Statistical Inference for Partially Observed Markov Processes


Documentation for package ‘pomp’ version 3.1.1.10

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    A B C D E F G H I K L M N O P R S T U V W

    pomp-package Inference for partially observed Markov processes

    -- A --

    abc Approximate Bayesian computation
    abc-data.frame Approximate Bayesian computation
    abc-method Approximate Bayesian computation
    abc-pomp Approximate Bayesian computation
    accumulators accumulators
    accumvars accumulators
    as-csnippet C snippets
    as-method Coerce to data frame
    as-method C snippets
    as.data.frame Coerce to data frame
    as.data.frame.abcList Coerce to data frame
    as.data.frame.bsmcd_pomp Coerce to data frame
    as.data.frame.kalmand_pomp Coerce to data frame
    as.data.frame.mif2List Coerce to data frame
    as.data.frame.pfilterd_pomp Coerce to data frame
    as.data.frame.pfilterList Coerce to data frame
    as.data.frame.pmcmcList Coerce to data frame
    as.data.frame.pomp Coerce to data frame
    as.data.frame.pompList Coerce to data frame
    as.data.frame.probed_pomp Coerce to data frame
    as.data.frame.wpfilterd_pomp Coerce to data frame

    -- B --

    bake Bake, stew, and freeze
    basic_components Basic POMP model components.
    basic_probes Useful probes for partially-observed Markov processes
    blowflies Nicholson's blowflies.
    blowflies1 Nicholson's blowflies.
    blowflies2 Nicholson's blowflies.
    bsflu Influenza outbreak in a boarding school
    bsmc2 The Liu and West Bayesian particle filter
    bsmc2-data.frame The Liu and West Bayesian particle filter
    bsmc2-method The Liu and West Bayesian particle filter
    bsmc2-pomp The Liu and West Bayesian particle filter
    bspline.basis B-spline bases
    bsplines B-spline bases

    -- C --

    coef Extract, set, or alter coefficients
    coef-listie Extract, set, or alter coefficients
    coef-method Extract, set, or alter coefficients
    coef-objfun Extract, set, or alter coefficients
    coef-pomp Extract, set, or alter coefficients
    coef<- Extract, set, or alter coefficients
    coef<--method Extract, set, or alter coefficients
    coef<--pomp Extract, set, or alter coefficients
    coerce-method Coerce to data frame
    coerce-method C snippets
    coerce-method Probes (AKA summary statistics)
    coerce-method Power spectrum
    coerce-objfun-data.frame Coerce to data frame
    coerce-pomp-data.frame Coerce to data frame
    coerce-probe_match_objfun-probed_pomp Probes (AKA summary statistics)
    coerce-spect_match_objfun-spectd_pomp Power spectrum
    cond.logLik Conditional log likelihood
    cond.logLik-bsmcd_pomp Conditional log likelihood
    cond.logLik-kalmand_pomp Conditional log likelihood
    cond.logLik-method Conditional log likelihood
    cond.logLik-pfilterd_pomp Conditional log likelihood
    cond.logLik-wpfilterd_pomp Conditional log likelihood
    continue Continue an iterative calculation
    continue-abcd_pomp Continue an iterative calculation
    continue-method Continue an iterative calculation
    continue-mif2d_pomp Continue an iterative calculation
    continue-pmcmcd_pomp Continue an iterative calculation
    covariate_table Covariates
    covariate_table-character-method Covariates
    covariate_table-method Covariates
    covariate_table-numeric-method Covariates
    covmat Estimate a covariance matrix from algorithm traces
    covmat-abcd_pomp Estimate a covariance matrix from algorithm traces
    covmat-abcList Estimate a covariance matrix from algorithm traces
    covmat-method Estimate a covariance matrix from algorithm traces
    covmat-pmcmcd_pomp Estimate a covariance matrix from algorithm traces
    covmat-pmcmcList Estimate a covariance matrix from algorithm traces
    covmat-probed_pomp Estimate a covariance matrix from algorithm traces
    Csnippet C snippets
    Csnippet-class C snippets

