CollocInfer: Collocation Inference for Dynamic Systems

These functions implement collocation-inference for continuous-time and discrete-time stochastic processes. They provide model-based smoothing, gradient-matching, generalized profiling and forwards prediction error methods.

Install the latest version of this package by entering the following in R:
install.packages("CollocInfer")
AuthorGiles Hooker <gjh27@cornell.edu>, Luo Xiao <lx42@cornell.edu>, James Ramsay <ramsay@psych.mcgill.ca>
Date of publication2016-11-07 08:12:33
MaintainerGiles Hooker <gjh27@cornell.edu>
LicenseGPL (>= 2)
Version1.0.4
http://www.bscb.cornell.edu/~hooker

View on CRAN

Functions

SplineCoefsDC Man page
SplineCoefsDC2 Man page
SplineCoefsDCDP Man page
SplineCoefsDP Man page
SplineCoefsErr Man page
SplineCoefsList Man page
SplineEst.NewtRaph Man page

Files

TODO
inst
inst/trymcmc.r
inst/todo.txt
inst/CITATION
inst/OldDemo
inst/OldDemo/CircleEx.r inst/OldDemo/HenonEx.R inst/OldDemo/FhNEx.Jim.r inst/OldDemo/Circle.r inst/OldDemo/SEIREX.r
inst/OldDemo/gillespieInc.csv
inst/OldDemo/FhNEx3.R inst/OldDemo/FhN.diagnostics.R inst/OldDemo/exp2fhn.r inst/OldDemo/FhNEx2.r inst/OldDemo/gillespie.r
inst/OldDemo/ChemoData2.rda
inst/OldDemo/FhNEx4.R inst/OldDemo/FhNEx.R
inst/MatlabCollocInfer
inst/MatlabCollocInfer/make_Cproc.m
inst/MatlabCollocInfer/dataformat.m
inst/MatlabCollocInfer/demos
inst/MatlabCollocInfer/demos/ChemoStatDemo.m
inst/MatlabCollocInfer/demos/SEIRdata.txt
inst/MatlabCollocInfer/demos/SEIRDemo.m
inst/MatlabCollocInfer/demos/ChemoStatDemo_new.m
inst/MatlabCollocInfer/demos/SEIRdemo_Routput.txt
inst/MatlabCollocInfer/demos/groundwater.m
inst/MatlabCollocInfer/demos/ChemoData.txt
inst/MatlabCollocInfer/demos/NSdata.txt
inst/MatlabCollocInfer/demos/ChemoStatDemo_old.m
inst/MatlabCollocInfer/demos/ChemoStatDemo_new.asv
inst/MatlabCollocInfer/demos/ChemoStatDemo_tmp.m
inst/MatlabCollocInfer/demos/demos.m
inst/MatlabCollocInfer/demos/NSdemo.m
inst/MatlabCollocInfer/demos/groundwater.txt
inst/MatlabCollocInfer/demos/FhNDemo.m
inst/MatlabCollocInfer/demos/rainfall.txt
inst/MatlabCollocInfer/demos/SEIRcoefs2.txt
inst/MatlabCollocInfer/demos/demos.r
inst/MatlabCollocInfer/ssefunctions_tmp.m
inst/MatlabCollocInfer/SSE
inst/MatlabCollocInfer/SSE/dSSE_dp.m
inst/MatlabCollocInfer/SSE/make_SSEproc.m
inst/MatlabCollocInfer/SSE/d2SSE_proc_dc2.m
inst/MatlabCollocInfer/SSE/d2SSE_dydp.m
inst/MatlabCollocInfer/SSE/dSSE_proc_dp.m
inst/MatlabCollocInfer/SSE/dSSE_dy.m
inst/MatlabCollocInfer/SSE/d2SSE_dy2.m
inst/MatlabCollocInfer/SSE/d2SSE_dxdp.m
inst/MatlabCollocInfer/SSE/d2SSE_dxdy.m
inst/MatlabCollocInfer/SSE/SSE_proc.m
inst/MatlabCollocInfer/SSE/dSSE_proc_dc.m
inst/MatlabCollocInfer/SSE/make_SSElik.m
inst/MatlabCollocInfer/SSE/d2SSE_proc_dcdp.m
inst/MatlabCollocInfer/SSE/d2SSE_dx2.m
inst/MatlabCollocInfer/SSE/dSSE_dx.m
