build based on c43c18e

dev/index.html

@@ -7,4 +7,4 @@
 LogitLink
 LogLink
 ProbitLink
-SqrtLink</code></pre><h2 id="Manual-Outline"><a class="docs-heading-anchor" href="#Manual-Outline">Manual Outline</a><a id="Manual-Outline-1"></a><a class="docs-heading-anchor-permalink" href="#Manual-Outline" title="Permalink"></a></h2><ul><li><a href="man/getting_started/#Getting-started">Getting started</a></li><li class="no-marker"><ul><li><a href="man/getting_started/#Installation">Installation</a></li><li><a href="man/getting_started/#Typical-Workflow">Typical Workflow</a></li><li><a href="man/getting_started/#Parallel-computing">Parallel computing</a></li><li><a href="man/getting_started/#Running-from-command-line-as-script">Running from command line as script</a></li></ul></li><li><a href="man/examples/#Examples">Examples</a></li><li class="no-marker"><ul><li><a href="man/examples/#Using-MendelIHT.jl">Using MendelIHT.jl</a></li><li><a href="man/examples/#Parallel-computing">Parallel computing</a></li><li><a href="man/examples/#Example-1:-GWAS-with-PLINK/BGEN/VCF-files">Example 1: GWAS with PLINK/BGEN/VCF files</a></li><li><a href="man/examples/#Example-2:-How-to-simulate-data">Example 2: How to simulate data</a></li><li><a href="man/examples/#Example-3:-Logistic/Poisson/Negative-binomial-GWAS">Example 3: Logistic/Poisson/Negative-binomial GWAS</a></li><li><a href="man/examples/#Example-4:-Running-IHT-on-general-matrices">Example 4: Running IHT on general matrices</a></li><li><a href="man/examples/#Example-5:-Group-IHT">Example 5: Group IHT</a></li><li><a href="man/examples/#Example-6:-Linear-Regression-with-prior-weights">Example 6: Linear Regression with prior weights</a></li><li><a href="man/examples/#Example-7:-Multivariate-IHT">Example 7: Multivariate IHT</a></li><li><a href="man/examples/#Other-examples-and-functionalities">Other examples and functionalities</a></li></ul></li><li><a href="man/math/#Details-of-Parameter-Estimation">Details of Parameter Estimation</a></li><li class="no-marker"><ul><li><a href="man/math/#Generalized-linear-models">Generalized linear models</a></li><li><a href="man/math/#Loglikelihood,-gradient,-and-expected-information">Loglikelihood, gradient, and expected information</a></li><li><a href="man/math/#Iterative-hard-thresholding">Iterative hard thresholding</a></li><li><a href="man/math/#Nuisance-parameter-estimation">Nuisance parameter estimation</a></li></ul></li><li><a href="man/contributing/#Contributing">Contributing</a></li><li class="no-marker"><ul><li><a href="man/contributing/#Bug-Fixes-and-User-Support">Bug Fixes &amp; User Support</a></li><li><a href="man/contributing/#Citation">Citation</a></li></ul></li><li><a href="man/api/#API">API</a></li><li class="no-marker"><ul><li><a href="man/api/#Wrapper-Functions">Wrapper Functions</a></li><li><a href="man/api/#Core-Functions">Core Functions</a></li><li><a href="man/api/#Specifying-Groups-and-Weights">Specifying Groups and Weights</a></li><li><a href="man/api/#Simulation-Utilities">Simulation Utilities</a></li><li><a href="man/api/#Other-Useful-Functions">Other Useful Functions</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/getting_started/">Getting Started »</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="Saturday 9 September 2023 02:13">Saturday 9 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+SqrtLink</code></pre><h2 id="Manual-Outline"><a class="docs-heading-anchor" href="#Manual-Outline">Manual Outline</a><a id="Manual-Outline-1"></a><a class="docs-heading-anchor-permalink" href="#Manual-Outline" title="Permalink"></a></h2><ul><li><a href="man/getting_started/#Getting-started">Getting started</a></li><li class="no-marker"><ul><li><a href="man/getting_started/#Installation">Installation</a></li><li><a href="man/getting_started/#Typical-Workflow">Typical Workflow</a></li><li><a href="man/getting_started/#Parallel-computing">Parallel computing</a></li><li><a href="man/getting_started/#Running-from-command-line-as-script">Running from command line as script</a></li></ul></li><li><a href="man/examples/#Examples">Examples</a></li><li class="no-marker"><ul><li><a href="man/examples/#Using-MendelIHT.jl">Using MendelIHT.jl</a></li><li><a href="man/examples/#Parallel-computing">Parallel computing</a></li><li><a href="man/examples/#Example-1:-GWAS-with-PLINK/BGEN/VCF-files">Example 1: GWAS with PLINK/BGEN/VCF files</a></li><li><a href="man/examples/#Example-2:-How-to-simulate-data">Example 2: How to simulate data</a></li><li><a href="man/examples/#Example-3:-Logistic/Poisson/Negative-binomial-GWAS">Example 3: Logistic/Poisson/Negative-binomial GWAS</a></li><li><a href="man/examples/#Example-4:-Running-IHT-on-general-matrices">Example 4: Running IHT on general matrices</a></li><li><a href="man/examples/#Example-5:-Group-IHT">Example 5: Group IHT</a></li><li><a href="man/examples/#Example-6:-Linear-Regression-with-prior-weights">Example 6: Linear Regression with prior weights</a></li><li><a href="man/examples/#Example-7:-Multivariate-IHT">Example 7: Multivariate IHT</a></li><li><a href="man/examples/#Other-examples-and-functionalities">Other examples and functionalities</a></li></ul></li><li><a href="man/math/#Details-of-Parameter-Estimation">Details of Parameter Estimation</a></li><li class="no-marker"><ul><li><a href="man/math/#Generalized-linear-models">Generalized linear models</a></li><li><a href="man/math/#Loglikelihood,-gradient,-and-expected-information">Loglikelihood, gradient, and expected information</a></li><li><a href="man/math/#Iterative-hard-thresholding">Iterative hard thresholding</a></li><li><a href="man/math/#Nuisance-parameter-estimation">Nuisance parameter estimation</a></li></ul></li><li><a href="man/contributing/#Contributing">Contributing</a></li><li class="no-marker"><ul><li><a href="man/contributing/#Bug-Fixes-and-User-Support">Bug Fixes &amp; User Support</a></li><li><a href="man/contributing/#Citation">Citation</a></li></ul></li><li><a href="man/api/#API">API</a></li><li class="no-marker"><ul><li><a href="man/api/#Wrapper-Functions">Wrapper Functions</a></li><li><a href="man/api/#Core-Functions">Core Functions</a></li><li><a href="man/api/#Specifying-Groups-and-Weights">Specifying Groups and Weights</a></li><li><a href="man/api/#Simulation-Utilities">Simulation Utilities</a></li><li><a href="man/api/#Other-Useful-Functions">Other Useful Functions</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/getting_started/">Getting Started »</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="Sunday 10 September 2023 02:16">Sunday 10 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/man/FAQ/index.html

