Package: spatPomp 1.0.0
Edward Ionides
spatPomp: Inference for Spatiotemporal Partially Observed Markov Processes
Inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models. The 'spatPomp' package extends 'pomp' to include algorithms taking advantage of the spatial structure in order to assist with handling high dimensional processes. See Asfaw et al. (2024) <doi:10.48550/arXiv.2101.01157> for further description of the package.
Authors:
spatPomp_1.0.0.tar.gz
spatPomp_1.0.0.zip(r-4.5)spatPomp_1.0.0.zip(r-4.4)spatPomp_1.0.0.zip(r-4.3)
spatPomp_1.0.0.tgz(r-4.4-x86_64)spatPomp_1.0.0.tgz(r-4.4-arm64)spatPomp_1.0.0.tgz(r-4.3-x86_64)spatPomp_1.0.0.tgz(r-4.3-arm64)
spatPomp_1.0.0.tar.gz(r-4.5-noble)spatPomp_1.0.0.tar.gz(r-4.4-noble)
spatPomp_1.0.0.tgz(r-4.4-emscripten)spatPomp_1.0.0.tgz(r-4.3-emscripten)
spatPomp.pdf |spatPomp.html✨
spatPomp/json (API)
NEWS
| # Install 'spatPomp' in R: |
| install.packages('spatPomp', repos = c('https://spatpomp-org.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/spatpomp-org/spatpomp/issues
- city_data_UK - City data in the United Kingdom
- 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
- measlesUK - Measles in the United Kingdom
Last updated 6 days agofrom:c23552b93a. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 15 2024 |
| R-4.5-win-x86_64 | OK | Nov 15 2024 |
| R-4.5-linux-x86_64 | OK | Nov 15 2024 |
| R-4.4-win-x86_64 | OK | Nov 15 2024 |
| R-4.4-mac-x86_64 | OK | Nov 15 2024 |
| R-4.4-mac-aarch64 | OK | Nov 15 2024 |
| R-4.3-win-x86_64 | OK | Nov 15 2024 |
| R-4.3-mac-x86_64 | OK | Nov 15 2024 |
| R-4.3-mac-aarch64 | OK | Nov 15 2024 |
Exports:abfabfirarma_benchmarkbmbm_kalman_logLikbm2bm2_kalman_logLikbpfiltercontract_paramsdunit_measureenkfeunit_measureexpand_paramsgbmgirfhe10ibpfienkfigirfiubflogLiklorenzmean_by_unitmeaslesmeasles2munit_measureplotprintrunit_measuresimulatespatPompspatPomp_Csnippetunit_namesvec_dmeasurevec_rmeasurevunit_measure
Dependencies:abindclicodacodetoolscolorspacecpp11data.tabledeSolvedigestdplyrfansifarverforeachgenericsggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigpomppurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Inference for SpatPOMPs (Spatiotemporal Partially Observed Markov Processes) | spatPomp-package |
| Adapted Bagged Filter (ABF) | abf abf,abfd_spatPomp-method abf,spatPomp-method abf-abfd_spatPomp abf-spatPomp |
| Adapted Bagged Filter with Intermediate Resampling (ABF-IR) | abfir abfir,abfird_spatPomp-method abfir,spatPomp-method abfir-abfird_spatPomp abfir-spatPomp |
| Calculated log-ARMA log-likelihood benchmark for spatPomp models | arma_benchmark |
| Coerce to data frame | as.data.frame as.data.frame.spatPomp coerce,spatPomp,data.frame-method |
| Brownian motion spatPomp simulator | bm |
| Exact log-likelihood for Brownian motion spatPomp generator | bm_kalman_logLik |
| Brownian motion spatPomp generator with shared or unit-specific parameters | bm2 |
| Exact log-likelihood for Brownian motion spatPomp generator with shared or unit-specific parameters | bm2_kalman_logLik |
| Block particle filter (BPF) | bpfilter bpfilter,ANY-method bpfilter,bpfilterd_spatPomp-method bpfilter,missing-method bpfilter,spatPomp-method bpfilter-ANY bpfilter-bpfilterd_spatPomp bpfilter-missing bpfilter-spatPomp |
| City data in the United Kingdom | city_data_UK |
| Concatenate | c c.SpatPomp concat |
| dunit_measure 'dunit_measure' evaluates the unit measurement density of a unit's observation given the entire state | dunit_measure dunit_measure,spatPomp-method dunit_measure-spatPomp |
