rebuild of vignettes

mrke · Jul 29, 2021 · e1f844b · e1f844b
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diff --git a/inst/doc/deb-model-tutorial.html b/inst/doc/deb-model-tutorial.html
diff --git a/inst/doc/ectotherm-model-tutorial.html b/inst/doc/ectotherm-model-tutorial.html
diff --git a/inst/doc/endotherm-components-tutorial.html b/inst/doc/endotherm-components-tutorial.html
diff --git a/inst/doc/endotherm-model-equations.R b/inst/doc/endotherm-model-equations.R
@@ -4,12 +4,12 @@ knitr::opts_chunk$set(
 )
 library(knitr)
 
-## ---- echo=FALSE, out.width = "100%", fig.align="center", fig.cap = "Figure 1. A cross section system diagram for heat flow in an animal", fig.pos='!h'----
+## ---- echo=FALSE, out.width = "100%", fig.align="center", fig.cap = "A cross section system diagram for heat flow in an animal", fig.pos='!h'----
 include_graphics("Endo_System_Diagram.jpg")
 
-## ---- echo=FALSE, out.width = "100%", fig.align="center", fig.cap = "Figure 2. The relationship between subroutines of the endoR program in NicheMapR.", fig.pos='!h'----
+## ---- echo=FALSE, out.width = "100%", fig.align="center", fig.cap = "The relationship between subroutines of the endoR program in NicheMapR.", fig.pos='!h'----
 include_graphics("EndoR_scheme.jpg")
 
-## ---- echo=FALSE, out.width = "100%", fig.align="center", fig.cap = "Figure 3. The exchange of respiratory gases entering the respiratory tract at imagainary surface 1, with carbon dioxide and water vapour added from the body and oxygen consumed according to the metabolic rate and the remainder exiting the body at imaginary surface 2. Figure modified from Porter et al. (2000)", fig.pos='!h'----
+## ---- echo=FALSE, out.width = "100%", fig.align="center", fig.cap = "The exchange of respiratory gases entering the respiratory tract at imagainary surface 1, with carbon dioxide and water vapour added from the body and oxygen consumed according to the metabolic rate and the remainder exiting the body at imaginary surface 2. Figure modified from Porter et al. (2000)", fig.pos='!h'----
 include_graphics("Gas_System_Diagram.jpg")
 
diff --git a/inst/doc/endotherm-model-equations.Rmd b/inst/doc/endotherm-model-equations.Rmd
diff --git a/inst/doc/endotherm-model-equations.html b/inst/doc/endotherm-model-equations.html
diff --git a/inst/doc/endotherm-model-tutorial.html b/inst/doc/endotherm-model-tutorial.html
diff --git a/inst/doc/microclimate-IO.html b/inst/doc/microclimate-IO.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Michael Kearney" />
 
-<meta name="date" content="2021-07-20" />
+<meta name="date" content="2021-07-29" />
 
 <title>Inputs and outputs of the NicheMapR microclimate model</title>
 
@@ -241,7 +241,7 @@
 
 <h1 class="title toc-ignore">Inputs and outputs of the NicheMapR microclimate model</h1>
 <h4 class="author">Michael Kearney</h4>
-<h4 class="date">2021-07-20</h4>
+<h4 class="date">2021-07-29</h4>
 
 
 

diff --git a/inst/doc/microclimate-hourly-input-example.html b/inst/doc/microclimate-hourly-input-example.html
diff --git a/inst/doc/microclimate-model-theory-equations.html b/inst/doc/microclimate-model-theory-equations.html
diff --git a/inst/doc/microclimate-model-tutorial.html b/inst/doc/microclimate-model-tutorial.html
diff --git a/inst/doc/microclimate-monthly-input-example.html b/inst/doc/microclimate-monthly-input-example.html
diff --git a/inst/doc/microclimate_inputs.html b/inst/doc/microclimate_inputs.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Michael R. Kearney" />
 
-<meta name="date" content="2021-07-20" />
+<meta name="date" content="2021-07-29" />
 
 <title>Microclimate Model Input Data</title>
 
@@ -241,7 +241,7 @@
 
 <h1 class="title toc-ignore">Microclimate Model Input Data</h1>
 <h4 class="author">Michael R. Kearney</h4>
-<h4 class="date">2021-07-20</h4>
+<h4 class="date">2021-07-29</h4>
 
 
 

diff --git a/inst/doc/properties-of-air.html b/inst/doc/properties-of-air.html
diff --git a/inst/doc/transient-equation-derivations.html b/inst/doc/transient-equation-derivations.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Warren Porter &amp; Michael Kearney" />
 
-<meta name="date" content="2021-07-20" />
+<meta name="date" content="2021-07-29" />
 
 <title>Transient Equation Derivations</title>
 
@@ -241,7 +241,7 @@
 
 <h1 class="title toc-ignore">Transient Equation Derivations</h1>
 <h4 class="author">Warren Porter &amp; Michael Kearney</h4>
-<h4 class="date">2021-07-20</h4>
+<h4 class="date">2021-07-29</h4>
 
 
 
@@ -621,7 +621,7 @@ <h2>4. One lump or two? Computing internal to external resistance ratios</h2>
 <p>and <span class="math inline">\(R_b/R_e\)</span> = 0.006. Since <span class="math inline">\(R_e\)</span> is over 33 times greater than <span class="math inline">\(R_b\)</span>, <span class="math inline">\(R_e\)</span> is controlling heat loss and a 40 g lizard like the desert iguana may be treated as a single lump.</p>
 <p>Figure 3 shows calculations of Biot numbers for a range of body sizes.</p>
 <div class="figure">
-<img src="data:image/png;base64,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" alt />
+<img src="data:image/png;base64,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" alt />
 <p class="caption">The ratio of internal and external resistance (Biot number) for desert iguana-shaped lizards of different body mass at 0.45 m/s wind speed, 24 °C air and radiant temperature, 26 °C skin temperature, and flesh thermal conductivity of 0.5 W/mC.</p>
 </div>
 </div>