[Pomp-commits] r311 - in pkg: . pomp

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Aug 30 18:21:37 CEST 2010


Author: kingaa
Date: 2010-08-30 18:21:37 +0200 (Mon, 30 Aug 2010)
New Revision: 311

Added:
   pkg/DESCRIPTION
   pkg/NAMESPACE
   pkg/R/
   pkg/data/
   pkg/inst/
   pkg/man/
   pkg/src/
   pkg/tests/
Removed:
   pkg/pomp/DESCRIPTION
   pkg/pomp/NAMESPACE
   pkg/pomp/R/
   pkg/pomp/data/
   pkg/pomp/inst/
   pkg/pomp/man/
   pkg/pomp/src/
   pkg/pomp/tests/
Log:
- put everything in pkg/pomp back into pkg


Copied: pkg/DESCRIPTION (from rev 310, pkg/pomp/DESCRIPTION)
===================================================================
--- pkg/DESCRIPTION	                        (rev 0)
+++ pkg/DESCRIPTION	2010-08-30 16:21:37 UTC (rev 311)
@@ -0,0 +1,24 @@
+Package: pomp
+Type: Package
+Title: Statistical inference for partially observed Markov processes
+Version: 0.32-5
+Date: 2010-08-30
+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(>= 2.9.1), stats, methods, graphics
+Imports: mvtnorm, subplex, deSolve
+License: GPL(>= 2)
+LazyLoad: true
+LazyData: false
+Collate: eulermultinom.R euler.R plugins.R slice.R sobol.R bsplines.R 
+	 pomp-fun.R pomp.R pomp-methods.R rmeasure-pomp.R rprocess-pomp.R 
+	 dmeasure-pomp.R dprocess-pomp.R simulate-pomp.R skeleton-pomp.R 
+	 trajectory-pomp.R plot-pomp.R init.state-pomp.R 
+	 pfilter.R traj-match.R bsmc.R
+	 mif-class.R particles-mif.R pfilter-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-lql.R nlf-objfun.R nlf.R 
+	 probe.R probe-match.R basic-probes.R spect.R spect-match.R

Copied: pkg/NAMESPACE (from rev 310, pkg/pomp/NAMESPACE)
===================================================================
--- pkg/NAMESPACE	                        (rev 0)
+++ pkg/NAMESPACE	2010-08-30 16:21:37 UTC (rev 311)
@@ -0,0 +1,70 @@
+useDynLib(			
+          pomp,
+          bspline_basis,
+          periodic_bspline_basis,
+          bspline_basis_function,
+          systematic_resampling,
+          euler_model_simulator,
+          euler_model_density,
+          SSA_simulator,
+          R_Euler_Multinom,
+          D_Euler_Multinom,
+          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(deSolve,lsoda)
+importFrom(subplex,subplex)
+
+exportClasses('pomp','mif','pmcmc','probed.pomp','probe.matched.pomp','spect.pomp','spect.matched.pomp')
+
+exportMethods(
+              'plot','show','print','coerce',
+              'dprocess','rprocess','rmeasure','dmeasure','init.state','skeleton',
+              'data.array','summary','coef','logLik','time','time<-','timezero','timezero<-','window',
+              'simulate','pfilter',
+              'particles','mif','continue','coef<-','states','trajectory',
+              'pred.mean','pred.var','filter.mean','conv.rec',
+              'bsmc',
+              'pmcmc','dprior',
+              'spect','probe'
+              )
+
+export(
+       pomp,
+       reulermultinom,
+       deulermultinom,
+       euler.simulate,
+       onestep.simulate,
+       onestep.density,
+       euler.sim,
+       discrete.time.sim,
+       onestep.sim,
+       onestep.dens,
+       gillespie.sim,
+       sobol,
+       slice.design,
+       profile.design,
+       bspline.basis,
+       periodic.bspline.basis,
+       compare.mif,
+       nlf,
+       traj.match,
+       probe.mean,
+       probe.var,
+       probe.sd,
+       probe.period,
+       probe.quantile,
+       probe.acf,
+       probe.cov,
+       probe.cor,
+       probe.match,
+       spect.match
+       )

Deleted: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2010-08-30 16:17:49 UTC (rev 310)
+++ pkg/pomp/DESCRIPTION	2010-08-30 16:21:37 UTC (rev 311)
@@ -1,24 +0,0 @@
-Package: pomp
-Type: Package
-Title: Statistical inference for partially observed Markov processes
-Version: 0.32-5
-Date: 2010-08-30
-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(>= 2.9.1), stats, methods, graphics
-Imports: mvtnorm, subplex, deSolve
-License: GPL(>= 2)
-LazyLoad: true
-LazyData: false
-Collate: eulermultinom.R euler.R plugins.R slice.R sobol.R bsplines.R 
-	 pomp-fun.R pomp.R pomp-methods.R rmeasure-pomp.R rprocess-pomp.R 
-	 dmeasure-pomp.R dprocess-pomp.R simulate-pomp.R skeleton-pomp.R 
-	 trajectory-pomp.R plot-pomp.R init.state-pomp.R 
-	 pfilter.R traj-match.R bsmc.R
-	 mif-class.R particles-mif.R pfilter-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-lql.R nlf-objfun.R nlf.R 
-	 probe.R probe-match.R basic-probes.R spect.R spect-match.R

Deleted: pkg/pomp/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE	2010-08-30 16:17:49 UTC (rev 310)
+++ pkg/pomp/NAMESPACE	2010-08-30 16:21:37 UTC (rev 311)
@@ -1,70 +0,0 @@
-useDynLib(			
-          pomp,
-          bspline_basis,
-          periodic_bspline_basis,
-          bspline_basis_function,
-          systematic_resampling,
-          euler_model_simulator,
-          euler_model_density,
-          SSA_simulator,
-          R_Euler_Multinom,
-          D_Euler_Multinom,
-          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(deSolve,lsoda)
-importFrom(subplex,subplex)
-
-exportClasses('pomp','mif','pmcmc','probed.pomp','probe.matched.pomp','spect.pomp','spect.matched.pomp')
-
-exportMethods(
-              'plot','show','print','coerce',
-              'dprocess','rprocess','rmeasure','dmeasure','init.state','skeleton',
-              'data.array','summary','coef','logLik','time','time<-','timezero','timezero<-','window',
-              'simulate','pfilter',
-              'particles','mif','continue','coef<-','states','trajectory',
-              'pred.mean','pred.var','filter.mean','conv.rec',
-              'bsmc',
-              'pmcmc','dprior',
-              'spect','probe'
-              )
-
-export(
-       pomp,
-       reulermultinom,
-       deulermultinom,
-       euler.simulate,
-       onestep.simulate,
-       onestep.density,
-       euler.sim,
-       discrete.time.sim,
-       onestep.sim,
-       onestep.dens,
-       gillespie.sim,
-       sobol,
-       slice.design,
-       profile.design,
-       bspline.basis,
-       periodic.bspline.basis,
-       compare.mif,
-       nlf,
-       traj.match,
-       probe.mean,
-       probe.var,
-       probe.sd,
-       probe.period,
-       probe.quantile,
-       probe.acf,
-       probe.cov,
-       probe.cor,
-       probe.match,
-       spect.match
-       )



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