Package: CollocInfer 1.0.5

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.

Authors:Giles Hooker [aut, cre], Luo Xiao [aut], James Ramsay [ctb]

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CollocInfer.pdf |CollocInfer.html
CollocInfer/json (API)
NEWS

# Install 'CollocInfer' in R:
install.packages('CollocInfer', repos = c('https://gileshooker.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.51 score 1 stars 32 scripts 268 downloads 74 exports 50 dependencies

Last updated 17 days agofrom:dc7eb4be5d. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:blocks2matcheck.lik.proc.data.coefscheckweightschemo.funchemo.odeCollocInferPlotsFitMatchDCFitMatchDC2FitMatchErrFitMatchListFitMatchOptforward.prediction.errorinneroptIntegrateForwardLS.setupmake.Cprocmake.cvarmake.diagnosticsmake.Dprocmake.expmake.exp.Cprocmake.exp.Dprocmake.exptransmake.fhnmake.findif.loglikmake.findif.odemake.findif.varmake.genlinmake.Henonmake.idmake.logstate.likmake.logtransmake.multinormmake.NSmake.SEIRmake.SSElikmake.SSEprocmake.var.SEIRmatmultinorm.setupNewey.WestNeweyWest.VaroderhsouteroptParsMatchDPParsMatchErrParsMatchListParsMatchOptpomp.dmeasurepomp.skeletonProfile.covarianceProfile.GausNewtProfile.LSProfile.multinormProfileDPProfileDP.AllParProfileDP1ProfileErrProfileErr.AllParProfileErr1ProfileListProfileSSEProfileSSE.AllParSmooth.LSSmooth.multinormSplineCoefsDCSplineCoefsDC2SplineCoefsDC2sparseSplineCoefsDCDPSplineCoefsDPSplineCoefsErrSplineCoefsListSplineEst.NewtRaphtrimr

Dependencies:ashbitopscliclustercolorspacedeSolvedotCall64fansifarverfdafdsFNNggplot2gluegtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMASSMatrixmclustmgcvmulticoolmunsellmvtnormnlmepcaPPpillarpkgconfigpracmaR6rainbowRColorBrewerRcppRCurlrlangscalesspamtibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Collocation Inference in RCollocInfer-package CollocInfer
Chemostat Example DataChemoData ChemoParnames ChemoPars ChemoTime ChemoVarnames
Rosenzweig-MacArthur Model Applied to Chemostat DataChemoRMData ChemoRMPars ChemoRMTime RMparnames RMvarnames
Diagnostic PLots for CollocInferCollocInferPlots
FitzHugh-Nagumo dataFhNdata FhNparnames FhNpars FhNtimes FhNvarnames
Estimated Parameters for FitzHugh-Nagumo dataFhNest FhNestCoefs FhNestPars
Estimating Hidden StatesFitMatchDC FitMatchDC2 FitMatchErr FitMatchList FitMatchOpt
forward.prediction.errorforward.prediction.error
Inner Optimization Functionsinneropt
IntegrateForwardIntegrateForward
Finite Difference Functionsmake.findif make.findif.loglik make.findif.ode make.findif.var
Observation Process Distribution Functionmake.lik make.multinorm make.SSElik pomp.dmeasure
Log Transformsmake.exp.Cproc make.exp.Dproc make.exptrans make.logstate.lik make.logtrans
Process Distributionsmake.Cproc make.Dproc make.SSEproc
Transfer Functionschemo.fun make.diagnostics make.exp make.fhn make.genlin make.Henon make.id make.NS make.SEIR make.transfer pomp.skeleton
Variance Functionsmake.cvar make.var.SEIR make.variance
North Shore dataNSgroundwater NSrainfall NStimes
Outer Optimization Functionsouteropt
Estimate of Parameters from SmoothParsMatchDP ParsMatchErr ParsMatchList ParsMatchOpt
Profile.covarianceProfile.covariance
Profile Estimation with Collocation InferenceProfile.GausNewt ProfileDP ProfileErr ProfileList ProfileSSE
Profile Estimation FunctionsProfile.LS Profile.multinorm
SEIR dataSEIRdata SEIRparnames SEIRpars SEIRtimes SEIRvarnames
Setup Functions for proc and lik objectsLS.setup multinorm.setup setup
Model-Based Smoothing FunctionsSmooth.LS Smooth.multinorm
Spline Estimation FunctionsSplineCoefsDC SplineCoefsDC2 SplineCoefsDCDP SplineCoefsDP SplineCoefsErr SplineCoefsList SplineEst.NewtRaph