Package: mcstate 0.9.22

Rich FitzJohn

mcstate: Monte Carlo Methods for State Space Models

Implements Monte Carlo methods for state-space models such as 'SIR' models in epidemiology. Particle MCMC (pmcmc) and SMC2 methods are planned. This package is particularly designed to work with odin/dust models, but we will see how general it becomes.

Authors:Rich FitzJohn [aut, cre], Marc Baguelin [aut], Edward Knock [aut], Lilith Whittles [aut], John Lees [aut], Raphael Sonabend [aut], Imperial College of Science, Technology and Medicine [cph]

mcstate_0.9.22.tar.gz
mcstate_0.9.22.zip(r-4.7)mcstate_0.9.22.zip(r-4.6)mcstate_0.9.22.zip(r-4.5)
mcstate_0.9.22.tgz(r-4.6-any)mcstate_0.9.22.tgz(r-4.5-any)
mcstate_0.9.22.tar.gz(r-4.7-any)mcstate_0.9.22.tar.gz(r-4.6-any)
mcstate_0.9.22.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
mcstate/json (API)
NEWS

# Install 'mcstate' in R:

install.packages('mcstate', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/mcstate/issues

On CRAN:

7.31 score 19 stars 1 packages 100 scripts 34 exports 22 dependencies

Last updated from:3549d64ff9 (on master). Checks:5 ERROR, 2 OK, 2 NOTE. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	235
source / vignettes	OK	289
linux-release-x86_64	ERROR	223
macos-release-arm64	ERROR	190
macos-oldrel-arm64	NOTE	171
windows-devel	ERROR	316
windows-release	ERROR	303
windows-oldrel	NOTE	293
wasm-release	OK	139

Exports:adaptive_proposal_control array_bind array_drop array_flatten array_reshape if2 if2_control if2_parameter if2_parameters if2_sample multistage_epoch multistage_parameters particle_deterministic particle_filter particle_filter_data particle_filter_initial pmcmc pmcmc_chains_cleanup pmcmc_chains_collect pmcmc_chains_prepare pmcmc_chains_run pmcmc_combine pmcmc_control pmcmc_parameter pmcmc_parameters pmcmc_parameters_nested pmcmc_predict pmcmc_sample pmcmc_thin pmcmc_varied_parameter smc2 smc2_control smc2_parameter smc2_parameters

Dependencies:callr cli cpp11 crayon desc dust fs glue hms lifecycle pkgbuild pkgconfig pkgload prettyunits processx progress ps R6 rlang rprojroot vctrs withr

Deterministic models

Rendered fromdeterministic.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2022-01-28
Started: 2021-08-09

Fitting a continuous-time model

Rendered fromcontinuous.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2023-09-12
Started: 2023-09-12

Inference with iterated filtering

Rendered fromif2.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2022-01-28
Started: 2021-05-19

Nested SIR Models

Rendered fromnested_sir_models.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2022-01-28
Started: 2021-02-24

Parallelisation of inference

Rendered fromparallelisation.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2022-01-28
Started: 2020-10-26

Restarting pMCMC

Rendered fromrestart.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2022-11-10
Started: 2021-01-08

SIR models with odin, dust and mcstate

Rendered fromsir_models.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2022-11-10
Started: 2020-10-26

Validation of SMC using a Kalman filter

Rendered fromkalman.Rmdusingknitr::rmarkdownon May 13 2026.