inst/MatlabCollocInfer/SSE/SSE.m
inst/MatlabCollocInfer/Henon
inst/MatlabCollocInfer/Henon/make_Henon.m
inst/MatlabCollocInfer/outeropt.m
inst/MatlabCollocInfer/SEIRdata.txt
inst/MatlabCollocInfer/SplineCoefs.m
inst/MatlabCollocInfer/Profile_multinorm.m
inst/MatlabCollocInfer/blocks2mat.m
inst/MatlabCollocInfer/Smooth_LS.m
inst/MatlabCollocInfer/exptrans
inst/MatlabCollocInfer/exptrans/exptrans_d2fdxd.m
inst/MatlabCollocInfer/exptrans/exptrans_dfd.m
inst/MatlabCollocInfer/exptrans/exptrans_dfdx.m
inst/MatlabCollocInfer/exptrans/exptrans_fun.m
inst/MatlabCollocInfer/exptrans/make_exptrans.m
inst/MatlabCollocInfer/exptrans/exptrans_d2fdx2.m
inst/MatlabCollocInfer/exptrans/exptrans_dfdp.m
inst/MatlabCollocInfer/ProfileCovariance.asv
inst/MatlabCollocInfer/FHNtry.m
inst/MatlabCollocInfer/make_cvar.m
inst/MatlabCollocInfer/applysum.m
inst/MatlabCollocInfer/ParsMatch.m
inst/MatlabCollocInfer/checkmore_genlin.m
inst/MatlabCollocInfer/FitMatchOpt.m
inst/MatlabCollocInfer/CollocInferPlots.asv
inst/MatlabCollocInfer/inneropt.m
inst/MatlabCollocInfer/logstate_lik
inst/MatlabCollocInfer/logstate_lik/logstate_lik_d2fdx2.m
inst/MatlabCollocInfer/logstate_lik/make_logstate_lik.m
inst/MatlabCollocInfer/logstate_lik/logstate_lik_dfdx.m
inst/MatlabCollocInfer/logstate_lik/logstate_lik_dfdp.m
inst/MatlabCollocInfer/logstate_lik/logstate_lik_fun.m
inst/MatlabCollocInfer/logstate_lik/logstate_lik_d2fdxdp.m
inst/MatlabCollocInfer/CollocInfer.m
inst/MatlabCollocInfer/CollocInferUtility.m
inst/MatlabCollocInfer/checkmore_cvar.m
inst/MatlabCollocInfer/findif_var_d2fdxdp.m
inst/MatlabCollocInfer/findif
inst/MatlabCollocInfer/findif/make_findif_loglik.m
inst/MatlabCollocInfer/findif/make_findif_var.m
inst/MatlabCollocInfer/findif/findif_var_fun.m
inst/MatlabCollocInfer/findif/findif_loglik_fun.m
inst/MatlabCollocInfer/findif/findif_loglik_d2fdx2.m
inst/MatlabCollocInfer/findif/findif_ode_dfdp.m
inst/MatlabCollocInfer/findif/findif_ode_d2fdx2.m
inst/MatlabCollocInfer/findif/findif_ode_fn.m
inst/MatlabCollocInfer/findif/findif_var_dfdx.m
inst/MatlabCollocInfer/findif/findif_ode_d2fdxdp.m
inst/MatlabCollocInfer/findif/findif_ode_dfdx.m
inst/MatlabCollocInfer/findif/make_findif_ode.m
inst/MatlabCollocInfer/findif/findif_loglik_d2fdy2.m
inst/MatlabCollocInfer/findif/findif_loglik_dfdp.m
inst/MatlabCollocInfer/findif/findif_loglik_d2fdxdy.m
inst/MatlabCollocInfer/findif/findif_var_dfdp.m
inst/MatlabCollocInfer/findif/findif_var_d2fdx2.m
inst/MatlabCollocInfer/findif/findif_loglik_d2fdxdp.m
inst/MatlabCollocInfer/findif/findif_loglik_dfdy.m
inst/MatlabCollocInfer/findif/findif_loglik_d2fdydp.m
inst/MatlabCollocInfer/findif/findif_loglik_dfdx.m
inst/MatlabCollocInfer/ProfileErr.m
inst/MatlabCollocInfer/fhn
inst/MatlabCollocInfer/fhn/fhn_d2fdx2.m
inst/MatlabCollocInfer/fhn/fhn_fun_ode.m
inst/MatlabCollocInfer/fhn/fhn_dfdx.m
