Package: dust 0.15.3
Rich FitzJohn
dust: Iterate Multiple Realisations of Stochastic Models
An Engine for simulation of stochastic models. Includes support for running stochastic models in parallel, either with shared or varying parameters. Simulations are run efficiently in compiled code and can be run with a fraction of simulated states returned to R, allowing control over memory usage. Support is provided for building bootstrap particle filter for performing Sequential Monte Carlo (e.g., Gordon et al. 1993 <doi:10.1049/ip-f-2.1993.0015>). The core of the simulation engine is the 'xoshiro256**' algorithm (Blackman and Vigna <arxiv:1805.01407>), and the package is further described in FitzJohn et al 2021 <doi:10.12688/wellcomeopenres.16466.2>.
Authors:
dust_0.15.3.tar.gz
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dust.pdf |dust.html✨
dust/json (API)
NEWS
| # Install 'dust' in R: |
| install.packages('dust', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mrc-ide/dust/issues
Last updated 4 months agofrom:1bcce5f84c (on master). Checks:1 OK, 10 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 30 2025 |
| R-4.5-win-x86_64 | NOTE | Jan 30 2025 |
| R-4.5-mac-x86_64 | NOTE | Jan 30 2025 |
| R-4.5-mac-aarch64 | NOTE | Jan 30 2025 |
| R-4.5-linux-x86_64 | NOTE | Jan 30 2025 |
| R-4.4-win-x86_64 | NOTE | Jan 30 2025 |
| R-4.4-mac-x86_64 | NOTE | Jan 30 2025 |
| R-4.4-mac-aarch64 | NOTE | Jan 30 2025 |
| R-4.3-win-x86_64 | NOTE | Jan 30 2025 |
| R-4.3-mac-x86_64 | NOTE | Jan 30 2025 |
| R-4.3-mac-aarch64 | NOTE | Jan 30 2025 |
Exports:dustdust_cuda_configurationdust_cuda_optionsdust_datadust_exampledust_generatedust_ode_controldust_openmp_supportdust_openmp_threadsdust_packagedust_repair_environmentdust_rngdust_rng_distributed_pointerdust_rng_distributed_statedust_rng_pointer
Dependencies:callrclicpp11descfsgluelifecyclepkgbuildpkgloadprocessxpsR6rlangrprojrootwithr
Algorithms used to compute random numbers
Rendered fromrng_algorithms.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2021-11-16
Started: 2021-11-16
Comparing models and data
Rendered fromdata.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2023-06-28
Started: 2021-08-25
Distributed parallel random numbers
Rendered fromrng_distributed.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2022-11-08
Started: 2021-11-17
Introduction to dust
Rendered fromdust.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2023-04-27
Started: 2020-07-06
Multiple parameter sets
Rendered frommulti.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2021-10-20
Started: 2021-02-24
Principles and design of dust
Rendered fromdesign.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2023-03-17
Started: 2021-02-25
Random number generation
Rendered fromrng.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2022-11-02
Started: 2020-07-06
Running models on GPUs with CUDA
Rendered fromgpu.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2022-11-08
Started: 2021-11-08
Using RNGs from packages
Rendered fromrng_package.Rmdusingknitr::rmarkdownon Jan 30 2025.Last update: 2023-04-27
Started: 2021-11-12
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create a dust model from a C++ input file | dust |
| Detect CUDA configuration | dust_cuda_configuration |
| Create CUDA options | dust_cuda_options |
| Process data for dust | dust_data |
| Access dust's built-in examples | dust_example |
| Generate dust code | dust_generate |
| The dust class | dust_generator |
| Create a dust_ode_control object. | dust_ode_control |
| Information about OpenMP support | dust_openmp_support |
| Select number of threads | dust_openmp_threads |
| Create dust model in package | dust_package |
| Repair dust environment | dust_repair_environment |
| Dust Random Number Generator | dust_rng |
| Create a set of distributed seeds | dust_rng_distributed_pointer dust_rng_distributed_state |
| Create pointer to random number generator stream | dust_rng_pointer |
