[Pomp-commits] r992 - in pkg/pomp: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jul 2 13:31:09 CEST 2014
Author: kingaa
Date: 2014-07-02 13:31:08 +0200 (Wed, 02 Jul 2014)
New Revision: 992
Removed:
pkg/pomp/inst/CHANGES_0.29-1.txt
pkg/pomp/inst/ChangeLog
pkg/pomp/inst/O_CHANGES
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/inst/TODO
Log:
- clean up pomp/inst
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2014-07-01 11:50:53 UTC (rev 991)
+++ pkg/pomp/DESCRIPTION 2014-07-02 11:31:08 UTC (rev 992)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.53-1
-Date: 2014-06-27
+Version: 0.53-2
+Date: 2014-07-02
Authors at R: c(person(given=c("Aaron","A."),family="King",
role=c("aut","cre"),email="kingaa at umich.edu"),
person(given=c("Edward","L."),family="Ionides",role=c("aut")),
Deleted: pkg/pomp/inst/CHANGES_0.29-1.txt
===================================================================
--- pkg/pomp/inst/CHANGES_0.29-1.txt 2014-07-01 11:50:53 UTC (rev 991)
+++ pkg/pomp/inst/CHANGES_0.29-1.txt 2014-07-02 11:31:08 UTC (rev 992)
@@ -1,225 +0,0 @@
-There are three main changes in version 0.29-1.
-
-1. Substantial improvements to the documentation, including both the vignettes
-and the manual pages.
-
-2. A bigger, more intuitive, and easier-to-use set of "plugins" for filling the
-'rprocess' slot of a 'pomp' object.
-
-3. Changes to the C interface for 'rmeasure' and 'dmeasure' functions.
-
-The first and second changes preserve backward compatibility: your old codes
-will work fine even if you do not make use of the new functionality. Using the
-old-style plugins 'euler.simulate' or 'onestep.simulate' will result in annoying
-warnings about these functions being deprecated and suggesting that you migrate
-to the new-style plugins sometime soon. In a future release of pomp,
-'euler.simulate' and 'onestep.simulate' will disappear.
-
-The third change does NOT preserve backward compatibility. If you use compiled
-native routines for 'rmeasure' and/or 'dmeasure', you must modify those routines
-or your codes will not work properly (and will almost certainly crash) when used
-with versions 0.29-1 and later of pomp. The required modification is quite
-minor, however, and is detailed below.
-
-In more detail:
-
-Change 1.
-The vignettes have been completely rewritten to be useful as tutorials. The
-first vignette, "intro_to_pomp", is a step-by-step guide to the construction of
-a 'pomp' and simulation, particle filtering, trajectory-matching, iterated
-filtering, and nonlinear forecasting. View it by doing
-R> ?vignette("intro_to_pomp")
-The second vignette shows how to accelerate performance using compiled native
-routines and briefly introduces the developer interface to pomp. View it by
-doing
-R> ?vignette("advanced_topics_in_pomp")
-
-Change 2. New plugins.
-As you probably know very well, it can be challenging to implement a model in
-pomp. In particular, the most difficult bit is typically writing the process
-model simulator (rprocess). In an effort to make this more intuitive, I have
-provided several new "plugins": functions that write the 'rprocess' function for
-you given minimal input on the form of the model.
-
-For some time there has been some plugin functionality, but their structure has
-made them nonintuitive and their documentation difficult to understand from the
-user's point of view. The new plugins are much more straightforward to use and
-their documentation is clearer (I hope). The new plugins provide precisely the
-same functionality: only the interface has changed. To be clear: switching over
-to the new-style plugins will have no effect on the underlying model nor,
-therefore, on inferences that have been based on that model.
-
-If you have been using the old-style plugins (euler.simulate or
-onestep.simulate), you can continue to do so for the time being. However,
-warning messages will be generated to inform you that these functions are
-deprecated and will be removed in a later release of pomp.
-
-To switch over to the new-style plugins, you need only edit a few lines in the R
-code that constructs a pomp object. Specifically, if you use
-
-pomp(...,rprocess=euler.simulate,...,delta.t=dt,...,step.fun=foo,...,PACKAGE=bar, ...)
