[Pomp-commits] r674 - in pkg/pomp: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Apr 21 16:22:16 CEST 2012
Author: kingaa
Date: 2012-04-21 16:22:15 +0200 (Sat, 21 Apr 2012)
New Revision: 674
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/inst/ChangeLog
pkg/pomp/inst/NEWS
Log:
- bump version number since R 2.15.0 is now needed
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2012-04-21 14:02:33 UTC (rev 673)
+++ pkg/pomp/DESCRIPTION 2012-04-21 14:22:15 UTC (rev 674)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.41-6
-Date: 2012-04-18
+Version: 0.42-1
+Date: 2012-04-21
Revision: $Rev$
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
Maintainer: Aaron A. King <kingaa at umich.edu>
Modified: pkg/pomp/inst/ChangeLog
===================================================================
--- pkg/pomp/inst/ChangeLog 2012-04-21 14:02:33 UTC (rev 673)
+++ pkg/pomp/inst/ChangeLog 2012-04-21 14:22:15 UTC (rev 674)
@@ -1,2675 +1,20 @@
-2012-03-27 kingaa
+2012-04-21 kingaa
- * [r632] R/bsmc.R, inst/TODO, man/bsmc.Rd: - fix bug in plot method
- for 'bmscd.pomp'
- - parameter posterior means are now stored in the 'params' slot
- of 'bsmcd.pomp' objects
- * [r631] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
- inst/doc/manual.pdf: - compress the manual and fix some typos in
- the intro vignette
- * [r630] tests/ricker-bsmc.R, tests/ricker-bsmc.Rout.save: - units
- tests for new 'bsmc' facilities
- * [r629] DESCRIPTION, R/bsmc.R, R/mif-class.R, R/mif-methods.R,
- R/mif.R, R/nlf-objfun.R, R/nlf.R, R/pfilter.R, R/pmcmc.R,
- R/pomp.R, R/probe-match.R, R/traj-match.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/TODO, inst/data-R/dacca.R,
- inst/data-R/gompertz.R, inst/data-R/ricker.R, inst/data-R/sir.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/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/bsmc.Rd, man/dacca.Rd,
- man/mif-class.Rd, man/mif.Rd, man/nlf.Rd, man/pmcmc.Rd,
- man/probe.Rd, man/sir.Rd, man/traj-match.Rd, src/cholmodel.c,
- src/gompertz.c, src/ricker.c, src/sir.c, tests/dacca.R,
- tests/dacca.Rout.save, tests/dimchecks.R,
- tests/dimchecks.Rout.save, tests/gillespie.R,
- tests/gillespie.Rout.save, tests/gompertz.R,
- tests/gompertz.Rout.save, tests/ou2-mif.R,
- tests/ou2-mif.Rout.save, tests/ou2-pmcmc.R,
- tests/ou2-trajmatch.Rout.save, tests/partrans.R,
- tests/partrans.Rout.save, tests/pfilter.R,
- tests/pfilter.Rout.save, tests/pomppomp.R,
- tests/pomppomp.Rout.save, tests/ricker-probe.R,
- tests/ricker-probe.Rout.save, tests/ricker-spect.R,
- tests/ricker-spect.Rout.save, tests/ricker.R,
- tests/ricker.Rout.save, tests/skeleton.R,
- tests/skeleton.Rout.save, tests/steps.R, tests/steps.Rout.save: -
- put parameter transformation options into 'mif', 'bsmc', 'pmcmc',
- 'probe-match', 'traj-match', and 'nlf'
- - reverse direction of parameter transformations in
- data()-loadable examples
- - update documentation
- - make 'bsmc' into an S4 method
- - plot method for 'bsmcd.pomp' objects
+ * [r673] inst/NEWS, tests/pfilter.Rout.save: - update unit tests
+ and NEWS
-2012-03-21 kingaa
+2012-04-19 kingaa
- * [r628] DESCRIPTION, R/simulate-pomp.R: - bug fix in simulate code
- (with as.data.frame argument)
-
-2012-03-15 kingaa
-
- * [r627] DESCRIPTION, R/simulate-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/TODO, inst/data-R/euler.sir.R, inst/data-R/gillespie.sir.R,
- inst/data-R/sir.R, man/simulate-pomp.Rd, man/sir.Rd,
- man/trajectory-pomp.Rd, tests/dacca.R, tests/dacca.Rout.save,
- tests/ricker.R, tests/ricker.Rout.save: - add new 'as.data.frame'
- argument to 'simulate' and 'trajectory'
- - consolidate both SIR models in one inst/data-R file
-
-2012-03-09 kingaa
-
- * [r626] DESCRIPTION, R/pomp-methods.R, inst/TODO, src/partrans.c,
- src/simulate.c, tests/ou2-procmeas.Rout.save: - minor bugfixes
- * [r625] DESCRIPTION, NAMESPACE, R/init-state-pomp.R, R/pomp-fun.R,
- 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/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.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, inst/include/pomp.h,
- man/pomp-class.Rd, src/dmeasure.c, src/dprocess.c,
- src/initstate.c, src/partrans.c, src/pomp.h, src/pomp_internal.h,
- src/rmeasure.c, src/rprocess.c, src/skeleton.c,
- tests/dimchecks.R, tests/dimchecks.Rout.save, tests/logistic.R,
- tests/logistic.Rout.save, tests/ou2-procmeas.R,
- tests/ou2-procmeas.Rout.save, tests/rw2.Rout.save,
- tests/sir.Rout.save: - parameter transformations are handled
- through 'partrans'
- - all the horsemen now recycle parameters or states as
- appropriate
- * [r624] man/pomp-methods.Rd: - update documentation
- * [r623] R/mif-methods.R: - use new 'partrans' method
-
-2012-03-08 kingaa
-
- * [r622] src/euler.c: - fix incorrect comment
-
-2012-03-07 kingaa
-
- * [r621] R/pomp-fun.R: - minor tweak
- * [r620] DESCRIPTION, inst/NEWS, man/blowflies.Rd, man/pfilter.Rd:
- - update documentation of 'blowflies'
- - correct error in 'pfilter' documentation
-
-2012-03-06 kingaa
-
- * [r619] DESCRIPTION, R/parmat.R, inst/NEWS, man/parmat.Rd: -
- extend functionality of 'parmat' slightly
-
-2012-02-15 kingaa
-
- * [r618] R/probe-match.R, inst/NEWS: - same error as before, fixed
- now in 'probe.match'
- * [r617] R/probe.R, inst/NEWS: - catch error in 'probe' when nsim <
- nprobes
- * [r616] DESCRIPTION, 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/gillespie.sir.R: - fix the Gillespie
- example
- * [r615] inst/NEWS: - fix NEWS file
-
-2012-02-14 kingaa
-
- * [r614] DESCRIPTION: - back off of using svn keywords for the Date
- field
- * [r613] tests/partrans.R, tests/partrans.Rout.save: - add some
- units tests
- * [r612] DESCRIPTION, R/pomp-methods.R, R/pomp.R, inst/NEWS,
- inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
- - When a pomp object is updated using 'pomp', the 'params' slot
- will now be copied over (appropriately transformed). Before, it
- was simply dropped.