@@ -16,4 +16,4 @@
 @show add(0, 3)          # 0 + b + c using b = 3 and default value for c
 @show add(0, 5, c=10);   # 0 + b + c using b = 5 and c = 10</code></pre><pre><code class="nohighlight hljs">add(0) = 3
 add(0, 3) = 5
-add(0, 5, c = 10) = 15</code></pre><h2 id="Will-IHT-work-on-sequence/imputed-data?"><a class="docs-heading-anchor" href="#Will-IHT-work-on-sequence/imputed-data?">Will IHT work on sequence/imputed data?</a><a id="Will-IHT-work-on-sequence/imputed-data?-1"></a><a class="docs-heading-anchor-permalink" href="#Will-IHT-work-on-sequence/imputed-data?" title="Permalink"></a></h2><p>If someone can test this out and tell us, that would be extremely helpful.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../contributing/">« Contributing</a><a class="docs-footer-nextpage" href="../api/">API »</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="Saturday 9 September 2023 02:13">Saturday 9 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+add(0, 5, c = 10) = 15</code></pre><h2 id="Will-IHT-work-on-sequence/imputed-data?"><a class="docs-heading-anchor" href="#Will-IHT-work-on-sequence/imputed-data?">Will IHT work on sequence/imputed data?</a><a id="Will-IHT-work-on-sequence/imputed-data?-1"></a><a class="docs-heading-anchor-permalink" href="#Will-IHT-work-on-sequence/imputed-data?" title="Permalink"></a></h2><p>If someone can test this out and tell us, that would be extremely helpful.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../contributing/">« Contributing</a><a class="docs-footer-nextpage" href="../api/">API »</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="Sunday 10 September 2023 02:16">Sunday 10 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>