-
-where 'foo' is either an R function or the name of a compiled native routine,
-and 'bar' is the name of the shared-object library where the compiled native
-routine resides, you can achieve the same functionality by using
-
-pomp(...,rprocess=euler.sim(step.fun=foo,delta.t=dt,PACKAGE=bar),...)
-
-Similarly, if you use
-
-pomp(...,rprocess=onestep.simulate,...,step.fun=foo,...,PACKAGE=bar,...)
-
-replace it with
-
-pomp(...,rprocess=onestep.sim(step.fun=foo,PACKAGE=bar),...)
-
-Essentially, the new-style plugins are functions that return "customized"
-functions suitable for use in the 'rprocess' slot of a 'pomp' object.
-
-There are now new plugins that include a discrete-time model plugin
-('discrete.time.sim') and an implementation of the Gillespie algorithm
-('gillespie.sim'). The FORTRAN codes that underly 'gillespie.sim' are due to
-Helen Wearing. For documentation on the new functionality, see
-R> ?plugins
-or
-R>?euler.sim
-R>?gillespie.sim
-R>?onestep.sim
-R>?discrete.time.sim
-
-Change 3. New interface for C versions of 'rmeasure' and 'dmeasure'.
-
-This change only affects you if you use compiled native routines for the
-measurement portion of your model. If you specify your measurement model either
-using 'measurement.model=blah' or by specifying 'rmeasure' and/or 'dmeasure' as
-R functions, you need do nothing.
-
-If you have written C functions to implement your measurement model, you have
-written a C function of prototype
-
-void pomp_measure_model_simulator (double *y, double *x, double *p, int *stateindex,
-int *parindex, int *covindex, int ncovars, double *covars, double t);
-
-and/or a function of prototype
-
-void pomp_measure_model_density (double *lik, double *y, double *x, double *p,
-int give_log, int *stateindex, int *parindex, int *covindex, int ncovars, double
-*covars, double t);
-
-In the new version of 'pomp', you must modify these functions to have prototypes
-
-void pomp_measure_model_simulator (double *y, double *x, double *p,
-int *obsindex, int *stateindex, int *parindex, int *covindex, int ncovars,
-double *covars, double t);
-
-and
-
-void pomp_measure_model_density (double *lik, double *y, double *x, double *p,
-int give_log, int *obsindex, int *stateindex, int *parindex, int *covindex, int
-ncovars, double *covars, double t);
-
-The only difference is that you need to insert a new int* argument 'obsindex' in
-the appropriate place.
-
-If you simply insert the new argument and do nothing more, your codes should
-function as before. If you wish to take advantage of the new functionality, it
-should make your codes more robust. To do so, when constructing a 'pomp' object,
-specify the names of observed variables in the 'obsnames' argument to 'pomp'. If
-you have done this, upon any call to either your C 'dmeasure' or 'rmeasure'
-function, 'obsindex' will be a pointer to a set of integers that indicate the
-positions in 'y' that correspond to the variables in 'obsnames' in that order.
-Thus, 'obsindex' is exactly analogous to 'stateindex', 'parindex', and
-'covindex': 'obsindex' is to 'y' as 'stateindex' is to 'x' as 'parindex' is to
-'p' as 'covindex' is to 'covars'.