    -- D --

    dacca Model of cholera transmission for historic Bengal.
    design Design matrices for pomp calculations
    deulermultinom Probability distributions
    discrete_time The latent state process simulator
    distributions Probability distributions
    dmeasure dmeasure
    dmeasure-method dmeasure
    dmeasure-pomp dmeasure
    dmeasure_spec The measurement model density
    dprior dprior
    dprior-method dprior
    dprior-pomp dprior
    dprocess dprocess
    dprocess-method dprocess
    dprocess-pomp dprocess
    dprocess_spec The latent state process density

    -- E --

    eakf Ensemble Kalman filters
    eakf-data.frame Ensemble Kalman filters
    eakf-method Ensemble Kalman filters
    eakf-pomp Ensemble Kalman filters
    ebola Ebola outbreak, West Africa, 2014-2016
    ebolaModel Ebola outbreak, West Africa, 2014-2016
    ebolaWA2014 Ebola outbreak, West Africa, 2014-2016
    eff.sample.size Effective sample size
    eff.sample.size-bsmcd_pomp Effective sample size
    eff.sample.size-method Effective sample size
    eff.sample.size-pfilterd_pomp Effective sample size
    eff.sample.size-wpfilterd_pomp Effective sample size
    elementary_algorithms Elementary algorithms.
    enkf Ensemble Kalman filters
    enkf-data.frame Ensemble Kalman filters
    enkf-method Ensemble Kalman filters
    enkf-pomp Ensemble Kalman filters
    estimation_algorithms Estimation algorithms for POMP models.
    euler The latent state process simulator
    ewcitmeas Historical childhood disease incidence data
    ewmeas Historical childhood disease incidence data
    expit Transformations

    -- F --

    filter.mean Filtering mean
    filter.mean-kalmand_pomp Filtering mean
    filter.mean-method Filtering mean
    filter.mean-pfilterd_pomp Filtering mean
    filter.traj Filtering trajectories
    filter.traj-method Filtering trajectories
    filter.traj-pfilterd_pomp Filtering trajectories
    filter.traj-pfilterList Filtering trajectories
    filter.traj-pmcmcd_pomp Filtering trajectories
    filter.traj-pmcmcList Filtering trajectories
    flow Flow of a deterministic model
    flow-method Flow of a deterministic model
    flow-pomp Flow of a deterministic model
    forecast Forecast mean
    forecast-kalmand_pomp Forecast mean
    forecast-method Forecast mean
    freeze Bake, stew, and freeze

    -- G --

    gillespie The latent state process simulator
    gillespie_hl The latent state process simulator
    gompertz Gompertz model with log-normal observations.

    -- H --

    hitch Hitching C snippets and R functions to pomp_fun objects

    -- I --

    inv_log_barycentric Transformations

    -- K --

    kalman Ensemble Kalman filters

    -- L --

    logit Transformations
    logLik Log likelihood
    logLik-bsmcd_pomp Log likelihood
    logLik-kalmand_pomp Log likelihood
    logLik-method Log likelihood
    logLik-nlf_objfun Log likelihood
    logLik-objfun Log likelihood
    logLik-pfilterd_pomp Log likelihood
    logLik-pmcmcd_pomp Log likelihood
    logLik-probed_pomp Log likelihood
    logLik-spect_match_objfun Log likelihood
    logLik-wpfilterd_pomp Log likelihood
    logmeanexp The log-mean-exp trick
    log_barycentric Transformations
    LondonYorke Historical childhood disease incidence data

    -- M --

    map The deterministic skeleton of a model
    measles Historical childhood disease incidence data
    mif2 Iterated filtering: maximum likelihood by iterated, perturbed Bayes maps
    mif2-data.frame Iterated filtering: maximum likelihood by iterated, perturbed Bayes maps
    mif2-method Iterated filtering: maximum likelihood by iterated, perturbed Bayes maps
    mif2-mif2d_pomp Iterated filtering: maximum likelihood by iterated, perturbed Bayes maps
    mif2-pfilterd_pomp Iterated filtering: maximum likelihood by iterated, perturbed Bayes maps
    mif2-pomp Iterated filtering: maximum likelihood by iterated, perturbed Bayes maps
    mvn.diag.rw MCMC proposal distributions
    mvn.rw MCMC proposal distributions
    mvn.rw.adaptive MCMC proposal distributions

    -- N --

    nlf Nonlinear forecasting
    nlf_objfun Nonlinear forecasting
    nlf_objfun-data.frame Nonlinear forecasting
    nlf_objfun-method Nonlinear forecasting
    nlf_objfun-nlf_objfun Nonlinear forecasting
    nlf_objfun-pomp Nonlinear forecasting

