Inference for Spatiotemporal Partially Observed Markov Processes

Documentation for package ‘spatPomp’ version 0.35.0

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Inference for SpatPOMPs (Spatiotemporal Partially Observed Markov Processes)

-- A --

abf	Adapted Bagged Filter (ABF)
abf-abfd_spatPomp	Adapted Bagged Filter (ABF)
abf-method	Adapted Bagged Filter (ABF)
abf-spatPomp	Adapted Bagged Filter (ABF)
abfir	Adapted Bagged Filter with Intermediate Resampling (ABF-IR)
abfir-abfird_spatPomp	Adapted Bagged Filter with Intermediate Resampling (ABF-IR)
abfir-method	Adapted Bagged Filter with Intermediate Resampling (ABF-IR)
abfir-spatPomp	Adapted Bagged Filter with Intermediate Resampling (ABF-IR)
arma_benchmark	Calculated log-ARMA log-likelihood benchmark for spatPomp models
as.data.frame	Coerce to data frame
as.data.frame.spatPomp	Coerce to data frame

-- B --

bm	Brownian motion spatPomp simulator
bm2	Brownian motion spatPomp generator with shared or unit-specific parameters
bm2_kalman_logLik	Exact log-likelihood for Brownian motion spatPomp generator with shared or unit-specific parameters
bm_kalman_logLik	Exact log-likelihood for Brownian motion spatPomp generator
bpfilter	Block particle filter (BPF)
bpfilter-ANY	Block particle filter (BPF)
bpfilter-bpfilterd_spatPomp	Block particle filter (BPF)
bpfilter-method	Block particle filter (BPF)
bpfilter-missing	Block particle filter (BPF)
bpfilter-spatPomp	Block particle filter (BPF)

-- C --

c	Concatenate
c.SpatPomp	Concatenate
city_data_UK	City data in the United Kingdom
coerce-method	Coerce to data frame
concat	Concatenate
contract_params	Book-keeping functions for working with expanded parameters
contract_params,	Book-keeping functions for working with expanded parameters

-- D --

dunit_measure	dunit_measure 'dunit_measure' evaluates the unit measurement density of a unit's observation given the entire state
dunit_measure-method	dunit_measure 'dunit_measure' evaluates the unit measurement density of a unit's observation given the entire state
dunit_measure-spatPomp	dunit_measure 'dunit_measure' evaluates the unit measurement density of a unit's observation given the entire state

-- E --

enkf	Generalized Ensemble Kalman filter (EnKF)
enkf-method	Generalized Ensemble Kalman filter (EnKF)
enkf-spatPomp	Generalized Ensemble Kalman filter (EnKF)
eunit_measure	eunit_measure
eunit_measure-method	eunit_measure
eunit_measure-spatPomp	eunit_measure
expand_params	Book-keeping functions for working with expanded parameters
expand_params,	Book-keeping functions for working with expanded parameters

-- G --

gbm	Geometric Brownian motion spatPomp simulator
girf	Guided intermediate resampling filter (GIRF)
girf-ANY	Guided intermediate resampling filter (GIRF)
girf-girfd_spatPomp	Guided intermediate resampling filter (GIRF)
girf-method	Guided intermediate resampling filter (GIRF)
girf-missing	Guided intermediate resampling filter (GIRF)
girf-spatPomp	Guided intermediate resampling filter (GIRF)

-- H --

he10	Measles in UK: spatPomp generator with shared or unit-specific parameters
he10coordinates	City data in the United Kingdom
he10demography	Demographic data for 20 towns in the United Kingdom
he10measles	Measles in the United Kingdom
he10mle	Measles in the United Kingdom: MLE from He et al (2010)

-- I --

ibpf	Iterated block particle filter (IBPF)
ibpf-ANY	Iterated block particle filter (IBPF)
ibpf-bpfd_spatPomp	Iterated block particle filter (IBPF)
ibpf-ibpfd_spatPomp	Iterated block particle filter (IBPF)
ibpf-method	Iterated block particle filter (IBPF)
ibpf-missing	Iterated block particle filter (IBPF)
ibpf-spatPomp	Iterated block particle filter (IBPF)
ienkf	Iterated ensemble Kalman filter (IEnKF)
ienkf-method	Iterated ensemble Kalman filter (IEnKF)
ienkf-spatPomp	Iterated ensemble Kalman filter (IEnKF)
igirf	Iterated guided intermediate resampling filter (IGIRF)
igirf-ANY	Iterated guided intermediate resampling filter (IGIRF)
igirf-igirfd_spatPomp	Iterated guided intermediate resampling filter (IGIRF)
igirf-method	Iterated guided intermediate resampling filter (IGIRF)
igirf-missing	Iterated guided intermediate resampling filter (IGIRF)
igirf-spatPomp	Iterated guided intermediate resampling filter (IGIRF)
iubf	Iterated Unadapted Bagged Filter (IUBF)
iubf-method	Iterated Unadapted Bagged Filter (IUBF)
iubf-spatPomp	Iterated Unadapted Bagged Filter (IUBF)

-- L --

-- M --

mean_by_unit	Book-keeping functions for working with expanded parameters
mean_by_unit,	Book-keeping functions for working with expanded parameters
measles	Measles in UK spatPomp generator
measles2	Measles in UK: spatPomp generator with shared or unit-specific parameters
measlesUK	Measles in the United Kingdom
munit_measure	munit_measure
munit_measure-method	munit_measure
munit_measure-spatPomp	munit_measure

-- P --

param_formats	Book-keeping functions for working with expanded parameters
plot	Plotting 'spatPomp' data
plot-igirfd_spatPomp	Plotting 'spatPomp' data
plot-method	Plotting 'spatPomp' data
plot-spatPomp	Plotting 'spatPomp' data
print	Print methods
print-method	Print methods
print-spatPomp	Print methods

-- R --

-- S --

simulate	Simulation of a spatiotemporal partially-observed Markov process
simulate-method	Simulation of a spatiotemporal partially-observed Markov process
simulate-spatPomp	Simulation of a spatiotemporal partially-observed Markov process
spatPomp	Constructor of the spatPomp object
spatPomp-class	An S4 class to represent a spatiotemporal POMP model and data.
spatPomp_Csnippet	C snippets
spatPomp_Csnippet-character	C snippets
spatPomp_Csnippet-method	C snippets

-- U --

unit_names	Unit names of a spatiotemporal model
unit_names-method	Unit names of a spatiotemporal model
unit_names-spatPomp	Unit names of a spatiotemporal model

-- V --

vec_dmeasure	Vector of measurement densities
vec_dmeasure-method	Vector of measurement densities
vec_dmeasure-spatPomp	Vector of measurement densities
vec_rmeasure	Vector of simulated measurements
vec_rmeasure-method	Vector of simulated measurements
vec_rmeasure-spatPomp	Vector of simulated measurements
vunit_measure	vunit_measure
vunit_measure-method	vunit_measure
vunit_measure-spatPomp	vunit_measure