-
-2012-02-10 kingaa
-
- * [r611] DESCRIPTION: - use svn keywords on date & svn revision
- * [r610] inst/NEWS: - cosmetics
-
-2012-02-09 kingaa
-
- * [r609] tests/ou2-mif-fp.R, tests/ou2-mif-fp.Rout.save: - some
- unit tests for new 'mif' functionality
- * [r608] .Rinstignore, DESCRIPTION, R/mif.R, inst/NEWS, man/mif.Rd,
- src/dprocess.c, src/euler.c, src/rmeasure.c, src/skeleton.c: -
- more informative error messages in cases where dimensionality of
- state space or data space differ internally
- - more flexible choice of update methods in 'mif' via the new
- argument 'method' which replaces the old 'weighted' flag
- - the 'weighted' flag of 'mif' is now deprecated
-
-2012-02-06 kingaa
-
- * [r607] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf,
- inst/doc/manual.pdf: - minor changes
-
-2012-01-19 kingaa
-
- * [r606] man/probe.Rd: - cosmetology
- * [r605] R/version.R: - add a 'version.string' to the return list
- * [r604] DESCRIPTION, NAMESPACE, R/probe-match.R, R/sannbox.R,
- R/traj-match.R, inst/NEWS, inst/doc/manual.pdf, man/probe.Rd,
- man/sannbox.Rd, man/traj-match.Rd, tests/ou2-trajmatch.R,
- tests/ou2-trajmatch.Rout.save, tests/ricker-probe.Rout.save: -
- add new 'traj.match.objfun' and 'probe.match.objfun' functions
- - rearrange existing 'traj.match' and 'probe.match' codes to make
- use of these
- - an improved 'sannbox' algorithm is now exported
- * [r603] R/bsmc.R: - use SVD method in 'rmvnorm' rather than
- 'eigen' method
- * [r602] DESCRIPTION, NAMESPACE, inst/NEWS:
- * [r601] inst/doc/Makefile, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf: - use png flag for big files
- * [r600] tests/ou2-bsmc.R, tests/ou2-bsmc.Rout.save: - change the
- seed in an attempt to forestall errors under windows R-devel
- * [r599] man/ricker.Rd: - cosmetics
- * [r598] R/eulermultinom.R, inst/include/pomp.h,
- man/eulermultinom.Rd, src/eulermultinom.c, src/pomp.h: - add an R
- interface to the 'rgammawn' function
- * [r597] .Rinstignore: - add .Rinstignore file
-
-2012-01-16 kingaa
-
- * [r596] DESCRIPTION, inst/doc/gompertz-multi-mif.rda,
- inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: - fix
- SD/SE of pfilter log-likelihoods in 'intro_to_pomp'
-
-2012-01-15 kingaa
-
- * [r595] DESCRIPTION, inst/NEWS: - update DESCRIPTION & NEWS files
- * [r594] src/pomp.h: - add two inline helper functions: one for
- doing the exponential to geometric rate correction (see He et al.
- 2010),
- the other for computing the increment of an integrated gamma
- white-noise process (see Breto et al.)
-
-2012-01-12 kingaa
-
- * [r593] R/bsmc.R, inst/NEWS, man/bsmc.Rd, tests/ou2-bsmc.R,
- tests/ou2-bsmc.Rout.save: - Pierre Jacob's contributions to
- 'bsmc'
- * [r592] DESCRIPTION:
- * [r591] man/mif.Rd, man/slice-design.Rd: - minor documentation
- fixes
-
-2012-01-11 kingaa
-
- * [r590] DESCRIPTION, inst/ChangeLog, inst/NEWS, tests/steps.R,
- tests/steps.Rout.save: - version 0.40-2
- * [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,
+ * [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/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
+ 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)
-2011-12-24 kingaa
+2012-04-17 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'
+ * [r664] ., .Rbuildignore, .Rinstignore, DESCRIPTION, NAMESPACE, R,
+ data, demo, inst, man, src, tests: - move everything down one
+ level
-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
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 674
More information about the pomp-commits
mailing list