    -- O --

    obs obs
    obs-method obs
    obs-pomp obs
    onestep The latent state process simulator
    ou2 Two-dimensional discrete-time Ornstein-Uhlenbeck process

    -- P --

    parameter_trans Parameter transformations
    parameter_trans-character,character Parameter transformations
    parameter_trans-Csnippet,Csnippet Parameter transformations
    parameter_trans-function,function Parameter transformations
    parameter_trans-method Parameter transformations
    parameter_trans-missing,missing Parameter transformations
    parmat Create a matrix of parameters
    partrans partrans
    partrans-method partrans
    partrans-pomp partrans
    parus Parus major population dynamics
    periodic.bspline.basis B-spline bases
    pfilter Particle filter
    pfilter-data.frame Particle filter
    pfilter-method Particle filter
    pfilter-objfun Particle filter
    pfilter-pfilterd_pomp Particle filter
    pfilter-pomp Particle filter
    pfilterd_pomp Particle filter
    pfilterd_pomp-class Particle filter
    plot Plotting
    plot-Abc Plotting
    plot-bsmcd_pomp Plotting
    plot-method Plotting
    plot-Mif2 Plotting
    plot-pfilterd_pomp Plotting
    plot-Pmcmc Plotting
    plot-pomp Plotting
    plot-probed_pomp Plotting
    plot-probe_match_objfun Plotting
    plot-spectd_pomp Plotting
    plot-spect_match_objfun Plotting
    plot-wpfilterd_pomp Plotting
    pmcmc The particle Markov chain Metropolis-Hastings algorithm
    pmcmc-data.frame The particle Markov chain Metropolis-Hastings algorithm
    pmcmc-method The particle Markov chain Metropolis-Hastings algorithm
    pmcmc-pfilterd_pomp The particle Markov chain Metropolis-Hastings algorithm
    pmcmc-pmcmcd_pomp The particle Markov chain Metropolis-Hastings algorithm
    pmcmc-pomp The particle Markov chain Metropolis-Hastings algorithm
    pomp Constructor of the basic pomp object
    pomp,package Inference for partially observed Markov processes
    pompExample pomp_examples
    pompExamples pomp_examples
    pomp_example pomp_examples
    pomp_examples pomp_examples
    pred.mean Prediction mean
    pred.mean-kalmand_pomp Prediction mean
    pred.mean-method Prediction mean
    pred.mean-pfilterd_pomp Prediction mean
    pred.var Prediction variance
    pred.var-method Prediction variance
    pred.var-pfilterd_pomp Prediction variance
    print Print methods
    print-method Print methods
    prior_spec prior specification
    probe Probes (AKA summary statistics)
    probe-data.frame Probes (AKA summary statistics)
    probe-method Probes (AKA summary statistics)
    probe-objfun Probes (AKA summary statistics)
    probe-pomp Probes (AKA summary statistics)
    probe-probed_pomp Probes (AKA summary statistics)
    probe-probe_match_obfjun Probes (AKA summary statistics)
    probe.acf Useful probes for partially-observed Markov processes
    probe.ccf Useful probes for partially-observed Markov processes
    probe.marginal Useful probes for partially-observed Markov processes
    probe.match Probe matching
    probe.mean Useful probes for partially-observed Markov processes
    probe.median Useful probes for partially-observed Markov processes
    probe.nlar Useful probes for partially-observed Markov processes
    probe.period Useful probes for partially-observed Markov processes
    probe.quantile Useful probes for partially-observed Markov processes
    probe.sd Useful probes for partially-observed Markov processes
    probe.var Useful probes for partially-observed Markov processes
    probe_objfun Probe matching
    probe_objfun-data.frame Probe matching
    probe_objfun-method Probe matching
    probe_objfun-pomp Probe matching
    probe_objfun-probed_pomp Probe matching
    probe_objfun-probe_match_objfun Probe matching
    profile_design Design matrices for pomp calculations
    proposals MCMC proposal distributions