-
-Here is an example of one of my own codes. Before version 0.29-1, the code was:
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-#define TAU (p[parindex[0]])
-#define DEATHS (x[stateindex[4]])
-#define DATADEATHS (y[0])
-
-void norm_rmeasure (double *y, double *x, double *p,
- int *stateindex, int *parindex, int *covindex,
- int ncovars, double *covars, double t)
-{
- double v, tol = 1.0e-18;
- v = DEATHS*exp(TAU);
- if (!(R_FINITE(v))) {
- DATADEATHS = R_NaReal;
- } else {
- DATADEATHS = rnorm(DEATHS,v+tol);
- }
-}
-
-void norm_dmeasure (double *lik, double *y, double *x, double *p, int give_log,
- int *stateindex, int *parindex, int *covindex,
- int ncovars, double *covars, double t)
-{
- double v, tol = 1.0e-18;
- v = DEATHS*exp(TAU);
- if (!(R_FINITE(v))) {
- *lik = tol;
- } else {
- *lik = dnorm(DATADEATHS,DEATHS,v+tol,0)+tol;
- }
- if (give_log) *lik = log(*lik);
-}
-
-#undef TAU
-#undef DEATHS
-#undef DATADEATHS
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
-As of pomp version 0.29-1, the code is:
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-#define TAU (p[parindex[0]])
-#define DEATHS (x[stateindex[4]])
-#define DATADEATHS (y[obsindex[0]])
-
-void norm_rmeasure (double *y, double *x, double *p,
- int *obsindex, int *stateindex, int *parindex, int *covindex,
- int ncovars, double *covars, double t)
-{
- double v, tol = 1.0e-18;
- v = DEATHS*exp(TAU);
- if (!(R_FINITE(v))) {
- DATADEATHS = R_NaReal;
- } else {
- DATADEATHS = rnorm(DEATHS,v+tol);
- }
-}
-
-void norm_dmeasure (double *lik, double *y, double *x, double *p, int give_log,
- int *obsindex, int *stateindex, int *parindex, int *covindex,
- int ncovars, double *covars, double t)
-{
- double v, tol = 1.0e-18;
- v = DEATHS*exp(TAU);
- if (!(R_FINITE(v))) {
- *lik = tol;
- } else {
- *lik = dnorm(DATADEATHS,DEATHS,v+tol,0)+tol;
- }
- if (give_log) *lik = log(*lik);
-}
-
-#undef TAU
-#undef DEATHS
-#undef DATADEATHS
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
-A diff on these two shows just the changes:
-ddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddd
-3c3
-< #define DATADEATHS (y[0])
----
-> #define DATADEATHS (y[obsindex[0]])
-6c6
-< int *stateindex, int *parindex, int *covindex,
----
-> int *obsindex, int *stateindex, int *parindex, int *covindex,
-19c19
-< int *stateindex, int *parindex, int *covindex,
----
-> int *obsindex, int *stateindex, int *parindex, int *covindex,
-ddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddd
\ No newline at end of file
Deleted: pkg/pomp/inst/ChangeLog
===================================================================
--- pkg/pomp/inst/ChangeLog 2014-07-01 11:50:53 UTC (rev 991)
+++ pkg/pomp/inst/ChangeLog 2014-07-02 11:31:08 UTC (rev 992)
@@ -1,427 +0,0 @@
-2013-01-09 kingaa
-
- * [r806] R/mif-class.R, R/mif.R, R/pfilter.R, R/pmcmc.R, inst/NEWS,
- man/mif-class.Rd, man/mif.Rd, man/pfilter.Rd, tests/ou2-mif2.R,
- tests/ou2-mif2.Rout.save: - integrate MIF2
- * [r805] R/example.R: - improved 'pompExample'
- * [r804] tests/bbs-trajmatch.R, tests/bbs-trajmatch.Rout.save,
- tests/bbs.R, tests/bbs.Rout.save, tests/blowflies.R,
- tests/blowflies.Rout.save, 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-bsmc.R,
- tests/ou2-bsmc.Rout.save, tests/ou2-forecast.R,
- tests/ou2-forecast.Rout.save, tests/ou2-icfit.R,
- tests/ou2-icfit.Rout.save, tests/ou2-kalman.R,
