Statistical Inference for Partially Observed Markov Processes


Documentation for package ‘pomp’ version 5.11.0.0

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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-method Approximate Bayesian computation
accumvars accumulator variables

-- B --

bake Tools for reproducible computations
basic_components Basic POMP model components.
basic_probes Useful probes for partially-observed Markov processes
betabinomial Beta-binomial distribution
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-method The Liu and West Bayesian particle filter
bsplines B-spline bases
bspline_basis B-spline bases

-- C --

c Concatenate
c.Pomp Concatenate
childhood_disease_data Historical childhood disease incidence data
coef Extract, set, or alter coefficients
coef-method Extract, set, or alter coefficients
coef<- Extract, set, or alter coefficients
coef<--method Extract, set, or alter coefficients
compartmental_models Compartmental epidemiological models
concat Concatenate
cond_logLik Conditional log likelihood
cond_logLik-method Conditional log likelihood
continue Continue an iterative calculation
continue-method Continue an iterative calculation
covariates Covariates
covariate_table Covariates
covariate_table-method Covariates
covmat Estimate a covariance matrix from algorithm traces
covmat-method Estimate a covariance matrix from algorithm traces
Csnippet C snippets

-- D --

dacca Model of cholera transmission for historic Bengal.
dbetabinom Beta-binomial distribution
design Design matrices for pomp calculations
deulermultinom Eulermultinomial and gamma-whitenoise distributions
dinit dinit workhorse
dinit-method dinit workhorse
dinit_spec dinit specification
discrete_time rprocess specification
dmeasure dmeasure workhorse
dmeasure-method dmeasure workhorse
dmeasure_spec dmeasure specification
dprior dprior workhorse
dprior-method dprior workhorse
dprocess dprocess workhorse
dprocess-method dprocess workhorse
dprocess_spec dprocess specification

-- E --

eakf Ensemble Kalman filters
eakf-method 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-method Effective sample size
elementary_algorithms Elementary computations on POMP models.
emeasure emeasure workhorse
emeasure-method emeasure workhorse
emeasure_spec emeasure specification
enkf Ensemble Kalman filters
enkf-method Ensemble Kalman filters
estimation_algorithms Parameter estimation algorithms for POMP models.
euler rprocess specification
eulermultinom Eulermultinomial and gamma-whitenoise distributions
ewcitmeas Historical childhood disease incidence data
ewmeas Historical childhood disease incidence data
expit Transformations

-- F --

filter_mean Filtering mean
filter_mean-method Filtering mean
filter_traj Filtering trajectories
filter_traj-method Filtering trajectories
flow flow workhorse
flow-method flow workhorse
forecast Forecast mean
forecast-method Forecast mean
freeze Tools for reproducible computations

-- G --

gillespie rprocess specification
gillespie_hl rprocess specification
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
kalmanFilter Kalman filter

-- L --

logit Transformations
logLik Log likelihood
logLik-method Log likelihood
logmeanexp The log-mean-exp trick
log_barycentric Transformations
LondonYorke Historical childhood disease incidence data
lookup Lookup table

-- M --

map skeleton specification
mcap Monte Carlo adjusted profile
melt Melt
melt-method Melt
mif2 Iterated filtering: maximum likelihood by iterated, perturbed Bayes maps
mif2-method 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-method Nonlinear forecasting

-- O --

obs obs
obs-method obs
onestep rprocess specification
ou2 Two-dimensional discrete-time Ornstein-Uhlenbeck process

-- P --

parameter_trans parameter transformations
parameter_trans-method parameter transformations
parmat Create a matrix of parameters
parmat-method Create a matrix of parameters
partrans partrans workhorse
partrans-method partrans workhorse
parus Parus major population dynamics
periodic_bspline_basis B-spline bases
pfilter Particle filter
pfilter-method Particle filter
plot pomp plotting facilities
plot-method pomp plotting facilities
pmcmc The particle Markov chain Metropolis-Hastings algorithm
pmcmc-method The particle Markov chain Metropolis-Hastings algorithm
pomp Constructor of the basic pomp object
pomp,package Inference for partially observed Markov processes
pomp_constructor Constructor of the basic pomp object
pomp_examples pre-built pomp examples
pred_mean Prediction mean
pred_mean-method Prediction mean
pred_var Prediction variance
pred_var-method Prediction variance
priors prior specification
prior_spec prior specification
probe Probes (AKA summary statistics)
probe-method 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_objfun Probe matching
probe_objfun-method Probe matching
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
profile_design Design matrices for pomp calculations
proposals MCMC proposal distributions

-- R --

rbetabinom Beta-binomial distribution
repair_lookup_table Covariates
reproducibility_tools Tools for reproducible computations
reulermultinom Eulermultinomial and gamma-whitenoise distributions
rgammawn Eulermultinomial and gamma-whitenoise distributions
ricker Ricker model with Poisson observations.
rinit rinit workhorse
rinit-method rinit workhorse
rinit_spec rinit specification
rmeasure rmeasure workhorse
rmeasure-method rmeasure workhorse
rmeasure_spec rmeasure specification
rprior rprior workhorse
rprior-method rprior workhorse
rprocess rprocess workhorse
rprocess-method rprocess workhorse
rprocess_spec rprocess specification
runif_design Design matrices for pomp calculations
rw2 Two-dimensional random-walk process
rw_sd rw_sd

-- S --

sannbox Simulated annealing with box constraints.
saved_states Saved states
saved_states-method Saved states
simulate Simulations of a partially-observed Markov process
simulate-method Simulations of a partially-observed Markov process
sir Compartmental epidemiological models
sir2 Compartmental epidemiological models
SIR_models Compartmental epidemiological models
skeleton skeleton workhorse
skeleton-method skeleton workhorse
skeleton_spec skeleton specification
slice_design Design matrices for pomp calculations
sobol_design Design matrices for pomp calculations
spect Power spectrum
spect-method Power spectrum
spect_match Spectrum matching
spect_objfun Spectrum matching
spect_objfun-method Spectrum matching
spy Spy
spy-method Spy
states Latent states
states-method Latent states
stew Tools for reproducible computations
summary Summary methods
summary-method Summary methods

-- T --

time Methods to extract and manipulate the obseration times
time-method Methods to extract and manipulate the obseration times
time<- Methods to extract and manipulate the obseration times
time<--method Methods to extract and manipulate the obseration times
timezero The zero time
timezero-method The zero time
timezero<- The zero time
timezero<--method The zero time
traces Traces
traces-method Traces
trajectory Trajectory of a deterministic model
trajectory-method Trajectory of a deterministic model
traj_match Trajectory matching
traj_objfun Trajectory matching
traj_objfun-method Trajectory matching
transformations Transformations

-- U --

userdata Facilities for making additional information to basic components

-- V --

vectorfield skeleton specification
verhulst Verhulst-Pearl model
vmeasure vmeasure workhorse
vmeasure-method vmeasure workhorse
vmeasure_spec vmeasure specification

-- W --

window Window
window-method Window
workhorses Workhorse functions for the 'pomp' algorithms.
wpfilter Weighted particle filter
wpfilter-method Weighted particle filter
wquant Weighted quantile function