Inference for Spatiotemporal Partially Observed Markov Processes


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Documentation for package ‘spatPomp’ version 1.0.0

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A B C D E G H I L M P R S U V

spatPomp-package 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 Expectation of the measurement model for one unit
eunit_measure-method Expectation of the measurement model for one unit
eunit_measure-spatPomp Expectation of the measurement model for one unit
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 --

logLik Log likelihood extractor
logLik-abfd_spatPomp Log likelihood extractor
logLik-abfird_spatPomp Log likelihood extractor
logLik-bpfilterd_spatPomp Log likelihood extractor
logLik-girfd_spatPomp Log likelihood extractor
logLik-igirfd_spatPomp Log likelihood extractor
logLik-iubfd_spatPomp Log likelihood extractor
logLik-method Log likelihood extractor
lorenz Lorenz '96 spatPomp constructor
lorenz96 Lorenz '96 spatPomp constructor

-- 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 Matching moments for the unit measurement model
munit_measure-method Matching moments for the unit measurement model
munit_measure-spatPomp Matching moments for the unit measurement model

-- P --

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

-- R --

runit_measure Random draw from the measurement model for one unit
runit_measure-method Random draw from the measurement model for one unit
runit_measure-spatPomp Random draw from the measurement model for one unit

-- 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 unit measurement densities for each unit
vec_dmeasure-method Vector of unit measurement densities for each unit
vec_dmeasure-spatPomp Vector of unit measurement densities for each unit
vec_rmeasure Vector simulating measurements for each unit using 'runit_measure'
vec_rmeasure-method Vector simulating measurements for each unit using 'runit_measure'
vec_rmeasure-spatPomp Vector simulating measurements for each unit using 'runit_measure'
vunit_measure Conditional variance of the measurement on a single unit
vunit_measure-method Conditional variance of the measurement on a single unit
vunit_measure-spatPomp Conditional variance of the measurement on a single unit