Inference for Spatiotemporal Partially Observed Markov Processes
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Documentation for package ‘spatPomp’ version 1.0.0
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| 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 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 |