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| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Data · ArviZ.jl</title><script data-outdated-warner src="../../assets/warner.js"></script><link rel="canonical" href="stable/api/data/"/><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="../.."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../../assets/documenter.js"></script><script src="../../siteinfo.js"></script><script src="../../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../../assets/themeswap.js"></script><link href="../../assets/favicon.ico" rel="icon" type="image/x-icon"/><link href="../../assets/custom.css" rel="stylesheet" type="text/css"/></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../../"><img class="docs-light-only" src="../../assets/logo.png" alt="ArviZ.jl logo"/><img class="docs-dark-only" src="../../assets/logo-dark.png" alt="ArviZ.jl logo"/></a><form class="docs-search" action="../../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../../">Home</a></li><li><span class="tocitem">Getting Started</span><ul><li><a class="tocitem" href="../../quickstart/">Quickstart</a></li><li><a class="tocitem" href="../../working_with_inference_data/">Working with <code>InferenceData</code></a></li><li><a class="tocitem" href="../../creating_custom_plots/">Creating custom plots</a></li></ul></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="../stats/">Stats</a></li><li><a class="tocitem" href="../diagnostics/">Diagnostics</a></li><li class="is-active"><a class="tocitem" href>Data</a><ul class="internal"><li><a class="tocitem" href="#Inference-library-converters"><span>Inference library converters</span></a></li><li><a class="tocitem" href="#IO-/-Conversion"><span>IO / Conversion</span></a></li></ul></li><li><input class="collapse-toggle" id="menuitem-3-5" type="checkbox"/><label class="tocitem" for="menuitem-3-5"><span class="docs-label">InferenceObjects</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../inference_data/">InferenceData</a></li><li><a class="tocitem" href="../dataset/">Dataset</a></li></ul></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">API</a></li><li class="is-active"><a href>Data</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Data</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/arviz-devs/ArviZ.jl/blob/main/docs/src/api/data.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="data-api"><a class="docs-heading-anchor" href="#data-api">Data</a><a id="data-api-1"></a><a class="docs-heading-anchor-permalink" href="#data-api" title="Permalink"></a></h1><ul><li><a href="#ArviZ.from_mcmcchains"><code>ArviZ.from_mcmcchains</code></a></li><li><a href="#ArviZ.from_samplechains"><code>ArviZ.from_samplechains</code></a></li><li><a href="#InferenceObjects.from_netcdf"><code>InferenceObjects.from_netcdf</code></a></li><li><a href="#InferenceObjects.to_netcdf"><code>InferenceObjects.to_netcdf</code></a></li></ul><h2 id="Inference-library-converters"><a class="docs-heading-anchor" href="#Inference-library-converters">Inference library converters</a><a id="Inference-library-converters-1"></a><a class="docs-heading-anchor-permalink" href="#Inference-library-converters" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="ArviZ.from_mcmcchains" href="#ArviZ.from_mcmcchains"><code>ArviZ.from_mcmcchains</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">from_mcmcchains(posterior::MCMCChains.Chains; kwargs...) -> InferenceData | ||
| from_mcmcchains(; kwargs...) -> InferenceData | ||
| from_mcmcchains( | ||
| posterior::MCMCChains.Chains, | ||
| posterior_predictive, | ||
| predictions, | ||
| log_likelihood; | ||
| kwargs... | ||
| ) -> InferenceData</code></pre><p>Convert data in an <code>MCMCChains.Chains</code> format into an <a href="../inference_data/#InferenceObjects.InferenceData"><code>InferenceData</code></a>.</p><p>Any keyword argument below without an an explicitly annotated type above is allowed, so long as it can be passed to <a href="../inference_data/#InferenceObjects.convert_to_inference_data"><code>convert_to_inference_data</code></a>.</p><p><strong>Arguments</strong></p><ul><li><code>posterior::MCMCChains.Chains</code>: Draws from the posterior</li></ul><p><strong>Keywords</strong></p><ul><li><code>posterior_predictive::Any=nothing</code>: Draws from the posterior predictive distribution or name(s) of predictive variables in <code>posterior</code></li><li><code>predictions</code>: Out-of-sample predictions for the posterior.</li><li><code>prior</code>: Draws from the prior</li><li><code>prior_predictive</code>: Draws from the prior predictive distribution or name(s) of predictive variables in <code>prior</code></li><li><code>observed_data</code>: Observed data on which the <code>posterior</code> is conditional. It should only contain data which is modeled as a random variable. Keys are parameter names and values.</li><li><code>constant_data</code>: Model constants, data included in the model that are not modeled as random variables. Keys are parameter names.</li><li><code>predictions_constant_data</code>: Constants relevant to the model predictions (i.e. new <code>x</code> values in a linear regression).</li><li><code>log_likelihood</code>: Pointwise log-likelihood for the data. It is recommended to use this argument as a named tuple whose keys are observed variable names and whose values are log likelihood arrays. Alternatively, provide the name of variable in <code>posterior</code> containing log likelihoods.</li><li><code>library=MCMCChains</code>: Name of library that generated the chains</li><li><code>coords</code>: Map from named dimension to named indices</li><li><code>dims</code>: Map from variable name to names of its dimensions</li><li><code>eltypes</code>: Map from variable names to eltypes. This is primarily used to assign discrete eltypes to discrete variables that were stored in <code>Chains</code> as floats.</li></ul><p><strong>Returns</strong></p><ul><li><code>InferenceData</code>: The data with groups corresponding to the provided data</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/arviz-devs/ArviZ.jl/blob/923fdba683a76d0dde39f314a044016736783720/src/conversions.jl#L1-L48">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="ArviZ.from_samplechains" href="#ArviZ.from_samplechains"><code>ArviZ.from_samplechains</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">from_samplechains( | ||
