double' * [r703] DESCRIPTION, R/builder.R, R/trajectory-pomp.R, demo/sir.R: - fix bug in 'trajectory' for vectorfield case that shows up when 'zeronames' has length > 1 - re-work 'sir' demo so that it uses 'pompBuilder' 2012-05-02 kingaa * [r702] inst/ChangeLog: * [r701] R/trajectory-pomp.R, src/pomp_internal.h, src/skeleton.c, src/trajectory.c: - work on the guts of the 'skeleton' and 'trajectory' for speed up in vectorfield case * [r700] tests/demos.R: - remove automatic running of demos (since this fails under windows) * [r699] R/builder.R: - add declarations for 'get_pomp_userdata_int' and 'get_pomp_userdata_double' * [r698] src/rmeasure.c: - remove unused variables * [r697] DESCRIPTION, inst/ChangeLog: * [r696] demo/gompertz.R, demo/sir.R, src/dmeasure.c, src/euler.c, src/pomp_internal.h, src/rmeasure.c, src/skeleton.c, src/trajectory.c, tests/demos.R, tests/examples.R: - changes to eliminate pedantic warnings - put covariate table interpolation into vectorfield trajectory computation * [r695] inst/ChangeLog: * [r694] DESCRIPTION, R/trajectory-pomp.R, src/trajectory.c: - more work on the guts of 'trajectory' for the vectorfield case 2012-05-01 kingaa * [r693] src/trajectory.c: - make sure to set up 'userdata' access to user functions * [r692] inst/ChangeLog: * [r691] R/simulate-pomp.R, R/trajectory-pomp.R, tests/ricker.R, tests/ricker.Rout.save: - make 'sim' and 'traj' into factors when 'simulate' or 'trajectory' are called with 'as.data.frame=TRUE' 2012-04-30 kingaa * [r690] inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: * [r689] inst/ChangeLog: * [r688] DESCRIPTION, R/builder.R, inst/ChangeLog, man/builder.Rd, src/trajectory.c: - rework the guts of 'iterate_map' for much faster trajectory calculation 2012-04-29 kingaa * [r687] src/dmeasure.c, src/skeleton.c: - more work on the guts 2012-04-28 kingaa * [r686] DESCRIPTION, src/euler.c, src/rmeasure.c: - more changes to the guts 2012-04-27 kingaa * [r685] DESCRIPTION, R/pomp-fun.R, R/pomp.R, data/bbs.rda, data/blowflies.rda, data/dacca.rda, data/euler.sir.rda, data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda, data/ricker.rda, data/rw2.rda, data/verhulst.rda, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/bsmc-ricker-flat-prior.rda, inst/doc/gompertz-multi-mif.rda, inst/doc/gompertz-trajmatch.rda, inst/doc/intro_to_pomp.pdf, inst/doc/nlf-block-boot.rda, inst/doc/nlf-boot.rda, inst/doc/nlf-fit-from-truth.rda, inst/doc/nlf-fits.rda, inst/doc/nlf-lag-tests.rda, inst/doc/nlf-multi-short.rda, inst/doc/ricker-mif.rda, inst/doc/ricker-probe-match.rda, src/dmeasure.c, src/euler.c, src/lookup_table.c, src/partrans.c, src/pomp_fun.c, src/pomp_internal.h, src/rmeasure.c, src/skeleton.c: - changes to the guts of 'rmeasure', 'dmeasure', 'partrans', and the Euler rprocess plugins 2012-04-26 kingaa * [r684] R/builder.R, demo/gompertz.R, inst/ChangeLog: - zeronames argument in 'pompBuilder' is optional * [r683] DESCRIPTION, NAMESPACE, R/builder.R, data/bbs.rda, data/blowflies.rda, data/dacca.rda, data/euler.sir.rda, data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda, data/ricker.rda, data/rw2.rda, data/verhulst.rda, demo/gompertz.R, demo/logistic.R, inst/ChangeLog, inst/NEWS, inst/data-R/sir.R, inst/doc/advanced_topics_in_pomp.Rnw, inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf, inst/examples/gompertz.c, inst/include/pomp.h, man/builder.Rd, src/R_init_pomp.c, src/SSA_wrapper.c, src/dmeasure.c, src/euler.c, src/partrans.c, src/pomp.h, src/pomp_internal.h, src/rmeasure.c, src/sir.c, src/skeleton.c, src/userdata.c, tests/bbs.Rout.save, tests/pfilter.Rout.save, tests/skeleton.R, tests/skeleton.Rout.save: - add new facility for accessing 'userdata' from within user-defined native routines: get_pomp_userdata{,_int,_double} - change some data()-loadable examples to make use of this - make 'pompBuilder' visible - modify 'gompertz' demo to make use of 'pompBuilder' 2012-04-25 kingaa * [r682] inst/doc/advanced_topics_in_pomp.Rnw: - minor tweak to pompBuilder example * [r681] NAMESPACE, R/trajectory-pomp.R, src/trajectory.c: - put in a routine to reset external variables after deSolve call * [r680] src/bspline.c: - fix error message 2012-04-24 kingaa * [r679] DESCRIPTION, R/builder.R, inst/ChangeLog, inst/NEWS, inst/TODO, inst/doc/Makefile, inst/doc/advanced_topics_in_pomp.Rnw, inst/doc/advanced_topics_in_pomp.pdf: - put 'pompBuilder' demonstration into 'advanced topics' vignette * [r678] R/aaa.R, R/nlf-funcs.R, R/plot-pomp.R, R/pomp.R, R/probe-match.R, R/probe.R, R/spect.R: - use 'paste0' where appropriate. define 'paste0' for use with R <= 2.15.0 2012-04-23 kingaa * [r677] DESCRIPTION: - change Depends to 2.14.2 * [r676] DESCRIPTION, R/builder.R, data/bbs.rda, data/blowflies.rda, data/dacca.rda, data/euler.sir.rda, data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda, data/ricker.rda, data/rw2.rda, data/verhulst.rda, inst/NEWS, inst/data-R/blowflies.R, src/blowfly.c, tests/blowflies.R, tests/blowflies.Rout.save, tests/sir.Rout.save: - remove the delay 'tau' from the blowflies example - make the 'pompBuilder' work under 2.14.2 - update the data()-loadable examples 2012-04-21 kingaa * [r675] inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf: - update vignettes * [r674] DESCRIPTION, inst/ChangeLog, inst/NEWS: - bump version number since R 2.15.0 is now needed * [r673] inst/NEWS, tests/pfilter.Rout.save: - update unit tests and NEWS 2012-04-19 kingaa * [r670] DESCRIPTION, data/bbs.rda, data/blowflies.rda, data/dacca.rda, data/euler.sir.rda, data/gillespie.sir.rda, data/gompertz.rda, data/ou2.rda, data/ricker.rda, data/rw2.rda, data/verhulst.rda, inst/data-R/blowflies.R, src/blowfly.c: - fix segfault bug in blowfly example when tau is NA (thanks to Greg Minshall for finding the bug) 2012-04-17 kingaa * [r664] ., .Rbuildignore, .Rinstignore, DESCRIPTION, NAMESPACE, R, data, demo, inst, man, src, tests: - move everything down one level