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diff --git a/covariates.Rmd b/covariates.Rmd
@@ -1,4 +1,4 @@
-# Covariates {#covariates}
+# Covariates {#covariateschapter}
 
 ## Missing values
 

diff --git a/dispersal.Rmd b/dispersal.Rmd
@@ -1,4 +1,4 @@
-# Movements between sites, and states {#dispersal}
+# Sites and states {#dispersal}
 
 WORK IN PROGRESS. **I'm missing a section on gof w/ R2ucare and posterior predictive checks/Bayesian p-values.**
 

diff --git a/docs/404.html b/docs/404.html
@@ -78,12 +78,12 @@ <h1>
 <li><a class="" href="hmmcapturerecapture.html"><span class="header-section-number">3</span> Hidden Markov models</a></li>
 <li class="book-part">II. Transitions</li>
 <li><a class="" href="introduction-4.html">Introduction</a></li>
-<li><a class="" href="survival.html"><span class="header-section-number">4</span> Survival</a></li>
-<li><a class="" href="dispersal.html"><span class="header-section-number">5</span> Movements between sites, and states</a></li>
+<li><a class="" href="survival.html"><span class="header-section-number">4</span> Live and dead</a></li>
+<li><a class="" href="dispersal.html"><span class="header-section-number">5</span> Sites and states</a></li>
 <li class="book-part">III. Case studies</li>
 <li><a class="" href="introduction-7.html">Introduction</a></li>
 <li><a class="" href="tradeoffs.html"><span class="header-section-number">6</span> Life history</a></li>
-<li><a class="" href="covariates.html"><span class="header-section-number">7</span> Covariates</a></li>
+<li><a class="" href="covariateschapter.html"><span class="header-section-number">7</span> Covariates</a></li>
 <li><a class="" href="misc.html"><span class="header-section-number">8</span> Miscelleanous</a></li>
 <li><a class="" href="lackoffit.html"><span class="header-section-number">9</span> Lack of fit</a></li>
 <li class="book-part">IV. Conclusions</li>

diff --git a/docs/about-the-author.html b/docs/about-the-author.html
@@ -78,12 +78,12 @@ <h1>
 <li><a class="" href="hmmcapturerecapture.html"><span class="header-section-number">3</span> Hidden Markov models</a></li>
 <li class="book-part">II. Transitions</li>
 <li><a class="" href="introduction-4.html">Introduction</a></li>
-<li><a class="" href="survival.html"><span class="header-section-number">4</span> Survival</a></li>
-<li><a class="" href="dispersal.html"><span class="header-section-number">5</span> Movements between sites, and states</a></li>
+<li><a class="" href="survival.html"><span class="header-section-number">4</span> Live and dead</a></li>
+<li><a class="" href="dispersal.html"><span class="header-section-number">5</span> Sites and states</a></li>
 <li class="book-part">III. Case studies</li>
 <li><a class="" href="introduction-7.html">Introduction</a></li>
 <li><a class="" href="tradeoffs.html"><span class="header-section-number">6</span> Life history</a></li>
-<li><a class="" href="covariates.html"><span class="header-section-number">7</span> Covariates</a></li>
+<li><a class="" href="covariateschapter.html"><span class="header-section-number">7</span> Covariates</a></li>
 <li><a class="" href="misc.html"><span class="header-section-number">8</span> Miscelleanous</a></li>
 <li><a class="" href="lackoffit.html"><span class="header-section-number">9</span> Lack of fit</a></li>
 <li class="book-part">IV. Conclusions</li>

diff --git a/docs/covariates.html b/docs/covariates.html
@@ -79,7 +79,7 @@ <h1>
 <li class="book-part">II. Transitions</li>
 <li><a class="" href="introduction-4.html">Introduction</a></li>
 <li><a class="" href="survival.html"><span class="header-section-number">4</span> Survival</a></li>
-<li><a class="" href="dispersal.html"><span class="header-section-number">5</span> Movements between sites, and states</a></li>
+<li><a class="" href="dispersal.html"><span class="header-section-number">5</span> Of sites and states</a></li>
 <li class="book-part">III. Case studies</li>
 <li><a class="" href="introduction-7.html">Introduction</a></li>
 <li><a class="" href="tradeoffs.html"><span class="header-section-number">6</span> Life history</a></li>