| posterior=nothing; | ||
| prior=nothing, | ||
| library=SampleChains, | ||
| kwargs..., | ||
| ) -> InferenceData</code></pre><p>Convert SampleChains samples to an <code>InferenceData</code>.</p><p>Either <code>posterior</code> or <code>prior</code> may be a <code>SampleChains.AbstractChain</code> or <code>SampleChains.MultiChain</code> object.</p><p>For descriptions of remaining <code>kwargs</code>, see <a href="../inference_data/#InferenceObjects.from_namedtuple"><code>from_namedtuple</code></a>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/arviz-devs/ArviZ.jl/blob/923fdba683a76d0dde39f314a044016736783720/src/conversions.jl#L51-L65">source</a></section></article><h2 id="IO-/-Conversion"><a class="docs-heading-anchor" href="#IO-/-Conversion">IO / Conversion</a><a id="IO-/-Conversion-1"></a><a class="docs-heading-anchor-permalink" href="#IO-/-Conversion" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="InferenceObjects.from_netcdf" href="#InferenceObjects.from_netcdf"><code>InferenceObjects.from_netcdf</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">from_netcdf(path::AbstractString; kwargs...) -> InferenceData</code></pre><p>Load an <a href="../inference_data/#InferenceObjects.InferenceData"><code>InferenceData</code></a> from an unopened NetCDF file.</p><p>Remaining <code>kwargs</code> are passed to <a href="https://alexander-barth.github.io/NCDatasets.jl/stable/dataset/#NCDatasets.NCDataset"><code>NCDatasets.NCDataset</code></a>. This method loads data eagerly. To instead load data lazily, pass an opened <code>NCDataset</code> to <code>from_netcdf</code>.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>This method requires that NCDatasets is loaded before it can be used.</p></div></div><p><strong>Examples</strong></p><pre><code class="language-julia hljs">julia> using InferenceObjects, NCDatasets | ||
|
|
||
| julia> idata = from_netcdf("centered_eight.nc") | ||
| InferenceData with groups: | ||
| > posterior | ||
| > posterior_predictive | ||
| > sample_stats | ||
| > prior | ||
| > observed_data</code></pre><pre><code class="nohighlight hljs">from_netcdf(ds::NCDatasets.NCDataset; load_mode) -> InferenceData</code></pre><p>Load an <a href="../inference_data/#InferenceObjects.InferenceData"><code>InferenceData</code></a> from an opened NetCDF file.</p><p><code>load_mode</code> defaults to <code>:lazy</code>, which avoids reading variables into memory. Operations on these arrays will be slow. <code>load_mode</code> can also be <code>:eager</code>, which copies all variables into memory. It is then safe to close <code>ds</code>. If <code>load_mode</code> is <code>:lazy</code> and <code>ds</code> is closed after constructing <code>InferenceData</code>, using the variable arrays will have undefined behavior.</p><p><strong>Examples</strong></p><p>Here is how we might load an <code>InferenceData</code> from an <code>InferenceData</code> lazily from a web-hosted NetCDF file.</p><pre><code class="language-julia hljs">julia> using HTTP, InferenceObjects, NCDatasets | ||
|
|
||
| julia> resp = HTTP.get("https://github.com/arviz-devs/arviz_example_data/blob/main/data/centered_eight.nc?raw=true"); | ||
|
|
||
| julia> ds = NCDataset("centered_eight", "r"; memory = resp.body); | ||
|
|
||
| julia> idata = from_netcdf(ds) | ||
| InferenceData with groups: | ||
| > posterior | ||
| > posterior_predictive | ||
| > sample_stats | ||
| > prior | ||
| > observed_data | ||
|
|
||
| julia> idata_copy = copy(idata); # disconnect from the loaded dataset | ||
|
|
||
| julia> close(ds);</code></pre></div></section></article><article class="docstring"><header><a class="docstring-binding" id="InferenceObjects.to_netcdf" href="#InferenceObjects.to_netcdf"><code>InferenceObjects.to_netcdf</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">to_netcdf(data, dest::AbstractString; group::Symbol=:posterior, kwargs...) | ||
| to_netcdf(data, dest::NCDatasets.NCDataset; group::Symbol=:posterior)</code></pre><p>Write <code>data</code> to a NetCDF file.</p><p><code>data</code> is any type that can be converted to an <a href="../inference_data/#InferenceObjects.InferenceData"><code>InferenceData</code></a> using <a href="../inference_data/#InferenceObjects.convert_to_inference_data"><code>convert_to_inference_data</code></a>. If not an <code>InferenceData</code>, then <code>group</code> specifies which group the data represents.</p><p><code>dest</code> specifies either the path to the NetCDF file or an opened NetCDF file. If <code>dest</code> is a path, remaining <code>kwargs</code> are passed to <a href="https://alexander-barth.github.io/NCDatasets.jl/stable/dataset/#NCDatasets.NCDataset"><code>NCDatasets.NCDataset</code></a>.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>This method requires that NCDatasets is loaded before it can be used.</p></div></div><p><strong>Examples</strong></p><pre><code class="language-julia hljs">julia> using InferenceObjects, NCDatasets | ||
|
|
||
| julia> idata = from_namedtuple((; x = randn(4, 100, 3), z = randn(4, 100))) | ||
| InferenceData with groups: | ||
| > posterior | ||
|
|
||
| julia> to_netcdf(idata, "data.nc") | ||
| "data.nc"</code></pre></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../diagnostics/">« Diagnostics</a><a class="docs-footer-nextpage" href="../inference_data/">InferenceData »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 22 November 2023 08:06">Wednesday 22 November 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |
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