- tests/ou2-kalman.Rout.save, tests/ou2-mif-fp.R,
- tests/ou2-mif-fp.Rout.save, tests/ou2-mif.R,
- tests/ou2-mif.Rout.save, tests/ou2-nlf.R,
- tests/ou2-nlf.Rout.save, tests/ou2-pmcmc.R,
- tests/ou2-pmcmc.Rout.save, tests/ou2-probe.R,
- tests/ou2-probe.Rout.save, tests/ou2-procmeas.R,
- tests/ou2-procmeas.Rout.save, tests/ou2-simulate.R,
- tests/ou2-simulate.Rout.save, tests/ou2-trajmatch.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-bsmc.R,
- tests/ricker-bsmc.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/rw2.R, tests/rw2.Rout.save,
- tests/sir.R, tests/sir.Rout.save, tests/skeleton.R,
- tests/skeleton.Rout.save, tests/steps.R, tests/steps.Rout.save,
- tests/synlik.R, tests/synlik.Rout.save, tests/verhulst.R,
- tests/verhulst.Rout.save: - improved 'pompExample'
- * [r803] man/blowflies.Rd, man/dacca.Rd, man/example.Rd,
- man/gompertz.Rd, man/init.state-pomp.Rd, man/ou2.Rd,
- man/parmat.Rd, man/probe.Rd, man/ricker.Rd, man/rw2.Rd,
- man/simulate-pomp.Rd, man/sir.Rd, man/spect.Rd,
- man/traj-match.Rd, man/trajectory-pomp.Rd, man/verhulst.Rd: -
- improved 'pompExample'
- * [r802] man/pomp.Rd: - minor fix
- * [r801] .Rbuildignore, 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/examples/bbs.R, inst/examples/euler.sir.R,
- inst/examples/gillespie.sir.R, inst/examples/sir.R,
- man/blowflies.Rd, man/dacca.Rd, man/example.Rd, man/gompertz.Rd,
- man/init.state-pomp.Rd, man/ou2.Rd, man/parmat.Rd, man/probe.Rd,
- man/ricker.Rd, man/rw2.Rd, man/simulate-pomp.Rd, man/sir.Rd,
- man/spect.Rd, man/traj-match.Rd, man/trajectory-pomp.Rd,
- man/verhulst.Rd, tests/bbs-trajmatch.R,
- tests/bbs-trajmatch.Rout.save, tests/bbs.R, tests/bbs.Rout.save,
- tests/blowflies.R, tests/blowflies.Rout.save, tests/dacca.R,
- tests/dacca.Rout.save, tests/dimchecks.R,
- tests/dimchecks.Rout.save, tests/fhn.Rout.save,
- tests/filtfail.Rout.save, tests/gillespie.R,
- tests/gillespie.Rout.save, tests/gompertz.R,
- tests/gompertz.Rout.save, tests/logistic.Rout.save,
- tests/ou2-bsmc.R, tests/ou2-bsmc.Rout.save, tests/ou2-forecast.R,
- tests/ou2-forecast.Rout.save, tests/ou2-icfit.R,
- tests/ou2-icfit.Rout.save, tests/ou2-kalman.R,
- tests/ou2-kalman.Rout.save, tests/ou2-mif-fp.R,
- tests/ou2-mif-fp.Rout.save, tests/ou2-mif.R,
- tests/ou2-mif.Rout.save, tests/ou2-nlf.R,
- tests/ou2-nlf.Rout.save, tests/ou2-pmcmc.R,
- tests/ou2-pmcmc.Rout.save, tests/ou2-probe.R,
- tests/ou2-probe.Rout.save, tests/ou2-procmeas.R,
- tests/ou2-procmeas.Rout.save, tests/ou2-simulate.R,
- tests/ou2-simulate.Rout.save, tests/ou2-trajmatch.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-bsmc.R,
- tests/ricker-bsmc.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/rw2.R, tests/rw2.Rout.save,
- tests/sir.R, tests/sir.Rout.save, tests/skeleton.R,
- tests/skeleton.Rout.save, tests/steps.R, tests/steps.Rout.save,
- tests/synlik.R, tests/synlik.Rout.save, tests/verhulst.R,
- tests/verhulst.Rout.save: - get rid of all data()-loadable pomp
- objects, replacing them with the new 'pompExample' facility
- * [r800] DESCRIPTION, NAMESPACE, R/example.R, inst/data-R,
- inst/examples/blowflies.R, inst/examples/dacca.R,
- inst/examples/ewmeas.csv, inst/examples/gompertz.R,
- inst/examples/ou2.R, inst/examples/ricker.R, inst/examples/rw2.R,
- inst/examples/sir.R, inst/examples/verhulst.R: - remove
- data()-loadable pomp objects in favor of the new 'pompExample'
- mechanism.
