# Inference for Spatiotemporal Partially Observed Markov Processes

## Documentation for package ‘spatPomp’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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