Package: dust2 0.3.28

Rich FitzJohn

dust2: Next Generation dust

Experimental sources for the next generation of dust, which will properly adopt the particle filter, have support for partial parameter updates, support for multiple parameter sets and hopefully better GPU/MPI support.

Authors:Rich FitzJohn [aut, cre], Imperial College of Science, Technology and Medicine [cph]

dust2_0.3.28.tar.gz
dust2_0.3.28.zip(r-4.7)dust2_0.3.28.zip(r-4.6)dust2_0.3.28.zip(r-4.5)
dust2_0.3.28.tgz(r-4.6-x86_64)dust2_0.3.28.tgz(r-4.6-arm64)dust2_0.3.28.tgz(r-4.5-x86_64)dust2_0.3.28.tgz(r-4.5-arm64)
dust2_0.3.28.tar.gz(r-4.7-arm64)dust2_0.3.28.tar.gz(r-4.7-x86_64)dust2_0.3.28.tar.gz(r-4.6-arm64)dust2_0.3.28.tar.gz(r-4.6-x86_64)
dust2_0.3.28.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
dust2/json (API)

# Install 'dust2' in R:
install.packages('dust2', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/dust2/issues

Pkgdown/docs site:https://mrc-ide.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

cppopenmp

7.11 score 6 packages 118 scripts 36 exports 4 dependencies

Last updated from:83721f78fd (on main). Checks:11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE228
linux-devel-x86_64NOTE213
source / vignettesOK320
linux-release-arm64NOTE223
linux-release-x86_64NOTE222
macos-release-arm64NOTE150
macos-release-x86_64NOTE316
macos-oldrel-arm64NOTE152
macos-oldrel-x86_64NOTE357
windows-develNOTE251
windows-releaseNOTE288
windows-oldrelNOTE250
wasm-releaseOK144

Exports:dust_browser_continuedust_browser_enableddust_browser_verbositydust_compiledust_exampledust_filter_createdust_filter_datadust_likelihood_last_gradientdust_likelihood_last_snapshotsdust_likelihood_last_statedust_likelihood_last_trajectoriesdust_likelihood_montydust_likelihood_rng_statedust_likelihood_rundust_likelihood_set_rng_statedust_ode_controldust_openmp_supportdust_openmp_threadsdust_packagedust_system_compare_datadust_system_createdust_system_internalsdust_system_reorderdust_system_rng_statedust_system_run_to_timedust_system_set_rng_statedust_system_set_statedust_system_set_state_initialdust_system_set_timedust_system_simulatedust_system_statedust_system_timedust_system_update_parsdust_unfilter_createdust_unpack_indexdust_unpack_state

Dependencies:clicpp11montyrlang

Writing dust2 systems
First steps, a random walk | Support code | Annotations | Type definitions | The methods | Multiple variables, the SIR revisited | Continuous time (ODE) models | Continuous time models with additional output | Continuous time models with special variables
Rendered fromwriting.Rmdusingknitr::rmarkdown

Last update: 2025-06-03
Started: 2024-10-15

Migrating from dust 1.x.x
Dude, where's my feature? | Change in meaning of time in discrete-time models | New interface | See also
Rendered frommigrating.Rmdusingknitr::rmarkdown

Last update: 2024-11-15
Started: 2024-11-04

Comparing dust systems to data
Rendered fromdata.Rmdusingknitr::rmarkdown

Last update: 2024-10-22
Started: 2024-10-15

Introduction to dust
A simple example - random walk | Running a model in parallel | A more interesting example | Other methods | Reordering particles | Set particle state
Rendered fromdust2.Rmdusingknitr::rmarkdown

Last update: 2024-10-21
Started: 2024-10-15

Details
Influential environment variables and options
Rendered fromdetails.Rmdusingknitr::rmarkdown

Last update: 2024-10-15
Started: 2024-10-02

Packaging dust systems
Rendered frompackaging.Rmdusingknitr::rmarkdown

Last update: 2024-10-15
Started: 2024-10-15

Principles and design of dust
Running multiple realisations | Parallelisation | Efficient running | Efficient state handling | Useful verbs | A compilation target
Rendered fromdesign.Rmdusingknitr::rmarkdown

Last update: 2024-10-15
Started: 2024-10-15

Periodic variables details
Discrete time systems | Continuous time systems | Properties of resettable variables | Unresolved bits that might change
Rendered fromperiodic.Rmdusingknitr::rmarkdown

Last update: 2024-08-21
Started: 2024-07-10

Readme and manuals

Help Manual

Help pageTopics
The dust debuggerdust_browser dust_browser_continue dust_browser_enabled dust_browser_verbosity
Compile a dust2 systemdust_compile
Example generatorsdust_example
Create a particle filterdust_filter_create
Prepare datadust_filter_data
Create copy of a dust likelihood objectdust_likelihood_copy
Fetch last likelihood gradientdust_likelihood_last_gradient
Get likelihood snapshotsdust_likelihood_last_snapshots
Get likelihood statedust_likelihood_last_state
Fetch last likelihood trajectoriesdust_likelihood_last_trajectories
Create monty modeldust_likelihood_monty
Get filter RNG statedust_likelihood_rng_state dust_likelihood_set_rng_state
Compute likelihooddust_likelihood_run
Create a dust_ode_control object.dust_ode_control
Information about OpenMP supportdust_openmp_support
Select number of threadsdust_openmp_threads
Create dust system in packagedust_package
Compare system state against datadust_system_compare_data
Create a dust system objectdust_system_create
Fetch system internalsdust_system_internals
Reorder statesdust_system_reorder
Fetch and set rng statedust_system_rng_state dust_system_set_rng_state
Run systemdust_system_run_to_time
Set system statedust_system_set_state
Set system state to initial conditionsdust_system_set_state_initial
Set system timedust_system_set_time
Simulate systemdust_system_simulate
Extract system statedust_system_state
Fetch system timedust_system_time
Update parametersdust_system_update_pars
Create an unfilterdust_unfilter_create
Unpack statedust_unpack_index dust_unpack_state