[Pomp-commits] r664 - in pkg: . pomp
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 17 22:46:36 CEST 2012
Author: kingaa
Date: 2012-04-17 22:46:36 +0200 (Tue, 17 Apr 2012)
New Revision: 664
Added:
pkg/pomp/
pkg/pomp/.Rbuildignore
pkg/pomp/.Rinstignore
pkg/pomp/DESCRIPTION
pkg/pomp/NAMESPACE
pkg/pomp/R/
pkg/pomp/data/
pkg/pomp/demo/
pkg/pomp/inst/
pkg/pomp/man/
pkg/pomp/src/
pkg/pomp/tests/
Removed:
pkg/.Rbuildignore
pkg/.Rinstignore
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/
pkg/data/
pkg/demo/
pkg/inst/
pkg/man/
pkg/src/
pkg/tests/
Log:
- move everything down one level
Deleted: pkg/.Rbuildignore
===================================================================
--- pkg/.Rbuildignore 2012-04-16 14:03:44 UTC (rev 663)
+++ pkg/.Rbuildignore 2012-04-17 20:46:36 UTC (rev 664)
@@ -1,6 +0,0 @@
-inst/doc/Makefile
-inst/data-R/Makefile
-inst/data-R/make.R
-inst/doc/(.+?)\.bst$
-inst/doc/(.+?)\.R$
-inst/doc/(.+?)\.png$
Deleted: pkg/.Rinstignore
===================================================================
--- pkg/.Rinstignore 2012-04-16 14:03:44 UTC (rev 663)
+++ pkg/.Rinstignore 2012-04-17 20:46:36 UTC (rev 664)
@@ -1,3 +0,0 @@
-inst/doc/Makefile
-inst/doc/fullnat.bst
-inst/doc/(.+?)\.rda$
Deleted: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-04-16 14:03:44 UTC (rev 663)
+++ pkg/DESCRIPTION 2012-04-17 20:46:36 UTC (rev 664)
@@ -1,25 +0,0 @@
-Package: pomp
-Type: Package
-Title: Statistical inference for partially observed Markov processes
-Version: 0.41-6
-Date: 2012-04-16
-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>
-URL: http://pomp.r-forge.r-project.org
-Description: Inference methods for partially-observed Markov processes
-Depends: R(>= 2.15.0), stats, methods, graphics, mvtnorm, subplex, deSolve
-License: GPL(>= 2)
-LazyLoad: true
-LazyData: false
-BuildVignettes: no
-Collate: aaa.R version.R eulermultinom.R plugins.R
- parmat.R slice-design.R profile-design.R sobol.R bsplines.R sannbox.R
- pomp-fun.R pomp.R pomp-methods.R rmeasure-pomp.R rprocess-pomp.R init-state-pomp.R
- dmeasure-pomp.R dprocess-pomp.R skeleton-pomp.R simulate-pomp.R trajectory-pomp.R plot-pomp.R
- pfilter.R pfilter-methods.R traj-match.R bsmc.R
- mif-class.R particles-mif.R mif.R mif-methods.R compare-mif.R
- pmcmc.R pmcmc-methods.R compare-pmcmc.R
- nlf-funcs.R nlf-guts.R nlf-objfun.R nlf.R
- probe.R probe-match.R basic-probes.R spect.R spect-match.R
- builder.R
Deleted: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2012-04-16 14:03:44 UTC (rev 663)
+++ pkg/NAMESPACE 2012-04-17 20:46:36 UTC (rev 664)
@@ -1,94 +0,0 @@
-useDynLib(
- pomp,
- get_pomp_fun,
- bspline_basis,
- periodic_bspline_basis,
- bspline_basis_function,
- systematic_resampling,
- euler_model_simulator,
- euler_model_density,
- lookup_in_table,
- SSA_simulator,
- R_Euler_Multinom,D_Euler_Multinom,R_GammaWN,