| Generalized Ensemble Kalman filter (EnKF) | enkf enkf,ANY-method enkf,missing-method enkf,spatPomp-method enkf-spatPomp |
| Expectation of the measurement model for one unit | eunit_measure eunit_measure,spatPomp-method eunit_measure-spatPomp |
| Book-keeping functions for working with expanded parameters | contract_params contract_params, expand_params expand_params, mean_by_unit mean_by_unit, param_formats |
| Geometric Brownian motion spatPomp simulator | gbm |
| Guided intermediate resampling filter (GIRF) | girf girf,ANY-method girf,girfd_spatPomp-method girf,missing-method girf,spatPomp-method girf-ANY girf-girfd_spatPomp girf-missing girf-spatPomp |
| Measles in UK: spatPomp generator with shared or unit-specific parameters | he10 |
| City data in the United Kingdom | he10coordinates |
| Demographic data for 20 towns in the United Kingdom | he10demography |
| Measles in the United Kingdom | he10measles |
| Measles in the United Kingdom: MLE from He et al (2010) | he10mle |
| Iterated block particle filter (IBPF) | ibpf ibpf,ANY-method ibpf,bpfilterd_spatPomp-method ibpf,ibpfd_spatPomp-method ibpf,missing-method ibpf,spatPomp-method ibpf-ANY ibpf-bpfd_spatPomp ibpf-ibpfd_spatPomp ibpf-missing ibpf-spatPomp |
| Iterated ensemble Kalman filter (IEnKF) | ienkf ienkf,spatPomp-method ienkf-spatPomp |
| Iterated guided intermediate resampling filter (IGIRF) | igirf igirf,ANY-method igirf,igirfd_spatPomp-method igirf,missing-method igirf,spatPomp-method igirf-ANY igirf-igirfd_spatPomp igirf-missing igirf-spatPomp |
| Iterated Unadapted Bagged Filter (IUBF) | iubf iubf,spatPomp-method iubf-spatPomp |
| Log likelihood extractor | logLik logLik,abfd_spatPomp-method logLik,abfird_spatPomp-method logLik,bpfilterd_spatPomp-method logLik,girfd_spatPomp-method logLik,igirfd_spatPomp-method logLik,iubfd_spatPomp-method logLik-abfd_spatPomp logLik-abfird_spatPomp logLik-bpfilterd_spatPomp logLik-girfd_spatPomp logLik-igirfd_spatPomp logLik-iubfd_spatPomp |
| Lorenz '96 spatPomp constructor | lorenz lorenz96 |
| Measles in UK spatPomp generator | measles |
| Measles in UK: spatPomp generator with shared or unit-specific parameters | measles2 |
| Measles in the United Kingdom | measlesUK |
| Matching moments for the unit measurement model | munit_measure munit_measure,spatPomp-method munit_measure-spatPomp |
| Plot methods for 'spatPomp' objects | plot plot,igirfd_spatPomp-method plot,spatPomp-method plot-igirfd_spatPomp plot-spatPomp |
| Print methods | print print,spatPomp-method print-spatPomp |
| Random draw from the measurement model for one unit | runit_measure runit_measure,spatPomp-method runit_measure-spatPomp |
| Simulation of a spatiotemporal partially-observed Markov process | simulate simulate,spatPomp-method simulate-spatPomp |
| Constructor of the spatPomp object | spatPomp |
| C snippets | spatPomp_Csnippet spatPomp_Csnippet,character-method spatPomp_Csnippet-character |
| An S4 class to represent a spatiotemporal POMP model and data. | spatPomp-class |
| Unit names of a spatiotemporal model | unit_names unit_names,spatPomp-method unit_names-spatPomp |
| Vector of unit measurement densities for each unit | vec_dmeasure vec_dmeasure,spatPomp-method vec_dmeasure-spatPomp |
| Vector simulating measurements for each unit using 'runit_measure' | vec_rmeasure vec_rmeasure,spatPomp-method vec_rmeasure-spatPomp |
| Conditional variance of the measurement on a single unit | vunit_measure vunit_measure,spatPomp-method vunit_measure-spatPomp |
