Statistical Inference for Partially Observed Markov Processes


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Documentation for package ‘pomp’ version 2.3

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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

-- B --

bake Bake, stew, and freeze
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
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
enkf Ensemble Kalman filters
enkf-data.frame Ensemble Kalman filters
enkf-method Ensemble Kalman filters
enkf-pomp Ensemble Kalman filters
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 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
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
melt-method Coerce to data frame
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
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
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
profileDesign 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
runifDesign Design matrices for pomp calculations
rw.sd rw.sd
rw2 Two-dimensional random-walk process

-- S --

sannbox Simulated annealing with box constraints.
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
sliceDesign Design matrices for pomp calculations
sobolDesign 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.