- pfilter_computations,
- simulation_computations,
- iterate_map,traj_transp_and_copy,
- apply_probe_data,apply_probe_sim,
- probe_marginal_setup,probe_marginal_solve,
- probe_acf,probe_ccf,
- probe_nlar,
- synth_loglik,
- pomp_desolve_init,
- pomp_vf_eval,
- do_partrans,
- do_rprocess,
- do_dprocess,
- do_rmeasure,
- do_dmeasure,
- do_skeleton,
- do_init_state
- )
-
-importFrom(graphics,plot)
-importFrom(stats,simulate,time,coef,logLik,window)
-importFrom(mvtnorm,dmvnorm,rmvnorm)
-importFrom(subplex,subplex)
-importFrom(deSolve,ode)
-
-exportClasses(
- pomp,
- pfilterd.pomp,
- mif,
- pmcmc,
- traj.matched.pomp,
- probed.pomp,probe.matched.pomp,
- spect.pomp,spect.matched.pomp
- )
-
-exportMethods(
- pomp,
- plot,show,print,coerce,summary,logLik,window,"$",
- dprocess,rprocess,rmeasure,dmeasure,init.state,skeleton,
- data.array,obs,partrans,coef,"coef<-",time,"time<-",timezero,"timezero<-",
- simulate,pfilter,
- particles,mif,continue,states,trajectory,
- pred.mean,pred.var,filter.mean,conv.rec,
- bsmc,
- pmcmc,dprior,
- spect,probe,
- probe.match,traj.match
- )
-
-export(
- as.data.frame.pomp,
- reulermultinom,
- deulermultinom,
- rgammawn,
- euler.sim,
- discrete.time.sim,
- onestep.sim,
- onestep.dens,
- gillespie.sim,
- sobol,
- sobolDesign,
- sliceDesign,
- profileDesign,
- bspline.basis,
- periodic.bspline.basis,
- compare.mif,
- nlf,
- parmat,
- probe.mean,
- probe.median,
- probe.var,
- probe.sd,
- probe.period,
- probe.quantile,
- probe.acf,
- probe.ccf,
- probe.nlar,
- probe.marginal,
- sannbox,
- spect.match,
- traj.match.objfun
- )
Copied: pkg/pomp/.Rbuildignore (from rev 663, pkg/.Rbuildignore)
===================================================================
--- pkg/pomp/.Rbuildignore (rev 0)
+++ pkg/pomp/.Rbuildignore 2012-04-17 20:46:36 UTC (rev 664)
@@ -0,0 +1,6 @@
+inst/doc/Makefile
+inst/data-R/Makefile
+inst/data-R/make.R
+inst/doc/(.+?)\.bst$
+inst/doc/(.+?)\.R$
+inst/doc/(.+?)\.png$
Copied: pkg/pomp/.Rinstignore (from rev 663, pkg/.Rinstignore)
===================================================================
--- pkg/pomp/.Rinstignore (rev 0)
+++ pkg/pomp/.Rinstignore 2012-04-17 20:46:36 UTC (rev 664)
@@ -0,0 +1,3 @@
+inst/doc/Makefile
+inst/doc/fullnat.bst
+inst/doc/(.+?)\.rda$
Copied: pkg/pomp/DESCRIPTION (from rev 663, pkg/DESCRIPTION)
===================================================================
--- pkg/pomp/DESCRIPTION (rev 0)
+++ pkg/pomp/DESCRIPTION 2012-04-17 20:46:36 UTC (rev 664)
@@ -0,0 +1,25 @@
+Package: pomp
+Type: Package
+Title: Statistical inference for partially observed Markov processes
+Version: 0.41-6
+Date: 2012-04-16
+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>
+URL: http://pomp.r-forge.r-project.org
+Description: Inference methods for partially-observed Markov processes
