Package: odin2 0.3.46

Rich FitzJohn

odin2: Next generation odin

Temporary package for rewriting odin.

Authors:Rich FitzJohn [aut, cre], Wes Hinsley [aut], Thibaut Jombart [ctb], Ed Knock [ctb], Imperial College of Science, Technology and Medicine [cph]

odin2_0.3.46.tar.gz
odin2_0.3.46.zip(r-4.7)odin2_0.3.46.zip(r-4.6)odin2_0.3.46.zip(r-4.5)
odin2_0.3.46.tgz(r-4.6-any)odin2_0.3.46.tgz(r-4.5-any)
odin2_0.3.46.tar.gz(r-4.7-any)odin2_0.3.46.tar.gz(r-4.6-any)
odin2_0.3.46.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
odin2/json (API)

# Install 'odin2' in R:
install.packages('odin2', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/odin2/issues

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

On CRAN:

Conda:

7.72 score 10 stars 1 packages 111 scripts 6 exports 6 dependencies

Last updated from:94e7b52b0a (on main). Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK213
source / vignettesOK950
linux-release-x86_64OK212
macos-release-arm64OK182
macos-oldrel-arm64OK161
windows-develOK245
windows-releaseOK206
windows-oldrelOK292
wasm-releaseOK103

Exports:odinodin_error_explainodin_migrateodin_packageodin_showodin_validate

Dependencies:clicpp11dust2gluemontyrlang

Supported Functions
General syntax | Variables | Continuous time models | Basic operations | Conditionals | Operators | Mathematical functions and constants | Arrays | Array size | Special functions for arrays | Distribution functions | Semantics of random number draws | Special functions | Parameters | Data | Interpolation | Restricted names
Rendered fromfunctions.Rmdusingknitr::rmarkdown

Last update: 2026-01-20
Started: 2024-09-05

Details
Order of events | Options | odin2.compatibility | odin2.check_bounds | odin2.target
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Last update: 2025-10-20
Started: 2024-09-23

Getting started with odin2
Discrete time stochastic SIR model
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Last update: 2025-09-16
Started: 2024-08-12

Odin parse errors
E0001 | E1001 | E1002 | E1003 | E1004 | E1005 | E1006 | E1007 | E1008 | E1009 | E1010 | E1012 | E1013 | E1014 | E1015 | E1016 | E1017 | E1018 | E1019 | E1020 | E1021 | E1022 | E1023 | E1024 | E1025 | E1026 | E1027 | E1028 | E1029 | E1030 | E1031 | E1032 | E1033 | E1035 | E1036 | E1037 | E1038 | E1039 | E1040 | E1041 | E1042 | E1043 | E1044 | E1045 | E1046 | E1047 | E1048 | E1049 | E1050 | E1051 | E1052 | E1053 | E1054 | E1055 | E1056 | E1057 | E1058 | E1059 | E1060 | E1061 | E1062 | E1063 | E1064 | E1065 | E1066 | E1067 | E1068 | E1069 | E1070 | E2001 | E2002 | E2003 | E2004 | E2005 | E2006 | E2007 | E2008 | E2009 | E2010 | E2011 | E2012 | E2013 | E2014 | E2015 | E2016 | E2017 | E2018 | E2019 | E2020 | E2021 | E2023 | E2024 | E2025 | E2026 | E2027 | E2028 | E2029 | E3001 | E3002 | E3003
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Last update: 2025-09-12
Started: 2024-07-17

Fitting odin2 models to data
Setting the scene | Comparing to data | Stochastic likelihood with a particle filter | Inference with particle MCMC (pMCMC) | Effective sampling | Comparing against vectors of data | Deterministic models from stochastic | Differentiable models | Running multiple parameter sets at once | For dust2 systems | For dust2 filters/unfilters | For monty models | Further reading
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Last update: 2025-06-26
Started: 2024-08-12

Migrating from odin 1.x.x
New features | Planned | Hoped | Missing features | Changes in syntax | user() becomes parameter() | Compare keyword is now removed. | Vector parameters assign without array indices | Vector/matrix/array parameters whose size is determined by input require rank argument | Interpolate results assign without array indices | Discrete-time models have a more solid time basis | Assignments to dt | Assignments to time | Use of step | The name of the time variable in continuous time models has changed | Random number function calls have changed | System size cannot be changed after creation | Changes in the way arrays are handled | Changes to how delays are supported | delay() cannot be used in discrete time models | delay() results assign without array indices | The first argument to delay() must be the name of an equation | The 'default' argument to delay() has been removed | The delay time must be constant | General changes | Known limitations | Much slower compilation time | Loss of features from odin 1.x | Updating old code | Avoiding output() in discrete-time systems
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Last update: 2025-06-26
Started: 2024-08-12

Debugging
Using print() | print format strings | Conditional display | Controlling precision | Current limitations | Show the generated code | Use the interactive debugger
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Last update: 2024-11-06
Started: 2024-10-03

Packaging odin models
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Last update: 2024-11-06
Started: 2024-11-06