diff --git a/404.html b/404.html
index 3175dc2..001687b 100644
--- a/404.html
+++ b/404.html
@@ -18,7 +18,7 @@
 <link href="https://ruthkr.github.io/greatR/deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
 <!-- 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">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://ruthkr.github.io/greatR/pkgdown.js"></script><link href="https://ruthkr.github.io/greatR/extra.css" rel="stylesheet">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://ruthkr.github.io/greatR/pkgdown.js"></script><link href="https://ruthkr.github.io/greatR/extra.css" rel="stylesheet">
 <meta property="og:title" content="Page not found (404)">
 <meta property="og:image" content="https://ruthkr.github.io/greatR/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]>
@@ -30,11 +30,11 @@
     <a href="https://ruthkr.github.io/greatR/#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="https://ruthkr.github.io/greatR/index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -92,13 +92,11 @@ <h6 class="dropdown-header" data-toc-skip>Others</h6>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/LICENSE.html b/LICENSE.html
index 02cf55e..1bca0d1 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -1,16 +1,16 @@
 <!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, shrink-to-fit=no"><title>GNU General Public License • greatR</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"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet"><meta property="og:title" content="GNU General Public License"><meta property="og:image" content="https://ruthkr.github.io/greatR/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, shrink-to-fit=no"><title>GNU General Public License • greatR</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"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet"><meta property="og:title" content="GNU General Public License"><meta property="og:image" content="https://ruthkr.github.io/greatR/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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -258,11 +258,11 @@ <h2 id="how-to-apply-these-terms-to-your-new-programs">How to Apply These Terms
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/articles/data-requirement.html b/articles/data-requirement.html
index a5e26a0..875f39e 100644
--- a/articles/data-requirement.html
+++ b/articles/data-requirement.html
@@ -19,7 +19,7 @@
 <link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
 <!-- 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">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <meta property="og:title" content="Input data requirements">
 <meta property="og:description" content="greatR">
 <meta property="og:image" content="https://ruthkr.github.io/greatR/logo.png">
@@ -32,11 +32,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -256,13 +256,11 @@ <h2 id="a-list-of-vectors-as-an-input">A list of vectors as an input<a class="an
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/articles/index.html b/articles/index.html
index 0a0cca3..cb6bee8 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,16 +1,16 @@
 <!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, shrink-to-fit=no"><title>Articles • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Articles"><meta property="og:image" content="https://ruthkr.github.io/greatR/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, shrink-to-fit=no"><title>Articles • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Articles"><meta property="og:image" content="https://ruthkr.github.io/greatR/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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -57,7 +57,7 @@ <h6 class="dropdown-header" data-toc-skip>Others</h6>
 
     <div class="section ">
       <h3>Articles</h3>
-      <p class="section-desc"></p>
+      <div class="section-desc"></div>
 
       <dl><dt><a href="data-requirement.html">Input data requirements</a></dt>
         <dd>
@@ -68,7 +68,7 @@ <h3>Articles</h3>
       </dd></dl></div>
     <div class="section ">
       <h3>Articles</h3>
-      <p class="section-desc"></p>
+      <div class="section-desc"></div>
 
       <dl><dt><a href="register-data-manually.html">Registering data without optimisation</a></dt>
         <dd>
@@ -78,11 +78,11 @@ <h3>Articles</h3>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/articles/process-results.html b/articles/process-results.html
index 5388b18..d32a82a 100644
--- a/articles/process-results.html
+++ b/articles/process-results.html
@@ -19,7 +19,7 @@
 <link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
 <!-- 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">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <meta property="og:title" content="Processing results">
 <meta property="og:description" content="greatR">
 <meta property="og:image" content="https://ruthkr.github.io/greatR/logo.png">
@@ -32,11 +32,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -262,13 +262,11 @@ <h3 id="plot-heatmap-of-sample-distances">Plot heatmap of sample distances<a cla
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/articles/process-results_files/figure-html/plot-summary-results-1.png b/articles/process-results_files/figure-html/plot-summary-results-1.png
index d927c36..cbadab4 100644
Binary files a/articles/process-results_files/figure-html/plot-summary-results-1.png and b/articles/process-results_files/figure-html/plot-summary-results-1.png differ
diff --git a/articles/register-data-manually.html b/articles/register-data-manually.html
index 6a5cad0..3c73121 100644
--- a/articles/register-data-manually.html
+++ b/articles/register-data-manually.html
@@ -19,7 +19,7 @@
 <link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
 <!-- 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">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <meta property="og:title" content="Registering data without optimisation">
 <meta property="og:description" content="greatR">
 <meta property="og:image" content="https://ruthkr.github.io/greatR/logo.png">
@@ -32,11 +32,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -217,13 +217,11 @@ <h2 id="registering-multiple-gene-with-different-pre-defined-registration-parame
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/articles/register-data.html b/articles/register-data.html
index 75d1f23..69e57a2 100644
--- a/articles/register-data.html
+++ b/articles/register-data.html
@@ -19,7 +19,7 @@
 <link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
 <!-- 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">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <meta property="og:title" content="Registering data">
 <meta property="og:description" content="greatR">
 <meta property="og:image" content="https://ruthkr.github.io/greatR/logo.png">
@@ -32,11 +32,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -441,7 +441,7 @@ <h3 id="registration-results-1">Registration results<a class="anchor" aria-label
 <th align="left">registered</th>
 </tr></thead>
 <tbody><tr class="odd">
-<td align="left">5472143a</td>
+<td align="left">6058ef88</td>
 <td align="right">1.125762</td>
 <td align="right">0.074995</td>
 <td align="right">-6.115123</td>
@@ -457,13 +457,11 @@ <h3 id="registration-results-1">Registration results<a class="anchor" aria-label
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/authors.html b/authors.html
index e0f5c78..35181aa 100644
--- a/authors.html
+++ b/authors.html
@@ -1,16 +1,16 @@
 <!DOCTYPE html>
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 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -62,25 +62,21 @@ <h2>Authors</h2>
           <p><strong><a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a></strong>. Author, maintainer. <a href="https://orcid.org/0000-0003-1873-6203" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
         </li>
-        <li>
-          <p><strong>Alex Calderwood</strong>. Author. <a href="https://orcid.org/0000-0003-3749-035X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
-          </p>
-        </li>
       </ul></div>
 
     <div class="section level2 citation">
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/ruthkr/greatR/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
-      <p>Kristianingsih R, Calderwood A (2024).
+      <p>Kristianingsih R (2024).
 <em>greatR: Gene Registration from Expression and Time-Courses in R</em>.
-R package version 1.1.0.9000, https://github.com/ruthkr/greatR/, <a href="https://ruthkr.github.io/greatR/">https://ruthkr.github.io/greatR/</a>. 
+R package version 2.0.0, https://github.com/ruthkr/greatR/, <a href="https://ruthkr.github.io/greatR/">https://ruthkr.github.io/greatR/</a>. 
 </p>
       <pre>@Manual{,
   title = {greatR: Gene Registration from Expression and Time-Courses in R},
-  author = {Ruth Kristianingsih and Alex Calderwood},
+  author = {Ruth Kristianingsih},
   year = {2024},
-  note = {R package version 1.1.0.9000, https://github.com/ruthkr/greatR/},
+  note = {R package version 2.0.0, https://github.com/ruthkr/greatR/},
   url = {https://ruthkr.github.io/greatR/},
 }</pre>
     </div>
@@ -89,11 +85,11 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/deps/bootstrap-5.3.1/bootstrap.min.css b/deps/bootstrap-5.3.1/bootstrap.min.css
index cfdaecb..85eef2f 100644
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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1.1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(69,43,116,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #452B74;--bs-pagination-active-border-color: #452B74;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:calc(1.2625rem + .15vw);--bs-pagination-border-radius: var(--bs-border-radius-lg)}@media (min-width: 1200px){.pagination-lg{--bs-pagination-font-size:1.375rem}}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.9625rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: 1.2em;--bs-badge-padding-y: .6em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 400;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 0 solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.825rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #452B74;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #452B74;--bs-list-group-active-border-color: #452B74;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(69,43,116,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto 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#343a40;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #343a40;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #343a40;--bs-btn-bg: transparent;--bs-gradient: none}.btn-link{--bs-btn-font-weight: 400;--bs-btn-color: var(--bs-link-color);--bs-btn-bg: transparent;--bs-btn-border-color: transparent;--bs-btn-hover-color: var(--bs-link-hover-color);--bs-btn-hover-border-color: transparent;--bs-btn-active-color: var(--bs-link-hover-color);--bs-btn-active-border-color: transparent;--bs-btn-disabled-color: #868e96;--bs-btn-disabled-border-color: transparent;--bs-btn-box-shadow: 0 0 0 #000;--bs-btn-focus-shadow-rgb: 97,75,137;text-decoration:underline;-webkit-text-decoration:underline;-moz-text-decoration:underline;-ms-text-decoration:underline;-o-text-decoration:underline}.btn-link:focus-visible{color:var(--bs-btn-color)}.btn-link:hover{color:var(--bs-btn-hover-color)}.btn-lg,.btn-group-lg>.btn{--bs-btn-padding-y: .5rem;--bs-btn-padding-x: 1rem;--bs-btn-font-size:calc(1.2625rem + .15vw);--bs-btn-border-radius: 2.688em}@media (min-width: 1200px){.btn-lg,.btn-group-lg>.btn{--bs-btn-font-size:1.375rem}}.btn-sm,.btn-group-sm>.btn{--bs-btn-padding-y: .25rem;--bs-btn-padding-x: .5rem;--bs-btn-font-size:.688rem;--bs-btn-border-radius: .844em}.fade{transition:opacity 0.15s linear}@media (prefers-reduced-motion: reduce){.fade{transition:none}}.fade:not(.show){opacity:0}.collapse:not(.show){display:none}.collapsing{height:0;overflow:hidden;transition:height 0.35s ease}@media (prefers-reduced-motion: reduce){.collapsing{transition:none}}.collapsing.collapse-horizontal{width:0;height:auto;transition:width 0.35s ease}@media (prefers-reduced-motion: 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!important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand .navbar-toggler{display:none}.navbar-expand .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand .offcanvas .offcanvas-header{display:none}.navbar-expand .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}.navbar-dark,.navbar[data-bs-theme="dark"]{--bs-navbar-color: rgba(255,255,255,0.55);--bs-navbar-hover-color: rgba(255,255,255,0.75);--bs-navbar-disabled-color: rgba(255,255,255,0.25);--bs-navbar-active-color: #fff;--bs-navbar-brand-color: #fff;--bs-navbar-brand-hover-color: #fff;--bs-navbar-toggler-border-color: rgba(255,255,255,0.1);--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme="dark"] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: .5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: var(--bs-border-width);--bs-card-border-color: var(--bs-border-color-translucent);--bs-card-border-radius: var(--bs-border-radius);--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(var(--bs-body-color-rgb), 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url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%231c112e'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #a295ba;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(69,43,116,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1.1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%238f80ac'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%238f80ac'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1.1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(69,43,116,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #452B74;--bs-pagination-active-border-color: #452B74;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:calc(1.2625rem + .15vw);--bs-pagination-border-radius: var(--bs-border-radius-lg)}@media (min-width: 1200px){.pagination-lg{--bs-pagination-font-size:1.375rem}}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.9625rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: 1.2em;--bs-badge-padding-y: .6em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 400;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 0 solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.825rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #452B74;--bs-progress-bar-transition: width 0.6s 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var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #452B74;--bs-list-group-active-border-color: #452B74;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") 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var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * 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576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 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var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: 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var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: 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var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(69,43,116,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * 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diff --git a/index.html b/index.html
index 5414904..2e096cc 100644
--- a/index.html
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@@ -5,8 +5,7 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="A tool for registering (aligning) gene expression profiles
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+<meta name="description" content="A tool for registering (aligning) gene expression profiles between reference and query data.">
 <title>Gene Registration from Expression and Time-Courses in R • greatR</title>
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 <meta property="og:title" content="Gene Registration from Expression and Time-Courses in R">
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+<meta property="og:description" content="A tool for registering (aligning) gene expression profiles between reference and query data.">
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@@ -34,11 +32,11 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -182,7 +180,6 @@ <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
 <li>
 <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-1873-6203" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
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@@ -203,13 +200,11 @@ <h2 data-toc-skip>Dev status</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
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-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/news/index.html b/news/index.html
index 882aea4..a621437 100644
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+<!-- 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, shrink-to-fit=no"><title>Changelog • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Changelog"><meta property="og:image" content="https://ruthkr.github.io/greatR/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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -57,7 +57,7 @@ <h6 class="dropdown-header" data-toc-skip>Others</h6>
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="1.1.0.9000" id="greatr-1109000">greatR 1.1.0.9000<a class="anchor" aria-label="anchor" href="#greatr-1109000"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.0.0" id="greatr-200">greatR 2.0.0<a class="anchor" aria-label="anchor" href="#greatr-200"></a></h2><p class="text-muted">CRAN release: 2024-04-09</p>
 <ul><li>Added {patchwork} as a dependency.</li>
 <li>Updated {greatR} logo.</li>
 <li>Updated default <code>optimisation_method</code> in <code><a href="../reference/register.html">register()</a></code> to be “lbfgsb” (LBFSG-B) instead of “nm” (Nelder-Mead).</li>
@@ -67,7 +67,7 @@ <h2 class="pkg-version" data-toc-text="1.1.0.9000" id="greatr-1109000">greatR 1.
 <li>Updated <code><a href="../reference/calculate_distance.html">calculate_distance()</a></code> to return object of S3 class <code>dist_greatR</code>.</li>
 <li>Refactored <code>summarise_registration()</code> as <code><a href="../reference/summary.html">summary.res_greatR()</a></code> S3 method.</li>
 </ul><div class="section level3">
-<h3 id="improvements-1-1-0-9000">Improvements<a class="anchor" aria-label="anchor" href="#improvements-1-1-0-9000"></a></h3>
+<h3 id="improvements-2-0-0">Improvements<a class="anchor" aria-label="anchor" href="#improvements-2-0-0"></a></h3>
 <ul><li>Deprecate use of <code>time_delta</code> variable in registration process.</li>
 <li>Added <code>fun_args</code> (a list of arguments used when calling the function) in <code><a href="../reference/register.html">register()</a></code> results.</li>
 <li>Updated <code><a href="../reference/summary.html">summary.res_greatR()</a></code> to return <code>NA</code> instead of <code>[NA, NA]</code> when all genes are non-registered.</li>
@@ -84,14 +84,14 @@ <h3 id="improvements-1-1-0-9000">Improvements<a class="anchor" aria-label="ancho
 <li>Updated vignettes with additional examples, comments on arguments, and full coverage of all <code><a href="../reference/plot.html">plot()</a></code> methods.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="bug-fixes-1-1-0-9000">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-1-1-0-9000"></a></h3>
+<h3 id="bug-fixes-2-0-0">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-2-0-0"></a></h3>
 <ul><li>Fixed <code>get_shift_search_space_limits()</code> to adjust shift space limits accordingly to removal of <code>time_delta</code> variable (see 48c943cd).</li>
 <li>Fixed default <code>overlapping_percent = 0.5</code> (instead of 50) in <code>register_manually()</code>.</li>
 <li>Fixed <code>get_stretch_search_space_limits()</code> to correctly determine lower and upper limits when single stretch value is provided.</li>
 <li>Fixed issue in <code>get_shift_search_space_limits()</code> where range variables were not available when <code>calc_mode == "bound"</code>.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="new-functions-1-1-0-9000">New functions<a class="anchor" aria-label="anchor" href="#new-functions-1-1-0-9000"></a></h3>
+<h3 id="new-functions-2-0-0">New functions<a class="anchor" aria-label="anchor" href="#new-functions-2-0-0"></a></h3>
 <ul><li>
 <code>bind_results()</code> auxiliary function to merge results from <code><a href="../reference/register.html">register()</a></code>.</li>
 <li>
@@ -237,11 +237,11 @@ <h2 class="pkg-version" data-toc-text="0.1.0" id="greatr-010">greatR 0.1.0<a cla
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/pkgdown.js b/pkgdown.js
index 5fccd9c..9bd6621 100644
--- a/pkgdown.js
+++ b/pkgdown.js
@@ -30,10 +30,10 @@
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
+    var tooltipOriginalTitle=element.getAttribute('data-bs-original-title');
+    element.setAttribute('data-bs-original-title', msg);
     $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    element.setAttribute('data-bs-original-title', tooltipOriginalTitle);
   }
 
   if(ClipboardJS.isSupported()) {
@@ -60,7 +60,7 @@
         e.clearSelection();
       });
 
-      clipboard.on('error', function() {
+      clipboard.on('error', function(e) {
         changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
       });
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 7c2a56c..f9e0dd4 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,12 +1,12 @@
 pandoc: 3.1.11
-pkgdown: 2.0.7
+pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   data-requirement: data-requirement.html
   process-results: process-results.html
   register-data-manually: register-data-manually.html
   register-data: register-data.html
-last_built: 2024-03-25T22:02Z
+last_built: 2024-05-20T20:54Z
 urls:
   reference: https://ruthkr.github.io/greatR/reference
   article: https://ruthkr.github.io/greatR/articles
diff --git a/reference/calculate_distance.html b/reference/calculate_distance.html
index dcbac81..24fced7 100644
--- a/reference/calculate_distance.html
+++ b/reference/calculate_distance.html
@@ -1,7 +1,7 @@
 <!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, shrink-to-fit=no"><meta name="description" content="calculate_distance() is a function that allows users to calculate
 pairwise distances between samples from different time points to
-investigate the similarity of progression before or after registration."><title>Calculate distance between sample data before and after registration — calculate_distance • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Calculate distance between sample data before and after registration — calculate_distance"><meta property="og:description" content="calculate_distance() is a function that allows users to calculate
+investigate the similarity of progression before or after registration."><title>Calculate distance between sample data before and after registration — calculate_distance • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Calculate distance between sample data before and after registration — calculate_distance"><meta property="og:description" content="calculate_distance() is a function that allows users to calculate
 pairwise distances between samples from different time points to
 investigate the similarity of progression before or after registration."><meta property="og:image" content="https://ruthkr.github.io/greatR/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>
@@ -10,11 +10,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -104,11 +104,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/get_approximate_stretch.html b/reference/get_approximate_stretch.html
index 9d65d51..a9c48b7 100644
--- a/reference/get_approximate_stretch.html
+++ b/reference/get_approximate_stretch.html
@@ -2,7 +2,7 @@
 <!-- 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, shrink-to-fit=no"><meta name="description" content="get_approximate_stretch() is a function to get a stretch factor
 estimation given input data. This function will take the time point ranges
 of both reference and query data and compare them to estimate the stretch
-factor."><title>Get approximate stretch factor — get_approximate_stretch • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Get approximate stretch factor — get_approximate_stretch"><meta property="og:description" content="get_approximate_stretch() is a function to get a stretch factor
+factor."><title>Get approximate stretch factor — get_approximate_stretch • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Get approximate stretch factor — get_approximate_stretch"><meta property="og:description" content="get_approximate_stretch() is a function to get a stretch factor
 estimation given input data. This function will take the time point ranges
 of both reference and query data and compare them to estimate the stretch
 factor."><meta property="og:image" content="https://ruthkr.github.io/greatR/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]>
@@ -12,11 +12,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -101,11 +101,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/index.html b/reference/index.html
index 2d38cb6..0e0eeed 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,16 +1,16 @@
 <!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, shrink-to-fit=no"><title>Function reference • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Function reference"><meta property="og:image" content="https://ruthkr.github.io/greatR/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, shrink-to-fit=no"><title>Function reference • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Function reference"><meta property="og:image" content="https://ruthkr.github.io/greatR/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>
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 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -108,11 +108,11 @@ <h2 id="summarise-and-visualise-registration-results">Summarise and visualise re
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/plot.html b/reference/plot.html
index 488eea2..216cac9 100644
--- a/reference/plot.html
+++ b/reference/plot.html
@@ -1,16 +1,16 @@
 <!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, shrink-to-fit=no"><meta name="description" content="Visualise registration results"><title>Visualise registration results — plot • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Visualise registration results — plot"><meta property="og:description" content="Visualise registration results"><meta property="og:image" content="https://ruthkr.github.io/greatR/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, shrink-to-fit=no"><meta name="description" content="Visualise registration results"><title>Visualise registration results — plot • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Visualise registration results — plot"><meta property="og:description" content="Visualise registration results"><meta property="og:image" content="https://ruthkr.github.io/greatR/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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -166,11 +166,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/register.html b/reference/register.html
index 8892938..9219ed0 100644
--- a/reference/register.html
+++ b/reference/register.html
@@ -1,6 +1,6 @@
 <!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, shrink-to-fit=no"><meta name="description" content="register() is a function to register expression profiles a user
-wishes to compare."><title>Register or synchronize different expression profiles — register • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Register or synchronize different expression profiles — register"><meta property="og:description" content="register() is a function to register expression profiles a user
+wishes to compare."><title>Register or synchronize different expression profiles — register • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Register or synchronize different expression profiles — register"><meta property="og:description" content="register() is a function to register expression profiles a user
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -169,11 +169,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/summary.html b/reference/summary.html
index 78b92ac..f5c89bb 100644
--- a/reference/summary.html
+++ b/reference/summary.html
@@ -1,16 +1,16 @@
 <!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, shrink-to-fit=no"><meta name="description" content="Summarise registration results"><title>Summarise registration results — summary • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Summarise registration results — summary"><meta property="og:description" content="Summarise registration results"><meta property="og:image" content="https://ruthkr.github.io/greatR/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, shrink-to-fit=no"><meta name="description" content="Summarise registration results"><title>Summarise registration results — summary • greatR</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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Summarise registration results — summary"><meta property="og:description" content="Summarise registration results"><meta property="og:image" content="https://ruthkr.github.io/greatR/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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">greatR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -101,11 +101,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>, Alex Calderwood.</p>
+  <p>Developed by <a href="https://ruthkr.com" class="external-link">Ruth Kristianingsih</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/search.json b/search.json
index 9284654..382e5b1 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://ruthkr.github.io/greatR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://ruthkr.github.io/greatR/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://ruthkr.github.io/greatR/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://ruthkr.github.io/greatR/articles/data-requirement.html","id":"a-single-data-frame-input","dir":"Articles","previous_headings":"","what":"A single data frame input","title":"Input data requirements","text":"single data frame input data frame list must contain gene expression time-course data replicates. illustrative diagram shows required structure input.  data frame must contain reference query expression data, following five columns: gene_id: locus name unique ID gene. accession: accession name reference query data. timepoint: time points gene expression data. expression_value: desired expression values measure abundance gene transcripts. value can RPM, RPKM, FPKM, TPM, TMM, raw read counts. replicate: biological replicate ID expression value particular time point. example shows input data look like:","code":""},{"path":"https://ruthkr.github.io/greatR/articles/data-requirement.html","id":"a-list-of-data-frames-as-an-input","dir":"Articles","previous_headings":"","what":"A list of data frames as an input","title":"Input data requirements","text":"users data reference query joined IDs mapped one single data frame, option input data list data frames. shown illustrative diagram , list must contain reference query data frames columns required single data frame input (see previous section).  example shows input list data frames look like: Note elements list must named reference query, order element effect registration process.","code":"# Load data frames from the sample data brapa_ref_data <- system.file(\"extdata/brapa_SOC1_data.csv\", package = \"greatR\") |>   data.table::fread()  ara_query_data <- system.file(\"extdata/arabidopsis_SOC1_data.csv\", package = \"greatR\") |>   data.table::fread()  list_df <- list(   reference = brapa_ref_data,   query = ara_query_data )  list_df #> $reference #>             gene_id accession timepoint expression_value                    replicate #>              <char>    <char>     <int>            <num>                       <char> #> 1: BRAA03G023790.3C      Ro18        11         1.984367  ERR_ro18_rna_seq_v3_R18A1_1 #> 2: BRAA03G023790.3C      Ro18        11         1.474974  ERR_ro18_rna_seq_v3_R18A1_2 #> 3: BRAA03G023790.3C      Ro18        11         2.194917  ERR_ro18_rna_seq_v3_R18A1_3 #> 4: BRAA03G023790.3C      Ro18        29       113.797721 ERR_ro18_rna_seq_v3_R18A10_1 #> 5: BRAA03G023790.3C      Ro18        29        94.650207 ERR_ro18_rna_seq_v3_R18A10_2 #> 6: BRAA03G023790.3C      Ro18        29       129.176178 ERR_ro18_rna_seq_v3_R18A10_3 #>  #> $query #>      gene_id accession timepoint expression_value                   replicate #>       <char>    <char>     <int>            <num>                      <char> #> 1: AT2G45660      Col0        15         76.95936 ERR_ds_klepikova_SRR1688425 #> 2: AT2G45660      Col0        14         81.96151 ERR_ds_klepikova_SRR1688328 #> 3: AT2G45660      Col0        16         59.24077 ERR_ds_klepikova_SRR1688427 #> 4: AT2G45660      Col0        15         68.85581 ERR_ds_klepikova_SRR1688426 #> 5: AT2G45660      Col0        12         64.21780 ERR_ds_klepikova_SRR2106520 #> 6: AT2G45660      Col0        10         72.98476 ERR_ds_klepikova_SRR1661475"},{"path":"https://ruthkr.github.io/greatR/articles/data-requirement.html","id":"a-list-of-vectors-as-an-input","dir":"Articles","previous_headings":"","what":"A list of vectors as an input","title":"Input data requirements","text":"alternative list data frame input data, shown , users can also list numerical vectors input. illustrative diagram shows input look like:  example shows input list vectors can defined input: Note since ID specified vectors, greatR assign unique ID reference query pair data (see register data > Using inputs article).","code":"# Define expression value vectors ref_expressions <- c(1.9, 3.1, 7.8, 31.6, 33.7, 31.5, 131.4, 107.5, 116.7, 112.5, 109.7, 57.4, 50.9) query_expressions <- c(14, 12.1, 15.9, 47, 30.9, 50.5, 80.1, 67.4, 72.9, 61.7)  list_vector <- list(   reference = ref_expressions,   query = query_expressions )  list_vector #> $reference #>  [1]   1.9   3.1   7.8  31.6  33.7  31.5 131.4 107.5 116.7 112.5 109.7  57.4  50.9 #>  #> $query #>  [1] 14.0 12.1 15.9 47.0 30.9 50.5 80.1 67.4 72.9 61.7"},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"summarising-registration-results","dir":"Articles","previous_headings":"","what":"Summarising registration results","title":"Processing results","text":"total number registered non-registered genes can obtained running function summary() registration_results object input. function summary() returns list S3 class summary.res_greatR containing four different objects: summary data frame containing summary registration results (default S3 print). registered_genes vector gene IDs successfully registered. non_registered_genes vector non-registered gene IDs. reg_params data frame containing distribution registration parameters. list gene IDs registered non-registered can viewed calling:","code":"# Get registration summary reg_summary <- summary(registration_results)  reg_summary$summary |>   knitr::kable() reg_summary$registered_genes #> [1] \"BRAA02G043220.3C\" \"BRAA03G023790.3C\" \"BRAA03G051930.3C\" \"BRAA04G005470.3C\" #> [5] \"BRAA05G005370.3C\" \"BRAA06G025360.3C\" \"BRAA07G030470.3C\" \"BRAA07G034100.3C\" #> [9] \"BRAA09G045310.3C\" reg_summary$non_registered_genes #> [1] \"BRAA02G018970.3C\""},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"plot-distribution-of-registration-parameters","dir":"Articles","previous_headings":"Summarising registration results","what":"Plot distribution of registration parameters","title":"Processing results","text":"function plot() allows users plot bivariate distribution registration parameters. Non-registered genes can ignored selecting type = \"registered\" instead default type = \"\". Similarly, marginal distribution type can changed type_dist = \"histogram\" (default) type_dist = \"density\".","code":"plot(   reg_summary,   type = \"registered\" )"},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"plotting-registration-results","dir":"Articles","previous_headings":"","what":"Plotting registration results","title":"Processing results","text":"function plot() allows users plot registration results genes interest (default first 25 genes shown, control , use genes_list argument).  Notice plot includes label indicating particular genes registered non-registered, well registration parameters case registration successful. details function arguments, go plot().","code":"# Plot registration result plot(   registration_results,   ncol = 2 )"},{"path":[]},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"calculate-sample-distance","dir":"Articles","previous_headings":"Analysing similarity of expression profiles over time before and after registering","what":"Calculate sample distance","title":"Processing results","text":"registering data, users can compare overall similarity datasets registering using function calculate_distance(). default genes considered calculation, can changed using genes_list argument. function calculate_distance() returns list S3 class dist_greatR two data frames: result distance scaled reference query expressions using time points registration. original distance scaled reference query expressions using original time points registration.","code":"sample_distance <- calculate_distance(registration_results)"},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"plot-heatmap-of-sample-distances","dir":"Articles","previous_headings":"Analysing similarity of expression profiles over time before and after registering","what":"Plot heatmap of sample distances","title":"Processing results","text":"data frames can visualised using plot() function, selecting either type = \"result\" (default) type = \"original\".   Notice use match_timepoints = TRUE match registered query time points reference time points.","code":"# Plot heatmap of mean expression profiles distance before registration process plot(   sample_distance,   type = \"original\" ) # Plot heatmap of mean expression profiles distance after registration process plot(   sample_distance,   type = \"result\",   match_timepoints = TRUE )"},{"path":"https://ruthkr.github.io/greatR/articles/register-data-manually.html","id":"load-sample-data","dir":"Articles","previous_headings":"","what":"Load sample data","title":"Registering data without optimisation","text":"greatR provides example data frame containing two different species . thaliana B. rapa two three different replicates, respectively. data frame can read follows:","code":"# Load the package library(greatR) library(data.table) # Load a data frame from the sample data b_rapa_data <- system.file(\"extdata/brapa_arabidopsis_data.csv\", package = \"greatR\") |>   data.table::fread()"},{"path":"https://ruthkr.github.io/greatR/articles/register-data-manually.html","id":"registering-without-optimisation","dir":"Articles","previous_headings":"","what":"Registering without optimisation","title":"Registering data without optimisation","text":"illustrative table shows major differences runing register() without optimisation.  , use single gene gene_id = \"BRAA03G023790.3C\" sample data, feature can also used registering multiple genes. registering, can use helper function get_approximate_stretch() approximate stretch factor sample datasets. can now use estimated stretch calculated registration process . Users need set use_optimisation = FALSE disable automated optimisation process. check whether gene registered , can get summary results accessing model_comparison table registration result. can see, using given stretch shift parameter , B. rapa gene BRAA03G023790.3C can registered.","code":"gene_BRAA03G023790.3C_data <- b_rapa_data[gene_id == \"BRAA03G023790.3C\"] get_approximate_stretch(   gene_BRAA03G023790.3C_data,   reference = \"Ro18\",   query = \"Col0\" ) #> [1] 2.666667 registration_results <- register(   gene_BRAA03G023790.3C_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\",   stretches = 2.25,   shifts = -4.36,   use_optimisation = FALSE ) #> ── Validating input data ─────────────────────────────────────────────────────── #> ℹ Will process 1 gene. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #> #> ── Starting manual registration ──────────────────────────────────────────────── #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Applying registration for genes (1/1) [38ms] registration_results$model_comparison |>   knitr::kable()"},{"path":"https://ruthkr.github.io/greatR/articles/register-data-manually.html","id":"registering-multiple-gene-with-different-pre-defined-registration-parameters","dir":"Articles","previous_headings":"","what":"Registering multiple gene with different pre-defined registration parameters","title":"Registering data without optimisation","text":"Users can also specify list parameters rather single value. Similar registration process , users need set use_optimisation = FALSE disable automated optimisation process.","code":"registration_results <- register(   gene_BRAA03G023790.3C_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\",   stretches = seq(1, 3, 0.1),   shifts = seq(0, 4, 0.1),   use_optimisation = FALSE ) #> ── Validating input data ─────────────────────────────────────────────────────── #> ℹ Will process 1 gene. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #> #> ── Starting manual registration ──────────────────────────────────────────────── #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Applying registration for genes (1/1) [1.3s]"},{"path":[]},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"loading-sample-data","dir":"Articles","previous_headings":"Using data frame input","what":"Loading sample data","title":"Registering data","text":"greatR provides example data frame containing two different species . thaliana B. rapa two three different replicates, respectively. data frame can read follows: Note data five columns required package:","code":"# Load the package library(greatR) library(data.table) # Load a data frame from the sample data b_rapa_data <- system.file(\"extdata/brapa_arabidopsis_data.csv\", package = \"greatR\") |>   data.table::fread() b_rapa_data |>   knitr::kable()"},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"registering-the-data","dir":"Articles","previous_headings":"Using data frame input","what":"Registering the data","title":"Registering data","text":"align gene expression time-course Arabidopsis Col-0 B. rapa Ro18, can use function register(). using default use_optimisation = TRUE, greatR find best stretch shift parameters optimisation. details function arguments, go register(). dealing thousands genes, users may speed registration process using argument num_cores run registration using parallel processing.","code":"registration_results <- register(   b_rapa_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\" ) #> ── Validating input data ──────────────────────────────────────────────────────── #> ℹ Will process 10 genes. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #> #> ── Starting registration with optimisation ────────────────────────────────────── #> ℹ Using L-BFGS-B optimisation method. #> ℹ Using computed stretches and shifts search space limits. #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Optimising registration parameters for genes (10/10) [2s] parallel::detectCores() #> 8 registration_results <- register(   b_rapa_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\",   num_cores = 8 )"},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"registration-results","dir":"Articles","previous_headings":"Using data frame input","what":"Registration results","title":"Registering data","text":"function register() returns list S3 class res_greatR containing three different objects: data data frame containing expression data additional timepoint_reg column result registered time points applying registration parameters query data. model_comparison data frame containing () optimal stretch shift gene_id (b) difference Bayesian Information Criterion separate model combined model (BIC_diff) applying optimal registration parameters gene. value BIC_diff < 0, expression dynamics reference query data can registered (registered = TRUE). (Default S3 print). fun_args list arguments used calling function (reference, query, scaling_method, …). check whether gene registered , can get summary results accessing model_comparison table registration result. sample data , can see nine ten genes, registered = TRUE, meaning reference query data nine genes can aligned registered. data frame outputs can summarised visualised; see documentation processing registration results article.","code":"registration_results$model_comparison |>   knitr::kable()"},{"path":[]},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"loading-sample-data-1","dir":"Articles","previous_headings":"Using other inputs","what":"Loading sample data","title":"Registering data","text":"noted input data requirements article, register() also accepts list data frames list reference query vectors input:","code":"# Define expression value vectors ref_expressions <- c(1.9, 3.1, 7.8, 31.6, 33.7, 31.5, 131.4, 107.5, 116.7, 112.5, 109.7, 57.4, 50.9) query_expressions <- c(14, 12.1, 15.9, 47, 30.9, 50.5, 80.1, 67.4, 72.9, 61.7)  list_vector <- list(   reference = ref_expressions,   query = query_expressions )"},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"registering-the-data-1","dir":"Articles","previous_headings":"Using other inputs","what":"Registering the data","title":"Registering data","text":"previously shown, register input list, users can run function register():","code":"registration_results_vectors <- register(   list_vector,   reference = \"Ref\",   query = \"Query\",   scaling_method = \"z-score\" ) #> ── Validating input data ─────────────────────────────────────────────────────── #> ℹ Will process 1 gene. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #>  #> ── Starting registration with optimisation ───────────────────────────────────── #> ℹ Using L-BFGS-B optimisation method. #> ℹ Using computed stretches and shifts search space limits. #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Optimising registration parameters for genes (1/1) [170ms]"},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"registration-results-1","dir":"Articles","previous_headings":"Using other inputs","what":"Registration results","title":"Registering data","text":"registration result object structure using data frame input. Since ID explicitly defined input vector list, unique gene_id automatically generated reference query pair.","code":"registration_results_vectors$model_comparison |>   knitr::kable()"},{"path":"https://ruthkr.github.io/greatR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Ruth Kristianingsih. Author, maintainer. Alex Calderwood. Author.","code":""},{"path":"https://ruthkr.github.io/greatR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kristianingsih R, Calderwood (2024). greatR: Gene Registration Expression Time-Courses R. R package version 1.1.0.9000, https://github.com/ruthkr/greatR/, https://ruthkr.github.io/greatR/.","code":"@Manual{,   title = {greatR: Gene Registration from Expression and Time-Courses in R},   author = {Ruth Kristianingsih and Alex Calderwood},   year = {2024},   note = {R package version 1.1.0.9000, https://github.com/ruthkr/greatR/},   url = {https://ruthkr.github.io/greatR/}, }"},{"path":"https://ruthkr.github.io/greatR/index.html","id":"greatr-","dir":"","previous_headings":"","what":"Gene Registration from Expression and Time-Courses in R","title":"Gene Registration from Expression and Time-Courses in R","text":"greatR (Gene Registration Expression Time-courses R) tool register (align) two sets gene expression profiles users wish compare. gene profiles data referred query reference data. match time point ranges profiles, time points query profiles transformed stretching shifting process. tool uses statistical model comparison based Bayesian approach evaluate optimality gene expression profiles alignment.","code":""},{"path":"https://ruthkr.github.io/greatR/index.html","id":"package-workflow","dir":"","previous_headings":"","what":"Package workflow","title":"Gene Registration from Expression and Time-Courses in R","text":"flowchart illustrates workflow package given input data:  details use package available function documentations following vignettes: Input data requirements Register data Process registration results","code":""},{"path":"https://ruthkr.github.io/greatR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Gene Registration from Expression and Time-Courses in R","text":"can install stable version greatR CRAN : development version greatR GitHub :","code":"install.packages(\"greatR\") # install.packages(\"devtools\") devtools::install_github(\"ruthkr/greatR\")"},{"path":"https://ruthkr.github.io/greatR/index.html","id":"usage---quick-start","dir":"","previous_headings":"","what":"Usage - quick start","title":"Gene Registration from Expression and Time-Courses in R","text":"basic example shows register (align) gene expression profiles time:","code":"# Load the package library(greatR) # Load a data frame from the sample data b_rapa_data <- system.file(\"extdata/brapa_arabidopsis_data.csv\", package = \"greatR\") |>   utils::read.csv()  # Running the registration registration_results <- register(   b_rapa_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\" ) #> ── Validating input data ──────────────────────────────────────────────────────── #> ℹ Will process 10 genes. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #> #> ── Starting registration with optimisation ────────────────────────────────────── #> ℹ Using L-BFGS-B optimisation method. #> ℹ Using computed stretches and shifts search space limits. #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Optimising registration parameters for genes (10/10) [2s]"},{"path":"https://ruthkr.github.io/greatR/index.html","id":"reference","dir":"","previous_headings":"","what":"Reference","title":"Gene Registration from Expression and Time-Courses in R","text":"Calderwood, ., Hepworth, J., Woodhouse, … Morris, R. (2021). Comparative transcriptomics reveals desynchronisation gene expression floral transition Arabidopsis Brassica rapa cultivars. Quantitative Plant Biology, 2, E4. doi:10.1017/qpb.2021.6","code":""},{"path":"https://ruthkr.github.io/greatR/reference/calculate_distance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate distance between sample data before and after registration — calculate_distance","title":"Calculate distance between sample data before and after registration — calculate_distance","text":"calculate_distance() function allows users calculate pairwise distances samples different time points investigate similarity progression registration.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/calculate_distance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate distance between sample data before and after registration — calculate_distance","text":"","code":"calculate_distance(results, type = c(\"registered\", \"all\"), genes_list = NULL)"},{"path":"https://ruthkr.github.io/greatR/reference/calculate_distance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate distance between sample data before and after registration — calculate_distance","text":"results Result registration process using register(). type Whether calculate distance considering \"registered\" genes (default) \"\" genes. genes_list Optional vector indicating gene_id values considered.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/calculate_distance.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate distance between sample data before and after registration — calculate_distance","text":"function returns dist_greatR object containing two data frames: registered pairwise distance scaled reference query expressions using registered time points. original pairwise distance scaled reference query expressions using original time points.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/get_approximate_stretch.html","id":null,"dir":"Reference","previous_headings":"","what":"Get approximate stretch factor — get_approximate_stretch","title":"Get approximate stretch factor — get_approximate_stretch","text":"get_approximate_stretch() function get stretch factor estimation given input data. function take time point ranges reference query data compare estimate stretch factor.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/get_approximate_stretch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get approximate stretch factor — get_approximate_stretch","text":"","code":"get_approximate_stretch(data, reference = \"ref\", query = \"query\")"},{"path":"https://ruthkr.github.io/greatR/reference/get_approximate_stretch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get approximate stretch factor — get_approximate_stretch","text":"data Input data frame, either containing replicates gene expression . reference Accession name reference data. query Accession name query data.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/get_approximate_stretch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get approximate stretch factor — get_approximate_stretch","text":"function returns estimation stretch factor registering data.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Visualise registration results — plot","title":"Visualise registration results — plot","text":"Visualise registration results","code":""},{"path":"https://ruthkr.github.io/greatR/reference/plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Visualise registration results — plot","text":"","code":"# S3 method for res_greatR plot(   x,   type = c(\"result\", \"original\"),   genes_list = NULL,   show_rep_mean = FALSE,   ncol = NULL,   title = NULL,   ... )  # S3 method for dist_greatR plot(   x,   type = c(\"result\", \"original\"),   match_timepoints = TRUE,   title = NULL,   ... )  # S3 method for summary.res_greatR plot(   x,   type = c(\"all\", \"registered\"),   type_dist = c(\"histogram\", \"density\"),   genes_list = NULL,   bins = 30,   alpha = NA,   scatterplot_size = c(4, 3),   title = NULL,   ... )"},{"path":"https://ruthkr.github.io/greatR/reference/plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Visualise registration results — plot","text":"x Input object. plot.res_greatR(): registration results, output register() registration process. plot.summary.res_greatR(): registration results summary, output summary(). plot.dist_greatR(): pairwise distances reference query time points, output calculate_distance(). type Type plot. plot.res_greatR()  plot.dist_greatR(): whether use registration \"result\" (default) \"original\" time points. plot.summary.res_greatR(): whether show \"\" genes (default) \"registered\" ones. genes_list Optional vector indicating gene_id values plotted. show_rep_mean Whether show replicate mean values. ncol Number columns plot grid. default calculated automatically. title Optional plot title. ... Arguments passed methods (ignored). match_timepoints TRUE, match query time points reference time points. type_dist Type marginal distribution. Can either \"histogram\" (default), \"density\". bins Number bins use type_dist = \"histogram\". default, 30. alpha Optional opacity points scatterplot. scatterplot_size Vector c(width, height) specifying ratio width height scatterplot respect stretch shift distribution plots.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Visualise registration results — plot","text":"plot.res_greatR(): plot genes interest registration process (type = \"result\") showing original time points (type = \"original\"). plot.dist_greatR(): distance heatmap gene expression profiles time reference query. plot.summary.res_greatR(): TODO.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":null,"dir":"Reference","previous_headings":"","what":"Register or synchronize different expression profiles — register","title":"Register or synchronize different expression profiles — register","text":"register() function register expression profiles user wishes compare.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Register or synchronize different expression profiles — register","text":"","code":"register(   input,   stretches = NA,   shifts = NA,   reference,   query,   scaling_method = c(\"none\", \"z-score\", \"min-max\"),   overlapping_percent = 50,   use_optimisation = TRUE,   optimisation_method = c(\"lbfgsb\", \"nm\", \"sa\"),   optimisation_config = NULL,   exp_sd = NA,   num_cores = NA )"},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Register or synchronize different expression profiles — register","text":"input Input data frame containing replicates gene expression genotype time point. stretches Candidate registration stretch factors apply query data, required use_optimisation = FALSE. shifts Candidate registration shift values apply query data, required use_optimisation = FALSE. reference Accession name reference data. query Accession name query data. scaling_method Scaling method applied data prior registration process. Either none (default), z-score, min-max. overlapping_percent Minimum percentage overlapping time point range reference data. Shifts considered leaves least percentage overlapping time point range applying registration. use_optimisation Whether optimise registration parameters. default, TRUE. optimisation_method Optimisation method use. Either \"lbfgsb\" L-BFGS-B (default), \"nm\" Nelder-Mead, \"sa\" Simulated Annealing. optimisation_config Optional list arguments override default optimisation configuration. exp_sd Optional experimental standard deviation expression replicates. num_cores Number cores use user wants register genes asynchronously (parallel) background machine. default, NA, registration run without parallelisation.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Register or synchronize different expression profiles — register","text":"function returns res_greatR object containing: data table containing scaled input data additional timepoint_reg column applying registration parameters query data. model_comparison table comparing optimal registration function gene (based all_shifts_df scores) model registration applied. fun_args list arguments used calling function.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Register or synchronize different expression profiles — register","text":"","code":"if (FALSE) { # Load a data frame from the sample data data_path <- system.file(\"extdata/brapa_arabidopsis_data.csv\", package = \"greatR\") all_data <- utils::read.csv(data_path)  # Running the registration registration_results <- register(   input = all_data,   reference = \"Ro18\",   query = \"Col0\" ) }"},{"path":"https://ruthkr.github.io/greatR/reference/summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarise registration results — summary","title":"Summarise registration results — summary","text":"Summarise registration results","code":""},{"path":"https://ruthkr.github.io/greatR/reference/summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarise registration results — summary","text":"","code":"# S3 method for res_greatR summary(object, ...)"},{"path":"https://ruthkr.github.io/greatR/reference/summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarise registration results — summary","text":"object Registration results, output register() registration process. ... Arguments passed methods (ignored).","code":""},{"path":"https://ruthkr.github.io/greatR/reference/summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarise registration results — summary","text":"function returns list containing: summary table containing summary registration results. registered_genes vector gene accessions successfully registered. non_registered_genes vector non-registered gene accessions. reg_params table containing distribution registration parameters.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-1109000","dir":"Changelog","previous_headings":"","what":"greatR 1.1.0.9000","title":"greatR 1.1.0.9000","text":"Added {patchwork} dependency. Updated {greatR} logo. Updated default optimisation_method register() “lbfgsb” (LBFSG-B) instead “nm” (Nelder-Mead). Added sample SOC1 arabidopsis_SOC1_data.csv brapa_SOC1_data.csv extdata. Refactored optimise_registration_parameters argument register() use_optimisation. Updated register() return object S3 class res_greatR. Updated calculate_distance() return object S3 class dist_greatR. Refactored summarise_registration() summary.res_greatR() S3 method.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"improvements-1-1-0-9000","dir":"Changelog","previous_headings":"","what":"Improvements","title":"greatR 1.1.0.9000","text":"Deprecate use time_delta variable registration process. Added fun_args (list arguments used calling function) register() results. Updated summary.res_greatR() return NA instead [NA, NA] genes non-registered. Added reg_params (table containing distribution registration parameters) results list summary.res_greatR() method. Simplified calc_overlapping_percent() calculation. Take consideration overlapping_percent applying manual registration. Updated logic calc_variance() data replicates consider expression_value. Updated get_stretch_search_space_limits() get_shift_search_space_limits() exclude unexplorable regions search space. Improved calculate_distance() aux get_timepoint_comb_*_data() functions eliminate column selection renaming inside lapply() calls, reducing execution time 25%. Added type (“registered” “”) genes_list arguments calculate_distance() filter genes. Added new unit tests. Updated unit tests, added S3 class checks apropriate. Updated vignettes README diagrams figures. Updated vignettes additional examples, comments arguments, full coverage plot() methods.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"bug-fixes-1-1-0-9000","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"greatR 1.1.0.9000","text":"Fixed get_shift_search_space_limits() adjust shift space limits accordingly removal time_delta variable (see 48c943cd). Fixed default overlapping_percent = 0.5 (instead 50) register_manually(). Fixed get_stretch_search_space_limits() correctly determine lower upper limits single stretch value provided. Fixed issue get_shift_search_space_limits() range variables available calc_mode == \"bound\".","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"new-functions-1-1-0-9000","dir":"Changelog","previous_headings":"","what":"New functions","title":"greatR 1.1.0.9000","text":"bind_results() auxiliary function merge results register(). theme_greatR() function greatR_palettes list. transform_input() S3 generic accept different types input register(). plot.res_greatR() S3 method replace plot_registration_results(). plot.dist_greatR() S3 method replace plot_heatmap(). plot.summary.res_greatR() S3 method inspired WVPlots::ScatterHistC().","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-110","dir":"Changelog","previous_headings":"","what":"greatR 1.1.0","title":"greatR 1.1.0","text":"CRAN release: 2024-01-09 Added {furrr} {future} dependencies. Added num_cores parameter register() allow users run registration parallel. Added exp_sd parameter register() allow users manually set experimental gene expression variance. Updated scaling_method parameter register() scale_data() allow scaling (“none”, default), Z-score scaling (“z-score”), min-max scaling (“min-max”), updated unit tests accordingly.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"improvements-1-1-0","dir":"Changelog","previous_headings":"","what":"Improvements","title":"greatR 1.1.0","text":"Updated register() perform 3 sequential registrations using Nelder-Mead, improves results optimal stretch shift parameters. Updated calc_loglik() use sigma_squared every time point sum. Updated scaled_data() preprocess_data() return all_data object , instead list() containing all_data. Updated compare_H1_and_H2() return BIC_diff column (BIC_combined - BIC_separate), instead BIC_combined BIC_separate . Updated explore_manual_search_space() use BIC_diff instead BIC_combined calculate best_params model_comparison table. Updated register() perform 3 sequential registrations using Nelder-Mead, improves results optimal stretch shift parameters. may reverted tweaking neldermead() parameters ensure correct convergence. Added optional stretch_init shift_init get_search_space_limits(), updated optimise() allow different space_lims calculation settings: automatic, given boundary box, given initial coords (new). Removed unused mean_data calculation preprocess_data() argument scale_data(). Moved “process N genes” message register() preprocess_data() running filter_*() functions. Ensure results_list$data arranged/ordered correctly register(). Updated get_H*_model_curves() functions ensure model curves smooth. Updated parse_gene_facets() display BIC_diff facet strips. Added plot_mean_data parameter plot_registration_results(). Updated overlapping_percent parameter register() goes 0 100 (’s later normalised function avoid breakages line). Added scaling_method attribute data results register(), used plot_registration_results() build y-axis label according scaling method used. Updated brapa_arabidopsis_registration.rds file new pipeline results. Split get_search_space_limits() separate aux functions stretch shift, allows stretch shift input combinations. Updated validate_params(..., registration_type = \"optimisation\") allow stretch shift input combinations.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"bug-fixes-1-1-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"greatR 1.1.0","text":"Improved get_timepoint_comb_original_data() get_timepoint_comb_registered_data() perform cross_join() single gene_id time using lapply(), fixes “Error: vector memory exhausted (limit reached?)” error. Updated match_names() double setdiff() ensure name matching done two ways, updated corresponding unit test.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"new-functions-1-1-0","dir":"Changelog","previous_headings":"","what":"New functions","title":"greatR 1.1.0","text":"filter_incomplete_accession_pairs() filter genes missing one accession. calc_variance() preprocess data variance inside preprocess_data() instead calc_loglik(). Aux register_single_gene_*() functions inside register() simplify generalise pipeline parallel registration.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-100","dir":"Changelog","previous_headings":"","what":"greatR 1.0.0","title":"greatR 1.0.0","text":"CRAN release: 2023-07-19 Rewrote registration pipeline scratch, deprecating unnecessary, redundant auxiliary functions. Added L-BFGS-B Nelder-Mead (now default) optimisation methods {greatR}. Switched manual calculation log likelihood via calc_loglik() instead stats::logLik(). Reduced computation time 1000 times, (x30 speed-package rewrite, x35 speed-switching default optimisation method). Removed {dplyr}, {magrittr}, {purrr}, {rlang}, {stringr} package dependencies. Added {neldermead} package dependency. register() summarise_registration() get_approximate_stretch() plot_registration_results() plot_heatmap() calculate_distance()","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"improvements-1-0-0","dir":"Changelog","previous_headings":"","what":"Improvements","title":"greatR 1.0.0","text":"Simplified parameters main register() function, added scaling_method. Simplified structure output object register(). Simplified parameters summarise_registration(), plot_registration_results(), plot_heatmap(), calculate_distance() simply require results object register(), vastly simplifying usage. Improved messages, errors, progress indicators {cli}. Added correct pluralisation {cli} messages. Rewrote unit tests use {data.table} exclusively data manipulation. Added unit tests calc_loglik_H1(), calc_loglik_H2(), calc_overlapping_percent(), calculate_distance(), cross_join(), get_search_space_limits_from_params(), get_search_space_limits(), objective_fun(), optimise(), plot_heatmap(), plot_registration_results(), preprocess_data(), register_manually(), register(), summary_registration(), validate_params().","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"bug-fixes-1-0-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"greatR 1.0.0","text":"Fixed match_names() call validating accession names register() Fixed use deprecated aes_string() parsing timepoint_var using !!ggplot2::sym() call. Fixed preds left join plot_registration_results(). Fixed issue plot_registration_results() working genes unregistered type = \"registered\". Fixed calculation time_delta preprocess_data() ensure ’s grouped gene_id accession (just accession).","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-020","dir":"Changelog","previous_headings":"","what":"greatR 0.2.0","title":"greatR 0.2.0","text":"CRAN release: 2022-06-08 Added Alex Calderwood package co-author. Added vignette optimisation process. Refactored num_shifts shift_extreme parameters simplified shifts parameter.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"improvements-0-2-0","dir":"Changelog","previous_headings":"","what":"Improvements","title":"greatR 0.2.0","text":"Improved default parameter values exported functions. Added {optimization}, {purrr} package dependencies. Removed {cowplot}, {ggpubr}, {ggrepel}, {Rtsne}, {viridis} package dependencies. Cleaned {cli} messages. Removed legacy AIC references, longer used. Updated calculate_between_sample_distance() use registration_results primary parameter instead mean_df, mean_df_sc, imputed_mean_df. Added warning comparable time points found using users’ pre-defined parameters. Refactored optimise_shift_extreme maintain_min_num_overlapping_points, properly defined corrected boundary box number overlapping points whether needed maintained .","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"bug-fixes-0-2-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"greatR 0.2.0","text":"Check input accessions exist input data get_approximate_stretch(). Manually create time point sorting levels x_sample y_sample columns according plot_heatmap(). Properly handle - character accession names plot_heatmap() time points parsed correctly.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"new-features-0-2-0","dir":"Changelog","previous_headings":"","what":"New features","title":"greatR 0.2.0","text":"Added optional parameter optimisation process using Simulated Annealing optimise_registration_params().","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"new-functions-0-2-0","dir":"Changelog","previous_headings":"","what":"New functions","title":"greatR 0.2.0","text":"preprocess_data() simplify scale_and_register_data() code reuse logic elsewhere. get_best_stretch_and_shift_simplified(). get_BIC_from_registering_data(). get_boundary_box(). optimise_registration_params_single_gene(). optimise_registration_params() wrapper optimise_registration_params_single_gene() multiple genes. get_best_stretch_and_shift_after_optimisation().","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-010","dir":"Changelog","previous_headings":"","what":"greatR 0.1.0","title":"greatR 0.1.0","text":"CRAN release: 2022-01-12 Initial release. Added NEWS.md file track changes package.","code":""}]
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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://ruthkr.github.io/greatR/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. 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GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://ruthkr.github.io/greatR/articles/data-requirement.html","id":"a-single-data-frame-input","dir":"Articles","previous_headings":"","what":"A single data frame input","title":"Input data requirements","text":"single data frame input data frame list must contain gene expression time-course data replicates. illustrative diagram shows required structure input.  data frame must contain reference query expression data, following five columns: gene_id: locus name unique ID gene. accession: accession name reference query data. timepoint: time points gene expression data. expression_value: desired expression values measure abundance gene transcripts. value can RPM, RPKM, FPKM, TPM, TMM, raw read counts. replicate: biological replicate ID expression value particular time point. example shows input data look like:","code":""},{"path":"https://ruthkr.github.io/greatR/articles/data-requirement.html","id":"a-list-of-data-frames-as-an-input","dir":"Articles","previous_headings":"","what":"A list of data frames as an input","title":"Input data requirements","text":"users data reference query joined IDs mapped one single data frame, option input data list data frames. shown illustrative diagram , list must contain reference query data frames columns required single data frame input (see previous section).  example shows input list data frames look like: Note elements list must named reference query, order element effect registration process.","code":"# Load data frames from the sample data brapa_ref_data <- system.file(\"extdata/brapa_SOC1_data.csv\", package = \"greatR\") |>   data.table::fread()  ara_query_data <- system.file(\"extdata/arabidopsis_SOC1_data.csv\", package = \"greatR\") |>   data.table::fread()  list_df <- list(   reference = brapa_ref_data,   query = ara_query_data )  list_df #> $reference #>             gene_id accession timepoint expression_value                    replicate #>              <char>    <char>     <int>            <num>                       <char> #> 1: BRAA03G023790.3C      Ro18        11         1.984367  ERR_ro18_rna_seq_v3_R18A1_1 #> 2: BRAA03G023790.3C      Ro18        11         1.474974  ERR_ro18_rna_seq_v3_R18A1_2 #> 3: BRAA03G023790.3C      Ro18        11         2.194917  ERR_ro18_rna_seq_v3_R18A1_3 #> 4: BRAA03G023790.3C      Ro18        29       113.797721 ERR_ro18_rna_seq_v3_R18A10_1 #> 5: BRAA03G023790.3C      Ro18        29        94.650207 ERR_ro18_rna_seq_v3_R18A10_2 #> 6: BRAA03G023790.3C      Ro18        29       129.176178 ERR_ro18_rna_seq_v3_R18A10_3 #>  #> $query #>      gene_id accession timepoint expression_value                   replicate #>       <char>    <char>     <int>            <num>                      <char> #> 1: AT2G45660      Col0        15         76.95936 ERR_ds_klepikova_SRR1688425 #> 2: AT2G45660      Col0        14         81.96151 ERR_ds_klepikova_SRR1688328 #> 3: AT2G45660      Col0        16         59.24077 ERR_ds_klepikova_SRR1688427 #> 4: AT2G45660      Col0        15         68.85581 ERR_ds_klepikova_SRR1688426 #> 5: AT2G45660      Col0        12         64.21780 ERR_ds_klepikova_SRR2106520 #> 6: AT2G45660      Col0        10         72.98476 ERR_ds_klepikova_SRR1661475"},{"path":"https://ruthkr.github.io/greatR/articles/data-requirement.html","id":"a-list-of-vectors-as-an-input","dir":"Articles","previous_headings":"","what":"A list of vectors as an input","title":"Input data requirements","text":"alternative list data frame input data, shown , users can also list numerical vectors input. illustrative diagram shows input look like:  example shows input list vectors can defined input: Note since ID specified vectors, greatR assign unique ID reference query pair data (see register data > Using inputs article).","code":"# Define expression value vectors ref_expressions <- c(1.9, 3.1, 7.8, 31.6, 33.7, 31.5, 131.4, 107.5, 116.7, 112.5, 109.7, 57.4, 50.9) query_expressions <- c(14, 12.1, 15.9, 47, 30.9, 50.5, 80.1, 67.4, 72.9, 61.7)  list_vector <- list(   reference = ref_expressions,   query = query_expressions )  list_vector #> $reference #>  [1]   1.9   3.1   7.8  31.6  33.7  31.5 131.4 107.5 116.7 112.5 109.7  57.4  50.9 #>  #> $query #>  [1] 14.0 12.1 15.9 47.0 30.9 50.5 80.1 67.4 72.9 61.7"},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"summarising-registration-results","dir":"Articles","previous_headings":"","what":"Summarising registration results","title":"Processing results","text":"total number registered non-registered genes can obtained running function summary() registration_results object input. function summary() returns list S3 class summary.res_greatR containing four different objects: summary data frame containing summary registration results (default S3 print). registered_genes vector gene IDs successfully registered. non_registered_genes vector non-registered gene IDs. reg_params data frame containing distribution registration parameters. list gene IDs registered non-registered can viewed calling:","code":"# Get registration summary reg_summary <- summary(registration_results)  reg_summary$summary |>   knitr::kable() reg_summary$registered_genes #> [1] \"BRAA02G043220.3C\" \"BRAA03G023790.3C\" \"BRAA03G051930.3C\" \"BRAA04G005470.3C\" #> [5] \"BRAA05G005370.3C\" \"BRAA06G025360.3C\" \"BRAA07G030470.3C\" \"BRAA07G034100.3C\" #> [9] \"BRAA09G045310.3C\" reg_summary$non_registered_genes #> [1] \"BRAA02G018970.3C\""},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"plot-distribution-of-registration-parameters","dir":"Articles","previous_headings":"Summarising registration results","what":"Plot distribution of registration parameters","title":"Processing results","text":"function plot() allows users plot bivariate distribution registration parameters. Non-registered genes can ignored selecting type = \"registered\" instead default type = \"\". Similarly, marginal distribution type can changed type_dist = \"histogram\" (default) type_dist = \"density\".","code":"plot(   reg_summary,   type = \"registered\" )"},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"plotting-registration-results","dir":"Articles","previous_headings":"","what":"Plotting registration results","title":"Processing results","text":"function plot() allows users plot registration results genes interest (default first 25 genes shown, control , use genes_list argument).  Notice plot includes label indicating particular genes registered non-registered, well registration parameters case registration successful. details function arguments, go plot().","code":"# Plot registration result plot(   registration_results,   ncol = 2 )"},{"path":[]},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"calculate-sample-distance","dir":"Articles","previous_headings":"Analysing similarity of expression profiles over time before and after registering","what":"Calculate sample distance","title":"Processing results","text":"registering data, users can compare overall similarity datasets registering using function calculate_distance(). default genes considered calculation, can changed using genes_list argument. function calculate_distance() returns list S3 class dist_greatR two data frames: result distance scaled reference query expressions using time points registration. original distance scaled reference query expressions using original time points registration.","code":"sample_distance <- calculate_distance(registration_results)"},{"path":"https://ruthkr.github.io/greatR/articles/process-results.html","id":"plot-heatmap-of-sample-distances","dir":"Articles","previous_headings":"Analysing similarity of expression profiles over time before and after registering","what":"Plot heatmap of sample distances","title":"Processing results","text":"data frames can visualised using plot() function, selecting either type = \"result\" (default) type = \"original\".   Notice use match_timepoints = TRUE match registered query time points reference time points.","code":"# Plot heatmap of mean expression profiles distance before registration process plot(   sample_distance,   type = \"original\" ) # Plot heatmap of mean expression profiles distance after registration process plot(   sample_distance,   type = \"result\",   match_timepoints = TRUE )"},{"path":"https://ruthkr.github.io/greatR/articles/register-data-manually.html","id":"load-sample-data","dir":"Articles","previous_headings":"","what":"Load sample data","title":"Registering data without optimisation","text":"greatR provides example data frame containing two different species . thaliana B. rapa two three different replicates, respectively. data frame can read follows:","code":"# Load the package library(greatR) library(data.table) # Load a data frame from the sample data b_rapa_data <- system.file(\"extdata/brapa_arabidopsis_data.csv\", package = \"greatR\") |>   data.table::fread()"},{"path":"https://ruthkr.github.io/greatR/articles/register-data-manually.html","id":"registering-without-optimisation","dir":"Articles","previous_headings":"","what":"Registering without optimisation","title":"Registering data without optimisation","text":"illustrative table shows major differences runing register() without optimisation.  , use single gene gene_id = \"BRAA03G023790.3C\" sample data, feature can also used registering multiple genes. registering, can use helper function get_approximate_stretch() approximate stretch factor sample datasets. can now use estimated stretch calculated registration process . Users need set use_optimisation = FALSE disable automated optimisation process. check whether gene registered , can get summary results accessing model_comparison table registration result. can see, using given stretch shift parameter , B. rapa gene BRAA03G023790.3C can registered.","code":"gene_BRAA03G023790.3C_data <- b_rapa_data[gene_id == \"BRAA03G023790.3C\"] get_approximate_stretch(   gene_BRAA03G023790.3C_data,   reference = \"Ro18\",   query = \"Col0\" ) #> [1] 2.666667 registration_results <- register(   gene_BRAA03G023790.3C_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\",   stretches = 2.25,   shifts = -4.36,   use_optimisation = FALSE ) #> ── Validating input data ─────────────────────────────────────────────────────── #> ℹ Will process 1 gene. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #> #> ── Starting manual registration ──────────────────────────────────────────────── #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Applying registration for genes (1/1) [38ms] registration_results$model_comparison |>   knitr::kable()"},{"path":"https://ruthkr.github.io/greatR/articles/register-data-manually.html","id":"registering-multiple-gene-with-different-pre-defined-registration-parameters","dir":"Articles","previous_headings":"","what":"Registering multiple gene with different pre-defined registration parameters","title":"Registering data without optimisation","text":"Users can also specify list parameters rather single value. Similar registration process , users need set use_optimisation = FALSE disable automated optimisation process.","code":"registration_results <- register(   gene_BRAA03G023790.3C_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\",   stretches = seq(1, 3, 0.1),   shifts = seq(0, 4, 0.1),   use_optimisation = FALSE ) #> ── Validating input data ─────────────────────────────────────────────────────── #> ℹ Will process 1 gene. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #> #> ── Starting manual registration ──────────────────────────────────────────────── #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Applying registration for genes (1/1) [1.3s]"},{"path":[]},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"loading-sample-data","dir":"Articles","previous_headings":"Using data frame input","what":"Loading sample data","title":"Registering data","text":"greatR provides example data frame containing two different species . thaliana B. rapa two three different replicates, respectively. data frame can read follows: Note data five columns required package:","code":"# Load the package library(greatR) library(data.table) # Load a data frame from the sample data b_rapa_data <- system.file(\"extdata/brapa_arabidopsis_data.csv\", package = \"greatR\") |>   data.table::fread() b_rapa_data |>   knitr::kable()"},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"registering-the-data","dir":"Articles","previous_headings":"Using data frame input","what":"Registering the data","title":"Registering data","text":"align gene expression time-course Arabidopsis Col-0 B. rapa Ro18, can use function register(). using default use_optimisation = TRUE, greatR find best stretch shift parameters optimisation. details function arguments, go register(). dealing thousands genes, users may speed registration process using argument num_cores run registration using parallel processing.","code":"registration_results <- register(   b_rapa_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\" ) #> ── Validating input data ──────────────────────────────────────────────────────── #> ℹ Will process 10 genes. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #> #> ── Starting registration with optimisation ────────────────────────────────────── #> ℹ Using L-BFGS-B optimisation method. #> ℹ Using computed stretches and shifts search space limits. #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Optimising registration parameters for genes (10/10) [2s] parallel::detectCores() #> 8 registration_results <- register(   b_rapa_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\",   num_cores = 8 )"},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"registration-results","dir":"Articles","previous_headings":"Using data frame input","what":"Registration results","title":"Registering data","text":"function register() returns list S3 class res_greatR containing three different objects: data data frame containing expression data additional timepoint_reg column result registered time points applying registration parameters query data. model_comparison data frame containing () optimal stretch shift gene_id (b) difference Bayesian Information Criterion separate model combined model (BIC_diff) applying optimal registration parameters gene. value BIC_diff < 0, expression dynamics reference query data can registered (registered = TRUE). (Default S3 print). fun_args list arguments used calling function (reference, query, scaling_method, …). check whether gene registered , can get summary results accessing model_comparison table registration result. sample data , can see nine ten genes, registered = TRUE, meaning reference query data nine genes can aligned registered. data frame outputs can summarised visualised; see documentation processing registration results article.","code":"registration_results$model_comparison |>   knitr::kable()"},{"path":[]},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"loading-sample-data-1","dir":"Articles","previous_headings":"Using other inputs","what":"Loading sample data","title":"Registering data","text":"noted input data requirements article, register() also accepts list data frames list reference query vectors input:","code":"# Define expression value vectors ref_expressions <- c(1.9, 3.1, 7.8, 31.6, 33.7, 31.5, 131.4, 107.5, 116.7, 112.5, 109.7, 57.4, 50.9) query_expressions <- c(14, 12.1, 15.9, 47, 30.9, 50.5, 80.1, 67.4, 72.9, 61.7)  list_vector <- list(   reference = ref_expressions,   query = query_expressions )"},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"registering-the-data-1","dir":"Articles","previous_headings":"Using other inputs","what":"Registering the data","title":"Registering data","text":"previously shown, register input list, users can run function register():","code":"registration_results_vectors <- register(   list_vector,   reference = \"Ref\",   query = \"Query\",   scaling_method = \"z-score\" ) #> ── Validating input data ─────────────────────────────────────────────────────── #> ℹ Will process 1 gene. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #>  #> ── Starting registration with optimisation ───────────────────────────────────── #> ℹ Using L-BFGS-B optimisation method. #> ℹ Using computed stretches and shifts search space limits. #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Optimising registration parameters for genes (1/1) [170ms]"},{"path":"https://ruthkr.github.io/greatR/articles/register-data.html","id":"registration-results-1","dir":"Articles","previous_headings":"Using other inputs","what":"Registration results","title":"Registering data","text":"registration result object structure using data frame input. Since ID explicitly defined input vector list, unique gene_id automatically generated reference query pair.","code":"registration_results_vectors$model_comparison |>   knitr::kable()"},{"path":"https://ruthkr.github.io/greatR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Ruth Kristianingsih. Author, maintainer.","code":""},{"path":"https://ruthkr.github.io/greatR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kristianingsih R (2024). greatR: Gene Registration Expression Time-Courses R. R package version 2.0.0, https://github.com/ruthkr/greatR/, https://ruthkr.github.io/greatR/.","code":"@Manual{,   title = {greatR: Gene Registration from Expression and Time-Courses in R},   author = {Ruth Kristianingsih},   year = {2024},   note = {R package version 2.0.0, https://github.com/ruthkr/greatR/},   url = {https://ruthkr.github.io/greatR/}, }"},{"path":"https://ruthkr.github.io/greatR/index.html","id":"greatr-","dir":"","previous_headings":"","what":"Gene Registration from Expression and Time-Courses in R","title":"Gene Registration from Expression and Time-Courses in R","text":"greatR (Gene Registration Expression Time-courses R) tool register (align) two sets gene expression profiles users wish compare. gene profiles data referred query reference data. match time point ranges profiles, time points query profiles transformed stretching shifting process. tool uses statistical model comparison based Bayesian approach evaluate optimality gene expression profiles alignment.","code":""},{"path":"https://ruthkr.github.io/greatR/index.html","id":"package-workflow","dir":"","previous_headings":"","what":"Package workflow","title":"Gene Registration from Expression and Time-Courses in R","text":"flowchart illustrates workflow package given input data:  details use package available function documentations following vignettes: Input data requirements Register data Process registration results","code":""},{"path":"https://ruthkr.github.io/greatR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Gene Registration from Expression and Time-Courses in R","text":"can install stable version greatR CRAN : development version greatR GitHub :","code":"install.packages(\"greatR\") # install.packages(\"devtools\") devtools::install_github(\"ruthkr/greatR\")"},{"path":"https://ruthkr.github.io/greatR/index.html","id":"usage---quick-start","dir":"","previous_headings":"","what":"Usage - quick start","title":"Gene Registration from Expression and Time-Courses in R","text":"basic example shows register (align) gene expression profiles time:","code":"# Load the package library(greatR) # Load a data frame from the sample data b_rapa_data <- system.file(\"extdata/brapa_arabidopsis_data.csv\", package = \"greatR\") |>   utils::read.csv()  # Running the registration registration_results <- register(   b_rapa_data,   reference = \"Ro18\",   query = \"Col0\",   scaling_method = \"z-score\" ) #> ── Validating input data ──────────────────────────────────────────────────────── #> ℹ Will process 10 genes. #> ℹ Using estimated standard deviation, as no `exp_sd` was provided. #> ℹ Using `scaling_method` = \"z-score\". #> #> ── Starting registration with optimisation ────────────────────────────────────── #> ℹ Using L-BFGS-B optimisation method. #> ℹ Using computed stretches and shifts search space limits. #> ℹ Using `overlapping_percent` = 50% as a registration criterion. #> ✔ Optimising registration parameters for genes (10/10) [2s]"},{"path":"https://ruthkr.github.io/greatR/index.html","id":"reference","dir":"","previous_headings":"","what":"Reference","title":"Gene Registration from Expression and Time-Courses in R","text":"Calderwood, ., Hepworth, J., Woodhouse, … Morris, R. (2021). Comparative transcriptomics reveals desynchronisation gene expression floral transition Arabidopsis Brassica rapa cultivars. Quantitative Plant Biology, 2, E4. doi:10.1017/qpb.2021.6","code":""},{"path":"https://ruthkr.github.io/greatR/reference/calculate_distance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate distance between sample data before and after registration — calculate_distance","title":"Calculate distance between sample data before and after registration — calculate_distance","text":"calculate_distance() function allows users calculate pairwise distances samples different time points investigate similarity progression registration.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/calculate_distance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate distance between sample data before and after registration — calculate_distance","text":"","code":"calculate_distance(results, type = c(\"registered\", \"all\"), genes_list = NULL)"},{"path":"https://ruthkr.github.io/greatR/reference/calculate_distance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate distance between sample data before and after registration — calculate_distance","text":"results Result registration process using register(). type Whether calculate distance considering \"registered\" genes (default) \"\" genes. genes_list Optional vector indicating gene_id values considered.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/calculate_distance.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate distance between sample data before and after registration — calculate_distance","text":"function returns dist_greatR object containing two data frames: registered pairwise distance scaled reference query expressions using registered time points. original pairwise distance scaled reference query expressions using original time points.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/get_approximate_stretch.html","id":null,"dir":"Reference","previous_headings":"","what":"Get approximate stretch factor — get_approximate_stretch","title":"Get approximate stretch factor — get_approximate_stretch","text":"get_approximate_stretch() function get stretch factor estimation given input data. function take time point ranges reference query data compare estimate stretch factor.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/get_approximate_stretch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get approximate stretch factor — get_approximate_stretch","text":"","code":"get_approximate_stretch(data, reference = \"ref\", query = \"query\")"},{"path":"https://ruthkr.github.io/greatR/reference/get_approximate_stretch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get approximate stretch factor — get_approximate_stretch","text":"data Input data frame, either containing replicates gene expression . reference Accession name reference data. query Accession name query data.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/get_approximate_stretch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get approximate stretch factor — get_approximate_stretch","text":"function returns estimation stretch factor registering data.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Visualise registration results — plot","title":"Visualise registration results — plot","text":"Visualise registration results","code":""},{"path":"https://ruthkr.github.io/greatR/reference/plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Visualise registration results — plot","text":"","code":"# S3 method for res_greatR plot(   x,   type = c(\"result\", \"original\"),   genes_list = NULL,   show_rep_mean = FALSE,   ncol = NULL,   title = NULL,   ... )  # S3 method for dist_greatR plot(   x,   type = c(\"result\", \"original\"),   match_timepoints = TRUE,   title = NULL,   ... )  # S3 method for summary.res_greatR plot(   x,   type = c(\"all\", \"registered\"),   type_dist = c(\"histogram\", \"density\"),   genes_list = NULL,   bins = 30,   alpha = NA,   scatterplot_size = c(4, 3),   title = NULL,   ... )"},{"path":"https://ruthkr.github.io/greatR/reference/plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Visualise registration results — plot","text":"x Input object. plot.res_greatR(): registration results, output register() registration process. plot.summary.res_greatR(): registration results summary, output summary(). plot.dist_greatR(): pairwise distances reference query time points, output calculate_distance(). type Type plot. plot.res_greatR()  plot.dist_greatR(): whether use registration \"result\" (default) \"original\" time points. plot.summary.res_greatR(): whether show \"\" genes (default) \"registered\" ones. genes_list Optional vector indicating gene_id values plotted. show_rep_mean Whether show replicate mean values. ncol Number columns plot grid. default calculated automatically. title Optional plot title. ... Arguments passed methods (ignored). match_timepoints TRUE, match query time points reference time points. type_dist Type marginal distribution. Can either \"histogram\" (default), \"density\". bins Number bins use type_dist = \"histogram\". default, 30. alpha Optional opacity points scatterplot. scatterplot_size Vector c(width, height) specifying ratio width height scatterplot respect stretch shift distribution plots.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Visualise registration results — plot","text":"plot.res_greatR(): plot genes interest registration process (type = \"result\") showing original time points (type = \"original\"). plot.dist_greatR(): distance heatmap gene expression profiles time reference query. plot.summary.res_greatR(): TODO.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":null,"dir":"Reference","previous_headings":"","what":"Register or synchronize different expression profiles — register","title":"Register or synchronize different expression profiles — register","text":"register() function register expression profiles user wishes compare.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Register or synchronize different expression profiles — register","text":"","code":"register(   input,   stretches = NA,   shifts = NA,   reference,   query,   scaling_method = c(\"none\", \"z-score\", \"min-max\"),   overlapping_percent = 50,   use_optimisation = TRUE,   optimisation_method = c(\"lbfgsb\", \"nm\", \"sa\"),   optimisation_config = NULL,   exp_sd = NA,   num_cores = NA )"},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Register or synchronize different expression profiles — register","text":"input Input data frame containing replicates gene expression genotype time point. stretches Candidate registration stretch factors apply query data, required use_optimisation = FALSE. shifts Candidate registration shift values apply query data, required use_optimisation = FALSE. reference Accession name reference data. query Accession name query data. scaling_method Scaling method applied data prior registration process. Either none (default), z-score, min-max. overlapping_percent Minimum percentage overlapping time point range reference data. Shifts considered leaves least percentage overlapping time point range applying registration. use_optimisation Whether optimise registration parameters. default, TRUE. optimisation_method Optimisation method use. Either \"lbfgsb\" L-BFGS-B (default), \"nm\" Nelder-Mead, \"sa\" Simulated Annealing. optimisation_config Optional list arguments override default optimisation configuration. exp_sd Optional experimental standard deviation expression replicates. num_cores Number cores use user wants register genes asynchronously (parallel) background machine. default, NA, registration run without parallelisation.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Register or synchronize different expression profiles — register","text":"function returns res_greatR object containing: data table containing scaled input data additional timepoint_reg column applying registration parameters query data. model_comparison table comparing optimal registration function gene (based all_shifts_df scores) model registration applied. fun_args list arguments used calling function.","code":""},{"path":"https://ruthkr.github.io/greatR/reference/register.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Register or synchronize different expression profiles — register","text":"","code":"if (FALSE) { # Load a data frame from the sample data data_path <- system.file(\"extdata/brapa_arabidopsis_data.csv\", package = \"greatR\") all_data <- utils::read.csv(data_path)  # Running the registration registration_results <- register(   input = all_data,   reference = \"Ro18\",   query = \"Col0\" ) }"},{"path":"https://ruthkr.github.io/greatR/reference/summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarise registration results — summary","title":"Summarise registration results — summary","text":"Summarise registration results","code":""},{"path":"https://ruthkr.github.io/greatR/reference/summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarise registration results — summary","text":"","code":"# S3 method for res_greatR summary(object, ...)"},{"path":"https://ruthkr.github.io/greatR/reference/summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarise registration results — summary","text":"object Registration results, output register() registration process. ... Arguments passed methods (ignored).","code":""},{"path":"https://ruthkr.github.io/greatR/reference/summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarise registration results — summary","text":"function returns list containing: summary table containing summary registration results. registered_genes vector gene accessions successfully registered. non_registered_genes vector non-registered gene accessions. reg_params table containing distribution registration parameters.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-200","dir":"Changelog","previous_headings":"","what":"greatR 2.0.0","title":"greatR 2.0.0","text":"CRAN release: 2024-04-09 Added {patchwork} dependency. Updated {greatR} logo. Updated default optimisation_method register() “lbfgsb” (LBFSG-B) instead “nm” (Nelder-Mead). Added sample SOC1 arabidopsis_SOC1_data.csv brapa_SOC1_data.csv extdata. Refactored optimise_registration_parameters argument register() use_optimisation. Updated register() return object S3 class res_greatR. Updated calculate_distance() return object S3 class dist_greatR. Refactored summarise_registration() summary.res_greatR() S3 method.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"improvements-2-0-0","dir":"Changelog","previous_headings":"","what":"Improvements","title":"greatR 2.0.0","text":"Deprecate use time_delta variable registration process. Added fun_args (list arguments used calling function) register() results. Updated summary.res_greatR() return NA instead [NA, NA] genes non-registered. Added reg_params (table containing distribution registration parameters) results list summary.res_greatR() method. Simplified calc_overlapping_percent() calculation. Take consideration overlapping_percent applying manual registration. Updated logic calc_variance() data replicates consider expression_value. Updated get_stretch_search_space_limits() get_shift_search_space_limits() exclude unexplorable regions search space. Improved calculate_distance() aux get_timepoint_comb_*_data() functions eliminate column selection renaming inside lapply() calls, reducing execution time 25%. Added type (“registered” “”) genes_list arguments calculate_distance() filter genes. Added new unit tests. Updated unit tests, added S3 class checks apropriate. Updated vignettes README diagrams figures. Updated vignettes additional examples, comments arguments, full coverage plot() methods.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"bug-fixes-2-0-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"greatR 2.0.0","text":"Fixed get_shift_search_space_limits() adjust shift space limits accordingly removal time_delta variable (see 48c943cd). Fixed default overlapping_percent = 0.5 (instead 50) register_manually(). Fixed get_stretch_search_space_limits() correctly determine lower upper limits single stretch value provided. Fixed issue get_shift_search_space_limits() range variables available calc_mode == \"bound\".","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"new-functions-2-0-0","dir":"Changelog","previous_headings":"","what":"New functions","title":"greatR 2.0.0","text":"bind_results() auxiliary function merge results register(). theme_greatR() function greatR_palettes list. transform_input() S3 generic accept different types input register(). plot.res_greatR() S3 method replace plot_registration_results(). plot.dist_greatR() S3 method replace plot_heatmap(). plot.summary.res_greatR() S3 method inspired WVPlots::ScatterHistC().","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-110","dir":"Changelog","previous_headings":"","what":"greatR 1.1.0","title":"greatR 1.1.0","text":"CRAN release: 2024-01-09 Added {furrr} {future} dependencies. Added num_cores parameter register() allow users run registration parallel. Added exp_sd parameter register() allow users manually set experimental gene expression variance. Updated scaling_method parameter register() scale_data() allow scaling (“none”, default), Z-score scaling (“z-score”), min-max scaling (“min-max”), updated unit tests accordingly.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"improvements-1-1-0","dir":"Changelog","previous_headings":"","what":"Improvements","title":"greatR 1.1.0","text":"Updated register() perform 3 sequential registrations using Nelder-Mead, improves results optimal stretch shift parameters. Updated calc_loglik() use sigma_squared every time point sum. Updated scaled_data() preprocess_data() return all_data object , instead list() containing all_data. Updated compare_H1_and_H2() return BIC_diff column (BIC_combined - BIC_separate), instead BIC_combined BIC_separate . Updated explore_manual_search_space() use BIC_diff instead BIC_combined calculate best_params model_comparison table. Updated register() perform 3 sequential registrations using Nelder-Mead, improves results optimal stretch shift parameters. may reverted tweaking neldermead() parameters ensure correct convergence. Added optional stretch_init shift_init get_search_space_limits(), updated optimise() allow different space_lims calculation settings: automatic, given boundary box, given initial coords (new). Removed unused mean_data calculation preprocess_data() argument scale_data(). Moved “process N genes” message register() preprocess_data() running filter_*() functions. Ensure results_list$data arranged/ordered correctly register(). Updated get_H*_model_curves() functions ensure model curves smooth. Updated parse_gene_facets() display BIC_diff facet strips. Added plot_mean_data parameter plot_registration_results(). Updated overlapping_percent parameter register() goes 0 100 (’s later normalised function avoid breakages line). Added scaling_method attribute data results register(), used plot_registration_results() build y-axis label according scaling method used. Updated brapa_arabidopsis_registration.rds file new pipeline results. Split get_search_space_limits() separate aux functions stretch shift, allows stretch shift input combinations. Updated validate_params(..., registration_type = \"optimisation\") allow stretch shift input combinations.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"bug-fixes-1-1-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"greatR 1.1.0","text":"Improved get_timepoint_comb_original_data() get_timepoint_comb_registered_data() perform cross_join() single gene_id time using lapply(), fixes “Error: vector memory exhausted (limit reached?)” error. Updated match_names() double setdiff() ensure name matching done two ways, updated corresponding unit test.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"new-functions-1-1-0","dir":"Changelog","previous_headings":"","what":"New functions","title":"greatR 1.1.0","text":"filter_incomplete_accession_pairs() filter genes missing one accession. calc_variance() preprocess data variance inside preprocess_data() instead calc_loglik(). Aux register_single_gene_*() functions inside register() simplify generalise pipeline parallel registration.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-100","dir":"Changelog","previous_headings":"","what":"greatR 1.0.0","title":"greatR 1.0.0","text":"CRAN release: 2023-07-19 Rewrote registration pipeline scratch, deprecating unnecessary, redundant auxiliary functions. Added L-BFGS-B Nelder-Mead (now default) optimisation methods {greatR}. Switched manual calculation log likelihood via calc_loglik() instead stats::logLik(). Reduced computation time 1000 times, (x30 speed-package rewrite, x35 speed-switching default optimisation method). Removed {dplyr}, {magrittr}, {purrr}, {rlang}, {stringr} package dependencies. Added {neldermead} package dependency. register() summarise_registration() get_approximate_stretch() plot_registration_results() plot_heatmap() calculate_distance()","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"improvements-1-0-0","dir":"Changelog","previous_headings":"","what":"Improvements","title":"greatR 1.0.0","text":"Simplified parameters main register() function, added scaling_method. Simplified structure output object register(). Simplified parameters summarise_registration(), plot_registration_results(), plot_heatmap(), calculate_distance() simply require results object register(), vastly simplifying usage. Improved messages, errors, progress indicators {cli}. Added correct pluralisation {cli} messages. Rewrote unit tests use {data.table} exclusively data manipulation. Added unit tests calc_loglik_H1(), calc_loglik_H2(), calc_overlapping_percent(), calculate_distance(), cross_join(), get_search_space_limits_from_params(), get_search_space_limits(), objective_fun(), optimise(), plot_heatmap(), plot_registration_results(), preprocess_data(), register_manually(), register(), summary_registration(), validate_params().","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"bug-fixes-1-0-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"greatR 1.0.0","text":"Fixed match_names() call validating accession names register() Fixed use deprecated aes_string() parsing timepoint_var using !!ggplot2::sym() call. Fixed preds left join plot_registration_results(). Fixed issue plot_registration_results() working genes unregistered type = \"registered\". Fixed calculation time_delta preprocess_data() ensure ’s grouped gene_id accession (just accession).","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-020","dir":"Changelog","previous_headings":"","what":"greatR 0.2.0","title":"greatR 0.2.0","text":"CRAN release: 2022-06-08 Added Alex Calderwood package co-author. Added vignette optimisation process. Refactored num_shifts shift_extreme parameters simplified shifts parameter.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"improvements-0-2-0","dir":"Changelog","previous_headings":"","what":"Improvements","title":"greatR 0.2.0","text":"Improved default parameter values exported functions. Added {optimization}, {purrr} package dependencies. Removed {cowplot}, {ggpubr}, {ggrepel}, {Rtsne}, {viridis} package dependencies. Cleaned {cli} messages. Removed legacy AIC references, longer used. Updated calculate_between_sample_distance() use registration_results primary parameter instead mean_df, mean_df_sc, imputed_mean_df. Added warning comparable time points found using users’ pre-defined parameters. Refactored optimise_shift_extreme maintain_min_num_overlapping_points, properly defined corrected boundary box number overlapping points whether needed maintained .","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"bug-fixes-0-2-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"greatR 0.2.0","text":"Check input accessions exist input data get_approximate_stretch(). Manually create time point sorting levels x_sample y_sample columns according plot_heatmap(). Properly handle - character accession names plot_heatmap() time points parsed correctly.","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"new-features-0-2-0","dir":"Changelog","previous_headings":"","what":"New features","title":"greatR 0.2.0","text":"Added optional parameter optimisation process using Simulated Annealing optimise_registration_params().","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"new-functions-0-2-0","dir":"Changelog","previous_headings":"","what":"New functions","title":"greatR 0.2.0","text":"preprocess_data() simplify scale_and_register_data() code reuse logic elsewhere. get_best_stretch_and_shift_simplified(). get_BIC_from_registering_data(). get_boundary_box(). optimise_registration_params_single_gene(). optimise_registration_params() wrapper optimise_registration_params_single_gene() multiple genes. get_best_stretch_and_shift_after_optimisation().","code":""},{"path":"https://ruthkr.github.io/greatR/news/index.html","id":"greatr-010","dir":"Changelog","previous_headings":"","what":"greatR 0.1.0","title":"greatR 0.1.0","text":"CRAN release: 2022-01-12 Initial release. Added NEWS.md file track changes package.","code":""}]