DiffEqBayes.jl: Bayesian Parameter Estimation for Differential Equations
This repository is a set of extension functionality for estimating the parameters of differential equations using Bayesian methods. It allows the choice of using CmdStan.jl, Turing.jl, DynamicHMC.jl and ApproxBayes.jl to perform a Bayesian estimation of a differential equation problem specified via the DifferentialEquations.jl interface.
Installation
To install DiffEqBayes.jl, use the Julia package manager:
using Pkg
Pkg.add("DiffEqBayes")
Contributing
Please refer to the SciML ColPrac: Contributor's Guide on Collaborative Practices for Community Packages for guidance on PRs, issues, and other matters relating to contributing to SciML.
See the SciML Style Guide for common coding practices and other style decisions.
There are a few community forums:
- The #diffeq-bridged and #sciml-bridged channels in the Julia Slack
- The #diffeq-bridged and #sciml-bridged channels in the Julia Zulip
- On the Julia Discourse forums
- See also SciML Community page
Reproducibility
The documentation of this SciML package was built using these direct dependencies,
Status `~/work/DiffEqBayes.jl/DiffEqBayes.jl/docs/Project.toml`
[6e4b80f9] BenchmarkTools v1.4.0
[593b3428] CmdStan v6.6.0
[ebbdde9d] DiffEqBayes v3.6.1 `~/work/DiffEqBayes.jl/DiffEqBayes.jl`
[31c24e10] Distributions v0.25.104
⌅ [e30172f5] Documenter v0.27.25
[bbc10e6e] DynamicHMC v3.4.7
⌃ [1dea7af3] OrdinaryDiffEq v6.33.3
[65888b18] ParameterizedFunctions v5.16.0
[91a5bcdd] Plots v1.39.0
⌅ [731186ca] RecursiveArrayTools v2.32.3
[2913bbd2] StatsBase v0.34.2
[f3b207a7] StatsPlots v0.15.6
[84d833dd] TransformVariables v0.8.10
[8dfed614] Test
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated`
and using this machine and Julia version.
Julia Version 1.10.0
Commit 3120989f39b (2023-12-25 18:01 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 4 × AMD EPYC 7763 64-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 on 4 virtual cores
Environment:
JULIA_CMDSTAN_HOME = /home/runner/cmdstan-2.29.2/
A more complete overview of all dependencies and their versions is also provided.
Status `~/work/DiffEqBayes.jl/DiffEqBayes.jl/docs/Manifest.toml`
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[1a1c6b14] gperf_jll v3.1.1+0
[a4ae2306] libaom_jll v3.4.0+0
[0ac62f75] libass_jll v0.15.1+0
[2db6ffa8] libevdev_jll v1.11.0+0
[f638f0a6] libfdk_aac_jll v2.0.2+0
[36db933b] libinput_jll v1.18.0+0
[b53b4c65] libpng_jll v1.6.40+0
[f27f6e37] libvorbis_jll v1.3.7+1
[009596ad] mtdev_jll v1.1.6+0
[1270edf5] x264_jll v2021.5.5+0
[dfaa095f] x265_jll v3.5.0+0
[d8fb68d0] xkbcommon_jll v1.4.1+1
[0dad84c5] ArgTools v1.1.1
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8ba89e20] Distributed
[f43a241f] Downloads v1.6.0
[7b1f6079] FileWatching
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[4af54fe1] LazyArtifacts
[b27032c2] LibCURL v0.6.4
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[ca575930] NetworkOptions v1.2.0
[44cfe95a] Pkg v1.10.0
[de0858da] Printf
[9abbd945] Profile
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA v0.7.0
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays v1.10.0
[10745b16] Statistics v1.10.0
[4607b0f0] SuiteSparse
[fa267f1f] TOML v1.0.3
[a4e569a6] Tar v1.10.0
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[e66e0078] CompilerSupportLibraries_jll v1.0.5+1
[deac9b47] LibCURL_jll v8.4.0+0
[e37daf67] LibGit2_jll v1.6.4+0
[29816b5a] LibSSH2_jll v1.11.0+1
[c8ffd9c3] MbedTLS_jll v2.28.2+1
[14a3606d] MozillaCACerts_jll v2023.1.10
[4536629a] OpenBLAS_jll v0.3.23+2
[05823500] OpenLibm_jll v0.8.1+2
[efcefdf7] PCRE2_jll v10.42.0+1
[bea87d4a] SuiteSparse_jll v7.2.1+1
[83775a58] Zlib_jll v1.2.13+1
[8e850b90] libblastrampoline_jll v5.8.0+1
[8e850ede] nghttp2_jll v1.52.0+1
[3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`