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README.html
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<body>
<h1 id="rmoss-semiparametric-efficient-survival-analysis"><code>R</code>/MOSS: Semiparametric Efficient Survival Analysis</h1>
<p><a href="https://travis-ci.org/wilsoncai1992/MOSS"><img 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alt="Travis-CI Build Status" /></a> <a href="https://ci.appveyor.com/project/wilsoncai1992/MOSS"><img src="data:image/svg+xml;base64,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" alt="Appveyor Build Status" /></a> <a href="https://codecov.io/gh/wilsoncai1992/MOSS"><img src="data:image/svg+xml;base64,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" alt="codecov" /></a> <a href="https://www.repostatus.org/#active"><img src="data:image/svg+xml;base64,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" alt="Project Status: Active – The project has reached a stable, usable state and is being actively developed." /></a> <a href="https://www.gnu.org/licenses/gpl-2.0"><img src="data:image/svg+xml;charset=utf-8;base64,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" alt="License: GPL v2" /></a> <a href="http://cran.rstudio.com/web/packages/MOSS/index.html"><img src="data:image/svg+xml; charset=utf-8;base64,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" alt="CRAN_Status_Badge" /></a> <a href="http://cran.rstudio.com/web/packages/MOSS/index.html"><img src="data:image/svg+xml; 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<p>MOSS performs ensemble machine learning and Targeted Maximum Likelihood (TMLE) to estimate the counter-factual marginal survival functions, while non-parametrically adjusting for measured confounding. TMLE approach is employed to create a doubly robust and semi-parametrically efficient estimator. Simultaneous confidence bands of the entire curve is also available for inference. User can specify what kind of static intervention on treatment (exposure).</p>
<p>The following comparable methods are also included in the package for you to easily compare methods: - Inverse censoring probability weighted (IPCW) - Locally efficient one-step estimator (estimating equation methods)</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">install.packages</span>(<span class="st">'MOSS'</span>)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2">devtools<span class="op">::</span><span class="kw">install_github</span>(<span class="st">'wilsoncai1992/MOSS'</span>)</a></code></pre></div>
<h2 id="documentation">Documentation</h2>
<ul>
<li>To see all available package documentation:</li>
</ul>
<!-- end list -->
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">?MOSS</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">help</span>(<span class="dt">package =</span> <span class="st">'MOSS'</span>)</a></code></pre></div>
<h2 id="brief-overview">Brief overview</h2>
<h3 id="data-structure">Data structure</h3>
<p>The data input of all methods in the package should be an <code>R</code> <code>data.frame</code> in the following survival long data format:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># ID W A T.tilde delta</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># 1 1 0 0 95 1</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 2 2 1 1 1 0</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 3 3 0 0 215 1</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 4 4 1 1 15 1</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 5 5 0 0 73 1</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 6 6 0 0 15 1</span></a></code></pre></div>
<h3 id="steps-of-analysis">Steps of analysis</h3>
<ol>
<li>perform SuperLearner fit of the conditional survival function of failure event, conditional survival function of censoring event, propensity scores (<code>initial_sl_fit</code>)</li>
<li>perform TMLE adjustment of the conditional survival fit (<code>MOSS_hazard</code>)</li>
<li>simultaneous confidence band (<code>compute_simultaneous_ci</code>)</li>
</ol>
<h2 id="citation">Citation</h2>
<p>To cite <code>MOSS</code> in publications, please use:</p>
<blockquote>
<p>Cai W, van der Laan MJ (2019+). <em>One-step TMLE for time-to-event outcomes.</em> Working paper.</p>
</blockquote>
<h2 id="funding">Funding</h2>
<h2 id="copyright">Copyright</h2>
<p>This software is distributed under the GPL-2 license.</p>
<h2 id="community-guidelines">Community Guidelines</h2>
<p>Feedback, bug reports (and fixes!), and feature requests are welcome; file issues or seek support <a href="https://github.com/wilsoncai1992/MOSS/issues">here</a>.</p>
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