Package: dust2 0.2.4

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_0.2.4.tar.gz
dust2_0.2.4.zip(r-4.5)dust2_0.2.4.zip(r-4.4)dust2_0.2.4.zip(r-4.3)
dust2_0.2.4.tgz(r-4.4-x86_64)dust2_0.2.4.tgz(r-4.4-arm64)dust2_0.2.4.tgz(r-4.3-x86_64)dust2_0.2.4.tgz(r-4.3-arm64)
dust2_0.2.4.tar.gz(r-4.5-noble)dust2_0.2.4.tar.gz(r-4.4-noble)
dust2_0.2.4.tgz(r-4.4-emscripten)dust2_0.2.4.tgz(r-4.3-emscripten)
dust2.pdf |dust2.html
dust2/json (API)

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

Peer review:

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

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

On CRAN:

6.08 score 1 packages 21 scripts 35 exports 5 dependencies

Last updated 1 days agofrom:a2bfbd67f9 (on main). Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-win-x86_64NOTENov 07 2024
R-4.5-linux-x86_64NOTENov 07 2024
R-4.4-win-x86_64NOTENov 07 2024
R-4.4-mac-x86_64NOTENov 07 2024
R-4.4-mac-aarch64NOTENov 07 2024
R-4.3-win-x86_64NOTENov 07 2024
R-4.3-mac-x86_64NOTENov 07 2024
R-4.3-mac-aarch64NOTENov 07 2024

Exports:dust_browser_continuedust_browser_enableddust_browser_verbositydust_compiledust_exampledust_filter_createdust_filter_datadust_likelihood_last_gradientdust_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:clicpp11montyR6rlang

Comparing dust systems to data

Rendered fromdata.Rmdusingknitr::rmarkdownon Nov 07 2024.

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

Details

Rendered fromdetails.Rmdusingknitr::rmarkdownon Nov 07 2024.

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

Introduction to dust

Rendered fromdust2.Rmdusingknitr::rmarkdownon Nov 07 2024.

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

Migrating from dust 1.x.x

Rendered frommigrating.Rmdusingknitr::rmarkdownon Nov 07 2024.

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

Packaging dust systems

Rendered frompackaging.Rmdusingknitr::rmarkdownon Nov 07 2024.

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

Periodic variables details

Rendered fromperiodic.Rmdusingknitr::rmarkdownon Nov 07 2024.

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

Principles and design of dust

Rendered fromdesign.Rmdusingknitr::rmarkdownon Nov 07 2024.

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

Writing dust2 systems

Rendered fromwriting.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2024-10-28
Started: 2024-10-15

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 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