    -- R --

    reulermultinom Probability distributions
    rgammawn Probability distributions
    ricker Ricker model with Poisson observations.
    rinit rinit
    rinit-method rinit
    rinit-pomp rinit
    rinit_spec The initial-state distribution
    rmeasure rmeasure
    rmeasure-method rmeasure
    rmeasure-pomp rmeasure
    rmeasure_spec The measurement-model simulator
    rprior rprior
    rprior-method rprior
    rprior-pomp rprior
    rprocess rprocess
    rprocess-method rprocess
    rprocess-pomp rprocess
    rprocess_spec The latent state process simulator
    runif_design Design matrices for pomp calculations
    rw.sd rw.sd
    rw2 Two-dimensional random-walk process

    -- S --

    sannbox Simulated annealing with box constraints.
    saved.states Saved states
    saved.states-method Saved states
    saved.states-pfilterd_pomp Saved states
    saved.states-pfilterList Saved states
    simulate Simulations of a partially-observed Markov process
    simulate-data.frame Simulations of a partially-observed Markov process
    simulate-method Simulations of a partially-observed Markov process
    simulate-missing Simulations of a partially-observed Markov process
    simulate-objfun Simulations of a partially-observed Markov process
    simulate-pomp Simulations of a partially-observed Markov process
    sir Compartmental epidemiological models
    sir2 Compartmental epidemiological models
    sir_models Compartmental epidemiological models
    skeleton skeleton
    skeleton-method skeleton
    skeleton-pomp skeleton
    skeleton_spec The deterministic skeleton of a model
    slice_design Design matrices for pomp calculations
    sobol_design Design matrices for pomp calculations
    spect Power spectrum
    spect-data.frame Power spectrum
    spect-method Power spectrum
    spect-objfun Power spectrum
    spect-pomp Power spectrum
    spect-spectd_pomp Power spectrum
    spect-spect_match_objfun Power spectrum
    spect.match Spectrum matching
    spect_objfun Spectrum matching
    spect_objfun-data.frame Spectrum matching
    spect_objfun-method Spectrum matching
    spect_objfun-pomp Spectrum matching
    spect_objfun-spectd_pomp Spectrum matching
    spect_objfun-spect_match_objfun Spectrum matching
    spy Spy
    spy-method Spy
    states Latent states
    states-method Latent states
    states-pomp Latent states
    stew Bake, stew, and freeze
    summary Summary methods
    summary-method Summary methods
    summary-objfun Summary methods
    summary-probed_pomp Summary methods
    summary-spectd_pomp Summary methods

    -- T --

    time Methods to manipulate the obseration times
    time-method Methods to manipulate the obseration times
    time-pomp Methods to manipulate the obseration times
    time<- Methods to manipulate the obseration times
    time<--method Methods to manipulate the obseration times
    time<--pomp Methods to manipulate the obseration times
    timezero The zero time
    timezero-method The zero time
    timezero-pomp The zero time
    timezero<- The zero time
    timezero<--method The zero time
    timezero<--pomp The zero time
    traces Traces
    traces-Abc Traces
    traces-abcd_pomp Traces
    traces-abcList Traces
    traces-method Traces
    traces-Mif2 Traces
    traces-mif2d_pomp Traces
    traces-mif2List Traces
    traces-Pmcmc Traces
    traces-pmcmcd_pomp Traces
    traces-pmcmcList Traces
    traj.match Trajectory matching
    trajectory Trajectory of a deterministic model
    trajectory-method Trajectory of a deterministic model
    trajectory-pomp Trajectory of a deterministic model
    trajectory-traj_match_objfun Trajectory of a deterministic model
    traj_objfun Trajectory matching
    traj_objfun-data.frame Trajectory matching
    traj_objfun-method Trajectory matching
    traj_objfun-pomp Trajectory matching
    traj_objfun-traj_match_objfun Trajectory matching
    transformations Transformations

    -- U --

    userdata Facilities for making additional information to basic components

    -- V --

    vectorfield The deterministic skeleton of a model
    verhulst Verhulst-Pearl model

    -- W --

    window Window
    window-method Window
    window-pomp Window
    workhorses Workhorse functions for the 'pomp' algorithms.
    wpfilter Weighted particle filter
    wpfilter-data.frame Weighted particle filter
    wpfilter-method Weighted particle filter
    wpfilter-pomp Weighted particle filter
    wpfilter-wpfilterd_pomp Weighted particle filter
    wpfilterd_pomp Weighted particle filter
    wpfilterd_pomp-class Weighted particle filter