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| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · SurvivalBase.jl</title><meta name="title" content="Home · SurvivalBase.jl"/><meta property="og:title" content="Home · SurvivalBase.jl"/><meta property="twitter:title" content="Home · SurvivalBase.jl"/><meta name="description" content="Documentation for SurvivalBase.jl."/><meta property="og:description" content="Documentation for SurvivalBase.jl."/><meta property="twitter:description" content="Documentation for SurvivalBase.jl."/><meta property="og:url" content="https://JuliaSurv.github.io/SurvivalBase.jl/"/><meta property="twitter:url" content="https://JuliaSurv.github.io/SurvivalBase.jl/"/><link rel="canonical" href="https://JuliaSurv.github.io/SurvivalBase.jl/"/><script data-outdated-warner src="assets/warner.js"></script><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/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/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="search_index.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></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>SurvivalBase.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></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"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/JuliaSurv/SurvivalBase.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/JuliaSurv/SurvivalBase.jl/blob/main/docs/src/index.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="SurvivalBase"><a class="docs-heading-anchor" href="#SurvivalBase">SurvivalBase</a><a id="SurvivalBase-1"></a><a class="docs-heading-anchor-permalink" href="#SurvivalBase" title="Permalink"></a></h1><p>The <a href="https://github.com/JuliaSurv/SurvivalBase.jl"><code>SurvivalBase.jl</code></a> package is intended to hold internals and shared infrastructure for several other front-facing packages in the <a href="https://github.com/JuliaSurv">JuliaSurv</a> organization, while having the minimal set of dependencies. Please do not use it directly and instead used other front-facing packages and interfaces from the organization.</p><p>Right now, the main infrastructure consists of special functions <code>Surv</code> and <code>Strata</code> used in <a href="https://juliastats.org/StatsModels.jl/stable/api/"><code>StatsModels.jl</code></a>'s <code>@formula</code>s to be able to express as formulas strandard survival models. </p><p>The current implementation only provides bindings for right censored survivals times (with <code>Surv(T,Δ)</code>, left-hand-side of formulas) and <em>stratified</em> estimators (with <code>Strata(x)</code>, right-hand-side of formulas), but extensions to more complex survival times (e.g. truncation and/or censoring from right and/or left) is planned (note: it would be straightforward and non-breaking). </p><ul><li><a href="#SurvivalBase.Strata-Tuple{Any}"><code>SurvivalBase.Strata</code></a></li><li><a href="#SurvivalBase.Surv-Tuple{Float64, Bool}"><code>SurvivalBase.Surv</code></a></li></ul><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="SurvivalBase.Strata-Tuple{Any}" href="#SurvivalBase.Strata-Tuple{Any}"><code>SurvivalBase.Strata</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Strata(x::Symbol)</code></pre><p>Create a <code>StrataTerm</code> object that holds a variable in the construction of a formula to stratify an estimator. </p><p>The behavior of the stratification depends on the fitted estimator: is is usally used on the right hand side of formulas from <a href="https://github.com/JuliaStats/StatsModels.jl"><code>StatsModels.jl</code></a> as</p><pre><code class="nohighlight hljs">@formula(Surv(time,status) ~ Strata(covariate1) + covariate 2)</code></pre><p>It then has a behavior that unufortunately heavily depends on the estimator, e.g. stratification of a log-rank-type test. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaSurv/SurvivalBase.jl/blob/0a304e65065b078d42055eb960a394934b20780b/src/Strata.jl#L1-L11">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="SurvivalBase.Surv-Tuple{Float64, Bool}" href="#SurvivalBase.Surv-Tuple{Float64, Bool}"><code>SurvivalBase.Surv</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Surv(T::Symbol, Δ::Symbol)</code></pre><p>Create a <code>SurvTerm</code> object that holds a tuple of variables <code>(T,Δ)</code> in the construction of a formula, usually on the left-hand-side, representing a right-censored output time <code>T</code> with its status indicatrix <code>Δ</code>: Δ being true means that the time was indeed observed, while false means censoring. </p><p>This information, usually on the left hand side a formula, has then a behavior that may depend on the estimator. It allows to use formulas from <a href="https://github.com/JuliaStats/StatsModels.jl"><code>StatsModels.jl</code></a> as follow: </p><pre><code class="nohighlight hljs">@formula(Surv(time,status) ~ covariate1 + covariate 2)</code></pre><p>This usage is common in, e.g., cox models. However, note that the <em>meaning</em> of the formula heavily depends on the model : for hazard regession and maximum likelyhood estimation, this does not mean the same thing. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaSurv/SurvivalBase.jl/blob/0a304e65065b078d42055eb960a394934b20780b/src/Surv.jl#L1-L11">source</a></section></article></article><nav class="docs-footer"><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="auto">Automatic (OS)</option><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 1.4.1 on <span class="colophon-date" title="Saturday 8 June 2024 15:50">Saturday 8 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> | ||
| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · SurvivalBase.jl</title><meta name="title" content="Home · SurvivalBase.jl"/><meta property="og:title" content="Home · SurvivalBase.jl"/><meta property="twitter:title" content="Home · SurvivalBase.jl"/><meta name="description" content="Documentation for SurvivalBase.jl."/><meta property="og:description" content="Documentation for SurvivalBase.jl."/><meta property="twitter:description" content="Documentation for SurvivalBase.jl."/><meta property="og:url" content="https://JuliaSurv.github.io/SurvivalBase.jl/"/><meta property="twitter:url" content="https://JuliaSurv.github.io/SurvivalBase.jl/"/><link rel="canonical" href="https://JuliaSurv.github.io/SurvivalBase.jl/"/><script data-outdated-warner src="assets/warner.js"></script><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/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/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="search_index.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></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>SurvivalBase.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></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"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/JuliaSurv/SurvivalBase.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/JuliaSurv/SurvivalBase.jl/blob/main/docs/src/index.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="SurvivalBase"><a class="docs-heading-anchor" href="#SurvivalBase">SurvivalBase</a><a id="SurvivalBase-1"></a><a class="docs-heading-anchor-permalink" href="#SurvivalBase" title="Permalink"></a></h1><p>The <a href="https://github.com/JuliaSurv/SurvivalBase.jl"><code>SurvivalBase.jl</code></a> package is intended to hold internals and shared infrastructure for several other front-facing packages in the <a href="https://github.com/JuliaSurv">JuliaSurv</a> organization, while having the minimal set of dependencies. Please do not use it directly and instead used other front-facing packages and interfaces from the organization.</p><p>Right now, the main infrastructure consists of special functions <code>Surv</code> and <code>Strata</code> used in <a href="https://juliastats.org/StatsModels.jl/stable/api/"><code>StatsModels.jl</code></a>'s <code>@formula</code>s to be able to express as formulas strandard survival models. </p><p>The current implementation only provides bindings for right censored survivals times (with <code>Surv(T,Δ)</code>, left-hand-side of formulas) and <em>stratified</em> estimators (with <code>Strata(x)</code>, right-hand-side of formulas), but extensions to more complex survival times (e.g. truncation and/or censoring from right and/or left) is planned (note: it would be straightforward and non-breaking). </p><ul><li><a href="#SurvivalBase.Strata-Tuple{Any}"><code>SurvivalBase.Strata</code></a></li><li><a href="#SurvivalBase.Surv-Tuple{Float64, Bool}"><code>SurvivalBase.Surv</code></a></li></ul><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="SurvivalBase.Strata-Tuple{Any}" href="#SurvivalBase.Strata-Tuple{Any}"><code>SurvivalBase.Strata</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Strata(x::Symbol)</code></pre><p>Create a <code>StrataTerm</code> object that holds a variable in the construction of a formula to stratify an estimator. </p><p>The behavior of the stratification depends on the fitted estimator: is is usally used on the right hand side of formulas from <a href="https://github.com/JuliaStats/StatsModels.jl"><code>StatsModels.jl</code></a> as</p><pre><code class="nohighlight hljs">@formula(Surv(time,status) ~ Strata(covariate1) + covariate 2)</code></pre><p>It then has a behavior that unufortunately heavily depends on the estimator, e.g. stratification of a log-rank-type test. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaSurv/SurvivalBase.jl/blob/892945f509ddbc817c0d353963486ba5ae6395d6/src/Strata.jl#L1-L11">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="SurvivalBase.Surv-Tuple{Float64, Bool}" href="#SurvivalBase.Surv-Tuple{Float64, Bool}"><code>SurvivalBase.Surv</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Surv(T::Symbol, Δ::Symbol)</code></pre><p>Create a <code>SurvTerm</code> object that holds a tuple of variables <code>(T,Δ)</code> in the construction of a formula, usually on the left-hand-side, representing a right-censored output time <code>T</code> with its status indicatrix <code>Δ</code>: Δ being true means that the time was indeed observed, while false means censoring. </p><p>This information, usually on the left hand side a formula, has then a behavior that may depend on the estimator. It allows to use formulas from <a href="https://github.com/JuliaStats/StatsModels.jl"><code>StatsModels.jl</code></a> as follow: </p><pre><code class="nohighlight hljs">@formula(Surv(time,status) ~ covariate1 + covariate 2)</code></pre><p>This usage is common in, e.g., cox models. However, note that the <em>meaning</em> of the formula heavily depends on the model : for hazard regession and maximum likelyhood estimation, this does not mean the same thing. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaSurv/SurvivalBase.jl/blob/892945f509ddbc817c0d353963486ba5ae6395d6/src/Surv.jl#L1-L11">source</a></section></article></article><nav class="docs-footer"><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="auto">Automatic (OS)</option><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 1.4.1 on <span class="colophon-date" title="Monday 10 June 2024 18:53">Monday 10 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |