From a99fcb68f599ceec5b9ccf9207ad3eae87afe340 Mon Sep 17 00:00:00 2001
From: AparicioJohan <johan.aparicio@correounivalle.edu.co>
Date: Wed, 3 Jan 2024 10:13:00 -0600
Subject: [PATCH] Updates in documentation
---
docs/404.html | 2 +-
docs/CODE_OF_CONDUCT.html | 3 +-
docs/LICENSE-text.html | 2 +-
docs/LICENSE.html | 3 +-
docs/authors.html | 6 +-
docs/index.html | 36 +++++---
docs/news/index.html | 13 ++-
docs/pkgdown.yml | 6 +-
docs/reference/Dar16C_hiP.html | 61 +++++++++++--
docs/reference/GBLUPs.html | 10 +--
docs/reference/LSD.html | 125 +++++++++++++++++++++++++++
docs/reference/desireFormat.html | 2 +-
docs/reference/index.html | 12 ++-
docs/reference/marker_plot.html | 7 +-
docs/reference/mod.list.html | 91 +++++++++++++++++++
docs/reference/run_app.html | 2 +-
docs/reference/spatial.aud.html | 2 +-
docs/reference/spatial.selector.html | 2 +-
docs/reference/spatial.single.html | 2 +-
docs/reference/stageMET.html | 2 +-
docs/reference/stats.spatial.html | 2 +-
docs/sitemap.xml | 6 ++
22 files changed, 353 insertions(+), 44 deletions(-)
create mode 100644 docs/reference/LSD.html
create mode 100644 docs/reference/mod.list.html
diff --git a/docs/404.html b/docs/404.html
index a212296..1da34c3 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -96,7 +96,7 @@ <h1>Page not found (404)</h1>
<div class="pkgdown">
<p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer>
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
index 8ad4d49..610bca9 100644
--- a/docs/CODE_OF_CONDUCT.html
+++ b/docs/CODE_OF_CONDUCT.html
@@ -47,6 +47,7 @@ <h1>Contributor Code of Conduct</h1>
</div>
<div id="contributor-code-of-conduct" class="section level1">
+
<p>As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.</p>
<p>We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.</p>
<p>Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.</p>
@@ -70,7 +71,7 @@ <h1>Contributor Code of Conduct</h1>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index a673dc4..fb4618e 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -65,7 +65,7 @@ <h1>License</h1>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
index c8cb15d..53cc327 100644
--- a/docs/LICENSE.html
+++ b/docs/LICENSE.html
@@ -47,6 +47,7 @@ <h1>MIT License</h1>
</div>
<div id="mit-license" class="section level1">
+
<p>Copyright (c) 2020 Johan Aparicio</p>
<p>Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:</p>
<p>The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.</p>
@@ -68,7 +69,7 @@ <h1>MIT License</h1>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/authors.html b/docs/authors.html
index afc6723..cb15252 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -61,14 +61,14 @@ <h1 id="citation">Citation</h1>
</div>
- <p>Aparicio J (2022).
+ <p>Aparicio J (2024).
<em>MrBean: Web application for analyzing field experiments</em>.
R package version 2.0.9, <a href="https://github.com/AparicioJohan/MrBeanApp" class="external-link">https://github.com/AparicioJohan/MrBeanApp</a>.
</p>
<pre>@Manual{,
title = {MrBean: Web application for analyzing field experiments},
author = {Johan Aparicio},
- year = {2022},
+ year = {2024},
note = {R package version 2.0.9},
url = {https://github.com/AparicioJohan/MrBeanApp},
}</pre>
@@ -84,7 +84,7 @@ <h1 id="citation">Citation</h1>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/index.html b/docs/index.html
index 776e037..46b15ae 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -76,9 +76,9 @@
<div class="section level1">
<div class="page-header"><h1 id="mrbean-">MrBean <img src="reference/figures/hex-MrBean.png" width="120px" align="right"><a class="anchor" aria-label="anchor" href="#mrbean-"></a>
</h1></div>
-
+<p><a href="https://www.tidyverse.org/lifecycle/#experimental" class="external-link"><img src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt="Lifecycle: experimental"></a></p>
<p>Mr. Bean is an easy to use R-Shiny web-app that simplifies the analysis of large-scale plant breeding experimental analysis by using the power and versatility of Linear Mixed Models (LMM). This app combines the analytical robustness and speed of ASReml and SpATS with the visual power offered by R. Mr. Bean provides a graphical workflow for importing data, identifying outliers, and fitting field data using LMM with or without spatial correction. The results are BLUPs/BLUEs predictions and heritabilities for single-environmental experiments or multiple-environmental trial (MET) analysis. In addition, Mr. Bean also provides a module for exploring results from METs using several graphical and multivariate techniques.</p>
-<p><a href="https://mrpackages.netlify.app/" class="external-link">https://mrpackages.netlify.app/</a> <br><a href="https://apariciojohan.github.io/MrBeanApp/" class="external-link">https://apariciojohan.github.io/MrBeanApp/</a></p>
+<p><a href="https://apariciojohan.github.io/MrBeanApp/" class="external-link">https://apariciojohan.github.io/MrBeanApp/</a></p>
<div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h2>
@@ -100,10 +100,31 @@ <h2 id="example">Example<a class="anchor" aria-label="anchor" href="#example"></
<h2 id="demo">Demo<a class="anchor" aria-label="anchor" href="#demo"></a>
</h2>
<p>A running demo is on <a href="https://beanteam.shinyapps.io/MrBean_BETA/" class="external-link">shinyapps.io</a>.</p>
-<div class="row"><div class="card"><p><a href="https://beanteam.shinyapps.io/MrBean_BETA/" target="_blank" class="external-link"><img src="reference/figures/desktop_update.png"></a></p></div></div>
+<div class="row">
+<div class="card">
+<p><a href="https://beanteam.shinyapps.io/MrBean_BETA/" target="_blank" class="external-link"><img src="reference/figures/desktop_update.png"></a></p>
+</div>
+</div>
+<div class="section level3">
+<h3 id="citation">Citation<a class="anchor" aria-label="anchor" href="#citation"></a>
+</h3>
+<blockquote>
+<p><em>Aparicio J, Gezan SA, Ariza-Suarez D, Raatz B, Diaz S, Heilman-Morales A and Lobaton J (2024)</em> Mr.Bean: a comprehensive statistical and visualization application for modeling agricultural field trials data. <strong>Front. Plant Sci. 14:1290078.</strong>; <a href="https://doi.org/10.3389/fpls.2023.1290078" class="external-link">https://doi.org/10.3389/fpls.2023.1290078</a></p>
+</blockquote>
+</div>
+<div class="section level3">
+<h3 id="acknowledgments">Acknowledgments<a class="anchor" aria-label="anchor" href="#acknowledgments"></a>
+</h3>
+<blockquote>
+<ul>
+<li><a href="https://alliancebioversityciat.org/" class="external-link">Bean Breeding Program - International Center for Tropical Agriculture (CIAT)</a></li>
+<li><a href="https://sites.google.com/ndsu.edu/plsc-bpdm/home" class="external-link">Big Data Pipeline Unit (NDSU)</a></li>
+</ul>
+</blockquote>
<p><br></p>
<p>Please note that the ‘MrBean’ project is released with a <a href="CODE_OF_CONDUCT.html">Contributor Code of Conduct</a>. By contributing to this project, you agree to abide by its terms.</p>
</div>
+</div>
</div>
</div>
@@ -145,12 +166,7 @@ <h2 data-toc-skip>Developers</h2>
</ul>
</div>
-<div class="dev-status">
-<h2 data-toc-skip>Dev status</h2>
-<ul class="list-unstyled">
-<li><a href="https://www.tidyverse.org/lifecycle/#experimental" class="external-link"><img src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt="Lifecycle: experimental"></a></li>
-</ul>
-</div>
+
</div>
</div>
@@ -163,7 +179,7 @@ <h2 data-toc-skip>Dev status</h2>
<div class="pkgdown">
<p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer>
diff --git a/docs/news/index.html b/docs/news/index.html
index a6d8776..05c4b85 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -49,7 +49,10 @@ <h1 data-toc-skip>Changelog <small></small></h1>
<div class="section level2">
<h2 class="page-header" data-toc-text="2.0.9" id="mrbean-209">MrBean 2.0.9<a class="anchor" aria-label="anchor" href="#mrbean-209"></a></h2>
-<ul><li>Module GBLUP implemented.<ul><li>Added a plot and a table with variance components estimates.</li>
+<ul><li><p>LSD for single-site spatial analysis with SpATS.</p></li>
+<li>
+<p>Module GBLUP implemented.</p>
+<ul><li>Added a plot and a table with variance components estimates.</li>
<li>Added the estimation of genomic heritability or marker-based heritability.</li>
<li>Added a plot for checking the accuracy of the model by trait. (Observed values vs Predicted values).</li>
<li>Added action button for downloading a summary of the analysis.</li>
@@ -62,7 +65,8 @@ <h2 class="page-header" data-toc-text="2.0.9" id="mrbean-209">MrBean 2.0.9<a cla
<li>Added a plot with Estimated Squared-Marker effect for multiple traits. In addition, if the genetic map was imported you will be able to visualize this plot with colors by chromosome (similar to a manhattan plot).</li>
<li>Added action button for downloading markers effects.</li>
<li>Added an additional window for seeing the ranking of the GEBVs.</li>
-</ul></li></ul></div>
+</ul></li>
+</ul></div>
<div class="section level2">
<h2 class="page-header" data-toc-text="2.0.8" id="mrbean-208">MrBean 2.0.8<a class="anchor" aria-label="anchor" href="#mrbean-208"></a></h2>
<ul><li>Improved writing style.</li>
@@ -70,7 +74,8 @@ <h2 class="page-header" data-toc-text="2.0.8" id="mrbean-208">MrBean 2.0.8<a cla
</ul></div>
<div class="section level2">
<h2 class="page-header" data-toc-text="0.0.1" id="mrbean-001">MrBean 0.0.1<a class="anchor" aria-label="anchor" href="#mrbean-001"></a></h2>
-<ul><li>First version.</li></ul></div>
+<ul><li>First version.</li>
+</ul></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -85,7 +90,7 @@ <h2 class="page-header" data-toc-text="0.0.1" id="mrbean-001">MrBean 0.0.1<a cla
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index de0cde7..d7cee76 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,6 +1,6 @@
-pandoc: 2.14.0.3
-pkgdown: 2.0.6
+pandoc: 3.1.1
+pkgdown: 2.0.7
pkgdown_sha: ~
articles: {}
-last_built: 2022-08-08T19:12Z
+last_built: 2024-01-03T16:11Z
diff --git a/docs/reference/Dar16C_hiP.html b/docs/reference/Dar16C_hiP.html
index 353ae0b..a1c935a 100644
--- a/docs/reference/Dar16C_hiP.html
+++ b/docs/reference/Dar16C_hiP.html
@@ -1,5 +1,5 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Example data. — Dar16C_hiP • MrBean</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/paper/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Example data. — Dar16C_hiP"><meta property="og:description" content="A dataset containing an alpha lattice design."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>A dataset containing an alpha lattice design. — Dar16C_hiP • MrBean</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/paper/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="A dataset containing an alpha lattice design. — Dar16C_hiP"><meta property="og:description" content="A dataset containing an alpha lattice design."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -43,7 +43,7 @@
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Example data.</h1>
+ <h1>A dataset containing an alpha lattice design.</h1>
<small class="dont-index">Source: <a href="https://github.com/AparicioJohan/MrBeanApp/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="hidden name"><code>Dar16C_hiP.Rd</code></div>
</div>
@@ -58,8 +58,59 @@ <h1>Example data.</h1>
<div id="format">
<h2>Format</h2>
- <p>A data frame with 792 rows and 18 columns:</p>
- </div>
+ <p>data frame</p><dl><dt>dataset</dt>
+<dd><p>description here</p></dd>
+
+ <dt>unique_identifier</dt>
+<dd><p>description here</p></dd>
+
+ <dt>plot</dt>
+<dd><p>description here</p></dd>
+
+ <dt>line</dt>
+<dd><p>description here</p></dd>
+
+ <dt>rep</dt>
+<dd><p>description here</p></dd>
+
+ <dt>treatment</dt>
+<dd><p>description here</p></dd>
+
+ <dt>block</dt>
+<dd><p>description here</p></dd>
+
+ <dt>row</dt>
+<dd><p>description here</p></dd>
+
+ <dt>col</dt>
+<dd><p>description here</p></dd>
+
+ <dt>DF</dt>
+<dd><p>description here</p></dd>
+
+ <dt>DPM</dt>
+<dd><p>description here</p></dd>
+
+ <dt>PLHA</dt>
+<dd><p>description here</p></dd>
+
+ <dt>POM_c2</dt>
+<dd><p>description here</p></dd>
+
+ <dt>SW100</dt>
+<dd><p>description here</p></dd>
+
+ <dt>TSW</dt>
+<dd><p>description here</p></dd>
+
+ <dt>YDHA</dt>
+<dd><p>description here</p></dd>
+
+ <dt>YDHPL</dt>
+<dd><p>description here</p></dd>
+
+
+</dl></div>
<div id="source">
<h2>Source</h2>
<p><a href="CIAT:%20Bean%20Breeding%20Program">CIAT: Bean Breeding Program</a></p>
@@ -77,7 +128,7 @@ <h2>Source</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/GBLUPs.html b/docs/reference/GBLUPs.html
index 81df1d7..90d4376 100644
--- a/docs/reference/GBLUPs.html
+++ b/docs/reference/GBLUPs.html
@@ -73,6 +73,10 @@ <h2>Arguments</h2>
and the rest containing marker information in format (-1, 0 , 1).</p></dd>
+<dt>genotype</dt>
+<dd><p>string with the genotype name</p></dd>
+
+
<dt>traits</dt>
<dd><p>vector with the traits to be analyzed</p></dd>
@@ -80,10 +84,6 @@ <h2>Arguments</h2>
<dt>method</dt>
<dd><p>"GBLUP", "rrBLUP" or "mix" ("mix" in progress)</p></dd>
-
-<dt>genoype</dt>
-<dd><p>string with the genotype name</p></dd>
-
</dl></div>
<div id="value">
<h2>Value</h2>
@@ -117,7 +117,7 @@ <h2>Examples</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/LSD.html b/docs/reference/LSD.html
new file mode 100644
index 0000000..96b2824
--- /dev/null
+++ b/docs/reference/LSD.html
@@ -0,0 +1,125 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>LSD SpATS — LSD • MrBean</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/paper/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="LSD SpATS — LSD"><meta property="og:description" content="LSD SpATS"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
+
+ <div class="container template-reference-topic">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
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+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">MrBean</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">2.0.9</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav"><li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/AparicioJohan/MrBeanApp/" class="external-link">
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+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>LSD SpATS</h1>
+ <small class="dont-index">Source: <a href="https://github.com/AparicioJohan/MrBeanApp/blob/HEAD/R/SpATSplus.R" class="external-link"><code>R/SpATSplus.R</code></a></small>
+ <div class="hidden name"><code>LSD.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>LSD SpATS</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">LSD</span><span class="op">(</span><span class="va">model</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, data.frame <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>model</dt>
+<dd><p>an object of class SpATS as produced by SpATS()</p></dd>
+
+
+<dt>alpha</dt>
+<dd><p>Level of risk for the test (0.05 by default)</p></dd>
+
+
+<dt>data.frame</dt>
+<dd><p>whether return only the LSD value or a complete summary
+FALSE by default</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>data.frame or a lsd value depending on the data.frame argument</p>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># library(SpATS)</span></span></span>
+<span class="r-in"><span><span class="co"># data(wheatdata)</span></span></span>
+<span class="r-in"><span><span class="co"># wheatdata$R <- as.factor(wheatdata$row)</span></span></span>
+<span class="r-in"><span><span class="co"># wheatdata$C <- as.factor(wheatdata$col)</span></span></span>
+<span class="r-in"><span><span class="co">#</span></span></span>
+<span class="r-in"><span><span class="co"># m1 <- SpATS(</span></span></span>
+<span class="r-in"><span><span class="co"># response = "yield",</span></span></span>
+<span class="r-in"><span><span class="co"># spatial = ~ PSANOVA(col, row, nseg = c(10, 20), nest.div = 2),</span></span></span>
+<span class="r-in"><span><span class="co"># genotype = "geno",</span></span></span>
+<span class="r-in"><span><span class="co"># genotype.as.random = FALSE,</span></span></span>
+<span class="r-in"><span><span class="co"># fixed = ~ colcode + rowcode,</span></span></span>
+<span class="r-in"><span><span class="co"># random = ~ R + C,</span></span></span>
+<span class="r-in"><span><span class="co"># data = wheatdata,</span></span></span>
+<span class="r-in"><span><span class="co"># control = list(tolerance = 1e-03)</span></span></span>
+<span class="r-in"><span><span class="co"># )</span></span></span>
+<span class="r-in"><span><span class="co"># LSD(m1, data.frame = TRUE)</span></span></span>
+<span class="r-in"></span>
+</code></pre></div>
+ </div>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+ </nav></div>
+</div>
+
+
+ <footer><div class="copyright">
+ <p></p><p>Developed by Johan Aparicio.</p>
+</div>
+
+<div class="pkgdown">
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+ </footer></div>
+
+
+
+
+
+
+ </body></html>
+
diff --git a/docs/reference/desireFormat.html b/docs/reference/desireFormat.html
index 42e9edb..3a763a2 100644
--- a/docs/reference/desireFormat.html
+++ b/docs/reference/desireFormat.html
@@ -119,7 +119,7 @@ <h2>Examples</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 5c4719b..ec16828 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -53,7 +53,7 @@ <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" ari
</tr></tbody><tbody><tr><td>
<p><code><a href="Dar16C_hiP.html">Dar16C_hiP</a></code> </p>
</td>
- <td><p>Example data.</p></td>
+ <td><p>A dataset containing an alpha lattice design.</p></td>
</tr><tr><td>
<p><code><a href="desireFormat.html">desireFormat()</a></code> </p>
</td>
@@ -62,10 +62,18 @@ <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" ari
<p><code><a href="GBLUPs.html">GBLUPs()</a></code> </p>
</td>
<td><p>GBLUP and rrBLUP estimation</p></td>
+ </tr><tr><td>
+ <p><code><a href="LSD.html">LSD()</a></code> </p>
+ </td>
+ <td><p>LSD SpATS</p></td>
</tr><tr><td>
<p><code><a href="marker_plot.html">marker_plot()</a></code> </p>
</td>
<td><p>Marker Plot</p></td>
+ </tr><tr><td>
+ <p><code><a href="mod.list.html">mod.list</a></code> </p>
+ </td>
+ <td><p>A list of datasets</p></td>
</tr><tr><td>
<p><code><a href="run_app.html">run_app()</a></code> </p>
</td>
@@ -103,7 +111,7 @@ <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" ari
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/marker_plot.html b/docs/reference/marker_plot.html
index de7d010..34b225b 100644
--- a/docs/reference/marker_plot.html
+++ b/docs/reference/marker_plot.html
@@ -58,6 +58,7 @@ <h1>Marker Plot</h1>
<span> map <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> trait_selected <span class="op">=</span> <span class="st">""</span>,</span>
<span> type <span class="op">=</span> <span class="st">"point"</span>,</span>
+<span> point_size <span class="op">=</span> <span class="fl">4</span>,</span>
<span> legend_size <span class="op">=</span> <span class="fl">15</span>,</span>
<span> alpha <span class="op">=</span> <span class="fl">1</span></span>
<span><span class="op">)</span></span></code></pre></div>
@@ -82,6 +83,10 @@ <h2>Arguments</h2>
(point by default).</p></dd>