diff --git a/docs/covariateschapter.html b/docs/covariateschapter.html
@@ -0,0 +1,218 @@
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+<title>Chapter 7 Covariates | Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</title>
+<meta name="author" content="Olivier Gimenez">
+<meta name="description" content="7.1 Missing values NAs reprise du papier de Bonner, ou modèle de croissance poisson, ou rien hein… Work on missing values by Bonner et al. (2006) and Langrock and King (2013) and Worthington et...">
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+      <h1>
+        <a href="index.html" title="Theory and Case Studies in R">Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</a>:
+        <small class="text-muted">Theory and Case Studies in R</small>
+      </h1>
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+      <nav aria-label="Table of contents"><h2>Table of contents</h2>
+        <ul class="book-toc list-unstyled">
+<li><a class="" href="index.html">Welcome</a></li>
+<li><a class="" href="preface.html">Preface</a></li>
+<li><a class="" href="about-the-author.html">About the author</a></li>
+<li class="book-part">I. Foundations</li>
+<li><a class="" href="introduction.html">Introduction</a></li>
+<li><a class="" href="crashcourse.html"><span class="header-section-number">1</span> Bayesian statistics &amp; MCMC</a></li>
+<li><a class="" href="intronimble.html"><span class="header-section-number">2</span> NIMBLE tutorial</a></li>
+<li><a class="" href="hmmcapturerecapture.html"><span class="header-section-number">3</span> Hidden Markov models</a></li>
+<li class="book-part">II. Transitions</li>
+<li><a class="" href="introduction-4.html">Introduction</a></li>
+<li><a class="" href="survival.html"><span class="header-section-number">4</span> Live and dead</a></li>
+<li><a class="" href="dispersal.html"><span class="header-section-number">5</span> Sites and states</a></li>
+<li class="book-part">III. Case studies</li>
+<li><a class="" href="introduction-7.html">Introduction</a></li>
+<li><a class="" href="tradeoffs.html"><span class="header-section-number">6</span> Life history</a></li>
+<li><a class="active" href="covariateschapter.html"><span class="header-section-number">7</span> Covariates</a></li>
+<li><a class="" href="misc.html"><span class="header-section-number">8</span> Miscelleanous</a></li>
+<li><a class="" href="lackoffit.html"><span class="header-section-number">9</span> Lack of fit</a></li>
+<li class="book-part">IV. Conclusions</li>
+<li><a class="" href="introduction-8.html">Introduction</a></li>
+<li><a class="" href="take-home-messages.html">Take-home messages</a></li>
+<li><a class="" href="references.html">References</a></li>
+</ul>
+
+        <div class="book-extra">
+          <p><a id="book-repo" href="https://github.com/oliviergimenez/banana-book">View book source <i class="fab fa-github"></i></a></p>
+        </div>
+      </nav>
+</div>
+  </header><main class="col-sm-12 col-md-9 col-lg-7" id="content"><div id="covariateschapter" class="section level1" number="7">
+<h1>
+<span class="header-section-number">7</span> Covariates<a class="anchor" aria-label="anchor" href="#covariateschapter"><i class="fas fa-link"></i></a>
+</h1>
+<div id="missing-values" class="section level2" number="7.1">
+<h2>
+<span class="header-section-number">7.1</span> Missing values<a class="anchor" aria-label="anchor" href="#missing-values"><i class="fas fa-link"></i></a>
+</h2>
+<p>NAs reprise du papier de Bonner, ou modèle de croissance poisson, ou rien hein…</p>
+<p>Work on missing values by <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1541-0420.2005.00399.x">Bonner et al. (2006)</a> and <a href="https://projecteuclid.org/journals/annals-of-applied-statistics/volume-7/issue-3/Maximum-likelihood-estimation-of-markrecapturerecovery-models-in-the-presence-of/10.1214/13-AOAS644.full">Langrock and King (2013)</a> and <a href="https://link.springer.com/article/10.1007/s13253-014-0184-z">Worthington et al. (2015)</a>.</p>