inst/MatlabCollocInfer/fhn/fhn_d2fdxdp.m
inst/MatlabCollocInfer/fhn/fhn_dfdp.m
inst/MatlabCollocInfer/fhn/fhn_fun.m
inst/MatlabCollocInfer/fhn/make_fhn.m
inst/MatlabCollocInfer/ChemoStat
inst/MatlabCollocInfer/ChemoStat/chemo_obs.m
inst/MatlabCollocInfer/ChemoStat/chemo_fun.m
inst/MatlabCollocInfer/ChemoStat/chemo_ode.m
inst/MatlabCollocInfer/ChemoStat/chemo_fun_tmp.m
inst/MatlabCollocInfer/LS_setup.m
inst/MatlabCollocInfer/exp_d2Dproc_dcdp.m
inst/MatlabCollocInfer/oderhs.m
inst/MatlabCollocInfer/IntegrateForward.m
inst/MatlabCollocInfer/id
inst/MatlabCollocInfer/id/id_d2fdx2.m
inst/MatlabCollocInfer/id/id_dfdp.m
inst/MatlabCollocInfer/id/id_dfdx.m
inst/MatlabCollocInfer/id/id_d2fdxdp.m
inst/MatlabCollocInfer/id/id_fn.m
inst/MatlabCollocInfer/id/make_id.m
inst/MatlabCollocInfer/ProfileErr_AllPar.m
inst/MatlabCollocInfer/genlin
inst/MatlabCollocInfer/genlin/genlin_fun_ode.m
inst/MatlabCollocInfer/genlin/genlin_dfdx.m
inst/MatlabCollocInfer/genlin/make_genlin.m
inst/MatlabCollocInfer/genlin/genlin_d2fdx2.m
inst/MatlabCollocInfer/genlin/genlin_fn.m
inst/MatlabCollocInfer/genlin/genlin_dfdp.m
inst/MatlabCollocInfer/genlin/checkmore.m
inst/MatlabCollocInfer/genlin/genlin_d2fdxdp.m
inst/MatlabCollocInfer/exp
inst/MatlabCollocInfer/exp/exp_dCproc_dp.m
inst/MatlabCollocInfer/exp/exp_dfdx.m
inst/MatlabCollocInfer/exp/exp_dDproc_dp.m
inst/MatlabCollocInfer/exp/exp_Cproc.m
inst/MatlabCollocInfer/exp/make_exp.m
inst/MatlabCollocInfer/exp/exp_Dproc.m
inst/MatlabCollocInfer/exp/exp_dfdp.m
inst/MatlabCollocInfer/exp/exp_d2Dproc_dc2.m
inst/MatlabCollocInfer/exp/exp_d2Cproc_dcdp.m
inst/MatlabCollocInfer/exp/exp_d2fdx2.m
inst/MatlabCollocInfer/exp/exp_fn.m
inst/MatlabCollocInfer/exp/exp_d2Cproc_dc2.m
inst/MatlabCollocInfer/exp/exp_dDproc_dc.m
inst/MatlabCollocInfer/exp/make_exp_Dproc.m
inst/MatlabCollocInfer/exp/exp_d2fdxdp.m
inst/MatlabCollocInfer/exp/make_exp_Cproc.m
inst/MatlabCollocInfer/exp/exp_dCproc_dc.m
inst/MatlabCollocInfer/make_multinorm.m
inst/MatlabCollocInfer/LS_setup.asv
inst/MatlabCollocInfer/ParsMatchOpt.m
inst/MatlabCollocInfer/FHNdata.txt
inst/MatlabCollocInfer/CollocInferPlots.m
inst/MatlabCollocInfer/NS
inst/MatlabCollocInfer/NS/NS_d2fdxdp.m
inst/MatlabCollocInfer/NS/NS_fn.m
inst/MatlabCollocInfer/NS/NS_dfdx.m
inst/MatlabCollocInfer/NS/NS_ode.m
inst/MatlabCollocInfer/NS/NS_d2fdx2.m
inst/MatlabCollocInfer/NS/NS_fun.m
inst/MatlabCollocInfer/NS/NS_dfdp.m
inst/MatlabCollocInfer/NS/make_NS.m
inst/MatlabCollocInfer/Rcode