+Depends: R(>= 2.15.0), stats, methods, graphics, mvtnorm, subplex, deSolve
+License: GPL(>= 2)
+LazyLoad: true
+LazyData: false
+BuildVignettes: no
+Collate: aaa.R version.R eulermultinom.R plugins.R
+ parmat.R slice-design.R profile-design.R sobol.R bsplines.R sannbox.R
+ pomp-fun.R pomp.R pomp-methods.R rmeasure-pomp.R rprocess-pomp.R init-state-pomp.R
+ dmeasure-pomp.R dprocess-pomp.R skeleton-pomp.R simulate-pomp.R trajectory-pomp.R plot-pomp.R
+ pfilter.R pfilter-methods.R traj-match.R bsmc.R
+ mif-class.R particles-mif.R mif.R mif-methods.R compare-mif.R
+ pmcmc.R pmcmc-methods.R compare-pmcmc.R
+ nlf-funcs.R nlf-guts.R nlf-objfun.R nlf.R
+ probe.R probe-match.R basic-probes.R spect.R spect-match.R
+ builder.R
Copied: pkg/pomp/NAMESPACE (from rev 663, pkg/NAMESPACE)
===================================================================
--- pkg/pomp/NAMESPACE (rev 0)
+++ pkg/pomp/NAMESPACE 2012-04-17 20:46:36 UTC (rev 664)
@@ -0,0 +1,94 @@
+useDynLib(
+ pomp,
+ get_pomp_fun,
+ bspline_basis,
+ periodic_bspline_basis,
+ bspline_basis_function,
+ systematic_resampling,
+ euler_model_simulator,
+ euler_model_density,
+ lookup_in_table,
+ SSA_simulator,
+ R_Euler_Multinom,D_Euler_Multinom,R_GammaWN,
+ pfilter_computations,
+ simulation_computations,
+ iterate_map,traj_transp_and_copy,
+ apply_probe_data,apply_probe_sim,
+ probe_marginal_setup,probe_marginal_solve,
+ probe_acf,probe_ccf,
+ probe_nlar,
+ synth_loglik,
+ pomp_desolve_init,
+ pomp_vf_eval,
+ do_partrans,
+ do_rprocess,
+ do_dprocess,
+ do_rmeasure,
+ do_dmeasure,
+ do_skeleton,
+ do_init_state
+ )
+
+importFrom(graphics,plot)
+importFrom(stats,simulate,time,coef,logLik,window)
+importFrom(mvtnorm,dmvnorm,rmvnorm)
+importFrom(subplex,subplex)
+importFrom(deSolve,ode)
+
+exportClasses(
+ pomp,
+ pfilterd.pomp,
+ mif,
+ pmcmc,
+ traj.matched.pomp,
+ probed.pomp,probe.matched.pomp,
+ spect.pomp,spect.matched.pomp
+ )
+
+exportMethods(
+ pomp,
+ plot,show,print,coerce,summary,logLik,window,"$",
+ dprocess,rprocess,rmeasure,dmeasure,init.state,skeleton,
+ data.array,obs,partrans,coef,"coef<-",time,"time<-",timezero,"timezero<-",
+ simulate,pfilter,
+ particles,mif,continue,states,trajectory,
+ pred.mean,pred.var,filter.mean,conv.rec,
+ bsmc,
+ pmcmc,dprior,
+ spect,probe,
+ probe.match,traj.match
+ )
+
+export(
+ as.data.frame.pomp,
+ reulermultinom,
+ deulermultinom,
+ rgammawn,
+ euler.sim,
+ discrete.time.sim,
+ onestep.sim,
+ onestep.dens,
+ gillespie.sim,
+ sobol,
+ sobolDesign,
+ sliceDesign,
+ profileDesign,
+ bspline.basis,
+ periodic.bspline.basis,
+ compare.mif,
+ nlf,
+ parmat,
+ probe.mean,
+ probe.median,
+ probe.var,
+ probe.sd,
+ probe.period,
+ probe.quantile,
+ probe.acf,
+ probe.ccf,
+ probe.nlar,
+ probe.marginal,
+ sannbox,
+ spect.match,
+ traj.match.objfun
+ )
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