+</div>
+<div id="nonlinearities" class="section level2" number="7.2">
+<h2>
+<span class="header-section-number">7.2</span> Nonlinearities<a class="anchor" aria-label="anchor" href="#nonlinearities"><i class="fas fa-link"></i></a>
+</h2>
+<p>splines à la main et avec jagam, ex snow petrels</p>
+</div>
+<div id="covariate-selection" class="section level2" number="7.3">
+<h2>
+<span class="header-section-number">7.3</span> Covariate selection<a class="anchor" aria-label="anchor" href="#covariate-selection"><i class="fas fa-link"></i></a>
+</h2>
+<p>rjmcmc on turdus merila, papier Evolution Gimenez. Exemple cigognes, papier Gimenez WinBUGS.</p>
+</div>
+<div id="sex-uncertainty" class="section level2" number="7.4">
+<h2>
+<span class="header-section-number">7.4</span> Sex uncertainty<a class="anchor" aria-label="anchor" href="#sex-uncertainty"><i class="fas fa-link"></i></a>
+</h2>
+<p><span class="citation">Pradel et al. (<a href="references.html#ref-PradelEtAl2008">2008</a>)</span> and <span class="citation">Genovart, Pradel, and Oro (<a href="references.html#ref-genovart_exploiting_2012">2012</a>)</span></p>
+</div>
+<div id="actuarial-senescence" class="section level2" number="7.5">
+<h2>
+<span class="header-section-number">7.5</span> Actuarial senescence<a class="anchor" aria-label="anchor" href="#actuarial-senescence"><i class="fas fa-link"></i></a>
+</h2>
+<p><span class="citation">Choquet et al. (<a href="references.html#ref-choquet_semi-markov_2011">2011</a>)</span>, <span class="citation">Péron et al. (<a href="references.html#ref-peron_evidence_2016">2016</a>)</span>, Marzolin on dipper in Ecology.</p>
+</div>
+<div id="covariate-on-multinomial-logit-link" class="section level2" number="7.6">
+<h2>
+<span class="header-section-number">7.6</span> Covariate on multinomial logit link<a class="anchor" aria-label="anchor" href="#covariate-on-multinomial-logit-link"><i class="fas fa-link"></i></a>
+</h2>
+<p>papier Loreleï</p>
+</div>
+<div id="uncertainty-in-age" class="section level2" number="7.7">
+<h2>
+<span class="header-section-number">7.7</span> Uncertainty in age<a class="anchor" aria-label="anchor" href="#uncertainty-in-age"><i class="fas fa-link"></i></a>
+</h2>
+<p>Papier Vincenzo et d’autre papiers.</p>
+
+</div>
+</div>
+  <div class="chapter-nav">
+<div class="prev"><a href="tradeoffs.html"><span class="header-section-number">6</span> Life history</a></div>
+<div class="next"><a href="misc.html"><span class="header-section-number">8</span> Miscelleanous</a></div>
+</div></main><div class="col-md-3 col-lg-2 d-none d-md-block sidebar sidebar-chapter">
+    <nav id="toc" data-toggle="toc" aria-label="On this page"><h2>On this page</h2>
+      <ul class="nav navbar-nav">
+<li><a class="nav-link" href="#covariateschapter"><span class="header-section-number">7</span> Covariates</a></li>
+<li><a class="nav-link" href="#missing-values"><span class="header-section-number">7.1</span> Missing values</a></li>
+<li><a class="nav-link" href="#nonlinearities"><span class="header-section-number">7.2</span> Nonlinearities</a></li>
+<li><a class="nav-link" href="#covariate-selection"><span class="header-section-number">7.3</span> Covariate selection</a></li>
+<li><a class="nav-link" href="#sex-uncertainty"><span class="header-section-number">7.4</span> Sex uncertainty</a></li>
+<li><a class="nav-link" href="#actuarial-senescence"><span class="header-section-number">7.5</span> Actuarial senescence</a></li>
+<li><a class="nav-link" href="#covariate-on-multinomial-logit-link"><span class="header-section-number">7.6</span> Covariate on multinomial logit link</a></li>
+<li><a class="nav-link" href="#uncertainty-in-age"><span class="header-section-number">7.7</span> Uncertainty in age</a></li>
+</ul>
+
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