inst/MatlabCollocInfer/Rcode/ProfileR.R inst/MatlabCollocInfer/Rcode/LS.setup.R inst/MatlabCollocInfer/Rcode/fhn.R inst/MatlabCollocInfer/Rcode/inneropt.R inst/MatlabCollocInfer/Rcode/SSElik.R inst/MatlabCollocInfer/Rcode/FHN.try.R inst/MatlabCollocInfer/Rcode/InnerOptimization.r inst/MatlabCollocInfer/Rcode/SSEproc.R inst/MatlabCollocInfer/Rcode/Smooth.LS.R inst/MatlabCollocInfer/Rcode/findif.var.R inst/MatlabCollocInfer/Rcode/Henon.R inst/MatlabCollocInfer/Rcode/Profile.LS.R inst/MatlabCollocInfer/Rcode/Cproc.R inst/MatlabCollocInfer/Rcode/logtrans.R inst/MatlabCollocInfer/Rcode/Dproc.R inst/MatlabCollocInfer/Rcode/makeid.R inst/MatlabCollocInfer/Rcode/SEIR.r inst/MatlabCollocInfer/Rcode/make.fhn.R inst/MatlabCollocInfer/Rcode/ls.shortcut.r inst/MatlabCollocInfer/Rcode/multinorm.shortcut.r inst/MatlabCollocInfer/Rcode/exp.Cproc.R inst/MatlabCollocInfer/Rcode/Diagnostics.R inst/MatlabCollocInfer/Rcode/findif.ode.R inst/MatlabCollocInfer/Rcode/makeexp.R inst/MatlabCollocInfer/Rcode/Multinorm.R inst/MatlabCollocInfer/Rcode/logstate.lik.R inst/MatlabCollocInfer/Rcode/cvar.R inst/MatlabCollocInfer/Rcode/findif.loglik.R inst/MatlabCollocInfer/Rcode/exp.Dproc.R inst/MatlabCollocInfer/Rcode/genlin.R
inst/MatlabCollocInfer/checkweights.m
inst/MatlabCollocInfer/ProfileSSE_AllPar.m
inst/MatlabCollocInfer/FitMatchCoefs.m
inst/MatlabCollocInfer/groundwater.txt
inst/MatlabCollocInfer/make_Dproc.m
inst/MatlabCollocInfer/FhNdata
inst/MatlabCollocInfer/NorthShoreData.mat
inst/MatlabCollocInfer/Profile_GausNewt.m
inst/MatlabCollocInfer/ProfileSSE.m
inst/MatlabCollocInfer/SEIR
inst/MatlabCollocInfer/SEIR/SEIR_dfdp.m
inst/MatlabCollocInfer/SEIR/SEIR_d2fdxdp.m
inst/MatlabCollocInfer/SEIR/SEIR_dfdx.m
inst/MatlabCollocInfer/SEIR/SEIR_fun.m
inst/MatlabCollocInfer/SEIR/make_var_SEIR.m
inst/MatlabCollocInfer/SEIR/SEIR_var_fun.m
inst/MatlabCollocInfer/SEIR/SEIR_var_dfdx.m
inst/MatlabCollocInfer/SEIR/SEIR_var_d2fdx2.m
inst/MatlabCollocInfer/SEIR/SEIR_var_d2fdxdp.m
inst/MatlabCollocInfer/SEIR/SEIR_var_dfdp.m
inst/MatlabCollocInfer/SEIR/SEIR_d2fdx2.m
inst/MatlabCollocInfer/SEIR/SEIR_ode.m
inst/MatlabCollocInfer/SEIR/make_SEIR.m
inst/MatlabCollocInfer/devel
inst/MatlabCollocInfer/devel/ProfileCovariance.m
inst/MatlabCollocInfer/coefsformat.m
inst/MatlabCollocInfer/logtrans
inst/MatlabCollocInfer/logtrans/make_logtrans.m
inst/MatlabCollocInfer/logtrans/logtrans_dfdp.m
inst/MatlabCollocInfer/logtrans/logtrans_d2fdx2.m
inst/MatlabCollocInfer/logtrans/logtrans_dfdx.m
inst/MatlabCollocInfer/logtrans/logtrans_d2fdxdp.m
inst/MatlabCollocInfer/logtrans/logtrans_fun.m
inst/MatlabCollocInfer/make_diagnostics.m
inst/MatlabCollocInfer/ProfileErr_AllPar_scrap.m
inst/MatlabCollocInfer/rainfall.txt
inst/MatlabCollocInfer/SplineEst_NewtRaph.m
inst/MatlabCollocInfer/loggenlin
inst/MatlabCollocInfer/loggenlin/loggenlin_dfdx.m
inst/MatlabCollocInfer/loggenlin/loggenlin_fun_ode.m
inst/MatlabCollocInfer/loggenlin/loggenlin_d2fdxdp.m
inst/MatlabCollocInfer/loggenlin/loggenlin_fn.m
inst/MatlabCollocInfer/loggenlin/loggenlin_dfdp.m
inst/MatlabCollocInfer/loggenlin/make_loggenlin.m
inst/MatlabCollocInfer/loggenlin/loggenlin_d2fdx2.m
inst/MatlabCollocInfer/loggenlin/checkmore.m
inst/MatlabCollocInfer/FhNEx.m