-
-2013-01-08 kingaa
-
- * [r797] 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: -
- update data directory
- * [r794] DESCRIPTION, R/mif.R, tests/bbs.Rout.save,
- tests/gompertz.Rout.save, tests/ou2-bsmc.Rout.save,
- tests/ou2-mif.Rout.save: - update tests
- * [r793] DESCRIPTION, R/pfilter.R, R/pomp-class.R, R/pomp.R: - some
- changes preparatory to merging in mif2
-
-2012-09-14 kingaa
-
- * [r780] src/pomp_fun.c: - more informative error message when
- pomp_fun handler fails
-
-2012-08-22 kingaa
-
- * [r778] DESCRIPTION, inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/bsmc-ricker-flat-prior.rda,
- inst/doc/bsmc-ricker-normal-prior.rda,
- inst/doc/complex-sir-def.rda, inst/doc/fullnat.bst,
- inst/doc/gompertz-multi-mif.rda,
- inst/doc/gompertz-pfilter-guess.rda,
- inst/doc/gompertz-trajmatch.rda, inst/doc/intro_to_pomp.Rnw,
- 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/plugin-C-code.rda, inst/doc/plugin-R-code.rda,
- inst/doc/pomp.bib, inst/doc/ricker-comparison.rda,
- inst/doc/ricker-first-probe.rda, inst/doc/ricker-mif.rda,
- inst/doc/ricker-probe-match.rda, inst/doc/ricker-probe.rda,
- inst/doc/sim-sim.rda, inst/doc/sir-pomp-def.rda,
- inst/doc/vectorized-C-code.rda, inst/doc/vectorized-R-code.rda: -
- remove vignette codes
-
-2012-08-08 kingaa
-
- * [r765] DESCRIPTION, inst/doc/advanced_topics_in_pomp.Rnw,
- inst/doc/advanced_topics_in_pomp.pdf,
- inst/doc/bsmc-ricker-normal-prior.rda,
- inst/doc/complex-sir-def.rda,
- inst/doc/gompertz-pfilter-guess.rda, inst/doc/intro_to_pomp.Rnw,
- inst/doc/intro_to_pomp.pdf, inst/doc/plugin-C-code.rda,
- inst/doc/plugin-R-code.rda, inst/doc/ricker-comparison.rda,
- inst/doc/ricker-first-probe.rda, inst/doc/ricker-probe.rda,
- inst/doc/sim-sim.rda, inst/doc/sir-pomp-def.rda,
- inst/doc/vectorized-C-code.rda, inst/doc/vectorized-R-code.rda: -
- store more intermediate results in the building of the vignettes
- to make vignette-checking quicker
-
-2012-08-03 kingaa
-
- * [r757] tests/fhn.R, tests/fhn.Rout.save, tests/ricker-spect.R,
- tests/ricker-spect.Rout.save, tests/ricker.R,
- tests/ricker.Rout.save, tests/rw2.R, tests/rw2.Rout.save,
- tests/sir.R, tests/sir.Rout.save: - more modifications to test
- files
- * [r756] DESCRIPTION, inst/NEWS, tests/ou2-probe.R,
- tests/ou2-probe.Rout.save, tests/ricker-bsmc.R,
- tests/ricker-bsmc.Rout.save, tests/ricker-probe.R,
- tests/ricker-probe.Rout.save: - clean up tests
-
-2012-07-31 kingaa
-
- * [r753] DESCRIPTION, R/authors.R, inst/NEWS,
- man/pfilter-methods.Rd: - add authors list
- - add documentation of 'cond.logLik' and 'eff.sample.size'
-
-2012-07-13 kingaa
-
- * [r752] DESCRIPTION, NAMESPACE, R/aaa.R, R/mif.R,
- R/pfilter-methods.R, tests/gompertz.R, tests/gompertz.Rout.save,
- tests/ou2-mif.Rout.save: - add 'eff.sample.size' and
- 'cond.logLik' methods for 'pfilterd.pomp' objects
- - make 'non-finite parameters' warning message more informative
- * [r751] DESCRIPTION, src/dmeasure.c: - fix bug in 'dmeasure' when
- log=T. bug found by R. Reiner.
-
-2012-07-10 kingaa
-
- * [r750] DESCRIPTION, R/builder.R, inst/include/pomp.h, src/pomp.h,
- src/pomp_internal.h, src/sir.c: - fix bug with pompBuilder on mac
-
-2012-07-02 kingaa
-
- * [r744] DESCRIPTION: - require only R version >= 2.14.1
-
-2012-07-01 kingaa
-
- * [r743] DESCRIPTION, inst/ChangeLog: - update changelog & date
- * [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
-
Deleted: pkg/pomp/inst/O_CHANGES
===================================================================
--- pkg/pomp/inst/O_CHANGES 2014-07-01 11:50:53 UTC (rev 991)
+++ pkg/pomp/inst/O_CHANGES 2014-07-02 11:31:08 UTC (rev 992)
@@ -1,569 +0,0 @@
-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.
-
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 992
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