+<dt>point_size</dt>
+<dd><p>numeric value to define the size of the points</p></dd>
+
+
<dt>legend_size</dt>
<dd><p>numeric value to define the size of the theme
(15 by default).</p></dd>
@@ -122,7 +127,7 @@ <h2>Examples</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/mod.list.html b/docs/reference/mod.list.html
new file mode 100644
index 0000000..7ee3c04
--- /dev/null
+++ b/docs/reference/mod.list.html
@@ -0,0 +1,91 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>A list of datasets — mod.list • MrBean</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/paper/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="A list of datasets — mod.list"><meta property="og:description" content="mod.list is an object that pass a dataset to the environment variables"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
+
+ <div class="container template-reference-topic">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">MrBean</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">2.0.9</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav"><li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/AparicioJohan/MrBeanApp/" class="external-link">
+ <span class="fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>A list of datasets</h1>
+ <small class="dont-index">Source: <a href="https://github.com/AparicioJohan/MrBeanApp/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
+ <div class="hidden name"><code>mod.list.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>mod.list is an object that pass a dataset to the environment variables</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">mod.list</span></span></code></pre></div>
+ </div>
+
+ <div id="format">
+ <h2>Format</h2>
+ <p>a list</p>
+ </div>
+ <div id="source">
+ <h2>Source</h2>
+ <p><a href="CIAT:%20Bean%20Breeding%20Program">CIAT: Bean Breeding Program</a></p>
+ </div>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+ </nav></div>
+</div>
+
+
+ <footer><div class="copyright">
+ <p></p><p>Developed by Johan Aparicio.</p>
+</div>
+
+<div class="pkgdown">
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+ </footer></div>
+
+
+
+
+
+
+ </body></html>
+
diff --git a/docs/reference/run_app.html b/docs/reference/run_app.html
index 4b82c5a..96980f7 100644
--- a/docs/reference/run_app.html
+++ b/docs/reference/run_app.html
@@ -75,7 +75,7 @@ <h2>Arguments</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/spatial.aud.html b/docs/reference/spatial.aud.html
index f746ff4..2a41c73 100644
--- a/docs/reference/spatial.aud.html
+++ b/docs/reference/spatial.aud.html
@@ -178,7 +178,7 @@ <h2>Examples</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/spatial.selector.html b/docs/reference/spatial.selector.html
index 8d08c77..5ad7d12 100644
--- a/docs/reference/spatial.selector.html
+++ b/docs/reference/spatial.selector.html
@@ -219,7 +219,7 @@ <h2>Examples</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/spatial.single.html b/docs/reference/spatial.single.html
index 70c4837..675e299 100644
--- a/docs/reference/spatial.single.html
+++ b/docs/reference/spatial.single.html
@@ -236,7 +236,7 @@ <h2>Examples</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/stageMET.html b/docs/reference/stageMET.html
index 06fdda1..1b7797b 100644
--- a/docs/reference/stageMET.html
+++ b/docs/reference/stageMET.html
@@ -149,7 +149,7 @@ <h2>Examples</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/reference/stats.spatial.html b/docs/reference/stats.spatial.html
index b698a38..64480ef 100644
--- a/docs/reference/stats.spatial.html
+++ b/docs/reference/stats.spatial.html
@@ -129,7 +129,7 @@ <h2>Examples</h2>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 21196cb..391a268 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -33,9 +33,15 @@
<url>
<loc>/reference/index.html</loc>
</url>
+ <url>
+ <loc>/reference/LSD.html</loc>
+ </url>
<url>
<loc>/reference/marker_plot.html</loc>
</url>
+ <url>
+ <loc>/reference/mod.list.html</loc>
+ </url>
<url>
<loc>/reference/R.square.html</loc>
</url>