inst/MatlabCollocInfer/forward_prediction_error.m
inst/MatlabCollocInfer/Profile_LS.m
inst/MatlabCollocInfer/FHN_data.txt
inst/OldCode
inst/OldCode/sse.shortcut.R inst/OldCode/DE2x.R inst/OldCode/Dproc.shortcut.r
inst/OldCode/DE2x.rd
inst/OldCode/cproc.shortcut.r
inst/Devel
inst/Devel/Colloc.MCMCfixpar.r
inst/Devel/make.proc.rd
inst/Devel/Colloc.MCMC.R inst/Devel/testSRK2.r inst/Devel/pomp.interface.r inst/Devel/pomp.skeleton_test.r
inst/Devel/profile.covariance.rep.rd
inst/Devel/estep.r inst/Devel/Colloc.MCMC1.R inst/Devel/SEIR.r inst/Devel/EM.R
inst/Devel/setup.rd
inst/Devel/srk2.shortcut.r
inst/Devel/EM.rd
inst/Devel/ParsMatch.rep.rd
inst/Devel/SRK2proc.r
inst/Devel/Colloc.MCMC.rd
inst/Devel/FitMatch.rep.rd
inst/Devel/Colloc.MCMCtestoncoefs.r
inst/Devel/SplineCoefs.rep.rd
inst/Devel/datagenFhNex.r
inst/Devel/EM.rep.rd
inst/Devel/Profile.rep.rd
inst/Devel.Examples
inst/Devel.Examples/FhN.inputEx.R inst/Devel.Examples/SEIRRV.R
inst/Devel.Examples/LynxHare2.dat
inst/Devel.Examples/ChemoEx2.r inst/Devel.Examples/fhn.input.R inst/Devel.Examples/LVEX.R
inst/Devel.Examples/LynxHare.dat
inst/Devel.Examples/LV.R inst/Devel.Examples/pomp.sir.R inst/Devel.Examples/SEIRRVEX.R
inst/CollocInferManual.pdf
inst/trymcmc2.r
NAMESPACE
demo
demo/RMEx.r demo/ChemoRMEx.r
demo/OldDemo
demo/OldDemo/RMEx.r demo/OldDemo/HenonEx.R demo/OldDemo/ChemoEx2.r demo/OldDemo/FhNEx2.r demo/OldDemo/FhNEx.R demo/ChemoEx.R demo/SEIREX.r
demo/00Index
demo/HenonEx.r demo/FhNEx2.r demo/FhN.diagnostics.r demo/NorthShore.R
CHANGELOG
NEWS
data
data/SEIRdata.rda
data/NSdata.rda
data/ChemoData.rda
data/FhNdata.rda
data/ChemoRMData.rda
data/FhNest.rda
R
R/fhn.R R/SSElik.R R/SSEproc.R R/exptrans.r R/findif.var.R R/Henon.R R/pomp.skeleton.R R/Cproc.R R/logtrans.R R/check.lik.proc.data.coefs.r R/ParsMatchOptimization.R R/Dproc.R R/makeid.R R/SEIR.r R/NSfuns.R R/ls.shortcut.r R/multinorm.shortcut.r R/exp.Cproc.R R/forward.prediction.error.R R/IntegrateForward.R R/Diagnostics.R R/InnerOptimization.R R/findif.ode.R R/makeexp.R R/Multinorm.R R/CollocInferPlots.R R/Chemo.R R/FitMatchOptimization.R R/ProfileCovariance.R R/OuterOptimization.R R/logstate.lik.R R/cvar.R R/findif.loglik.R R/exp.Dproc.R R/genlin.R
MD5
DESCRIPTION
man
man/make.variance.rd
man/make.lik.rd
man/make.proc.rd
man/make.findif.rd
man/profile.covariance.rd
man/FhNest.rd
man/ParsMatch.rd
man/outeropt.rd
man/CollocInfer-package.rd
man/FhNdata.rd
man/make.logtrans.rd
man/ChemoData.rd
man/setup.rd
man/ChemoRMData.rd
man/inneropt.rd
man/ProfileObjective.rd
man/smooth.rd
man/SplineCoefs.Rd
man/CollocInferPlots.rd
man/NSdata.rd
man/CollocInfer-internal.rd
man/SEIRdata.rd
man/FitMatch.rd
man/IntegrateForward.rd
man/make.transform.rd
man/Profile.rd
man/forward.prediction.error.rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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