Updated pkgdown

_pkgdown.yml

@@ -35,17 +35,29 @@ home:
         title: Changelog
         text: <a href="news/index.html">News</a>
 reference:
-- title: Plot terms
+- title: Analytics
+- subtitle: Compute Scaling Relationships
   contents:
-  - plot_eirVpr
-  - lines_eirVpr
-  - plot_eirpr
-  - lines_eirpr
-- title: Human Infection Dynamics
-  contents: split_stratum_by_biting
-- subtitle: The SIS Model
-  contents: split_stratum_by_biting.SIS
-- title: The Adult Mosquito RMG Model
+  - xde_scaling
+  - xde_scaling_Z
+  - xde_scaling_eir
+  - xde_scaling_lambda
+  - pr2Lambda
+  - ssMYZ
+- subtitle: Convert Scaling Relationships
+  contents:
+  - xde_eir2ni
+  - xde_eir2pr
+  - xde_pr2eir
+  - xde_pr2ni
+  - xde_pr2m
+  - xde_pr2lambda
+- title: Adult Mosquito Models
+  desc: |
+     The model library for adult mosquito infection dynamics
+- subtitle: Utilities
+  contents:
+- subtitle: The Adult Mosquito RMG Model
   contents:
   - F_eggs.RMG
   - F_fqZ.RMG
@@ -62,7 +74,16 @@ reference:
   - setup_MYZpar.RMG
   - setup_MYZinits.RMG
   - update_inits_MYZ.RMG
-- title: The Garki model
+- title: Human / vertebrate host infection & Immunity
+  desc: |
+    The model library
+- subtitle: Utilities
+  contents:
+  - ssMYZ
+- subtitle: The SIS Model
+  contents:
+  - split_stratum_by_biting.SIS
+- subtitle: The Garki model
   contents:
   - F_X.garki
   - F_H.garki
@@ -80,7 +101,7 @@ reference:
   - HTC.garki
   - xde_plot_X.garki
   - xde_lines_X_garki
-- title: The SIR model
+- subtitle: The SIR model
   contents:
   - F_X.SIR
   - F_H.SIR
@@ -98,7 +119,7 @@ reference:
   - HTC.SIR
   - xde_plot_X.SIR
   - xde_lines_X_SIR
-- title: The SEIR model
+- subtitle: The SEIR model
   contents:
   - F_X.SEIR
   - F_H.SEIR
@@ -116,20 +137,9 @@ reference:
   - HTC.SEIR
   - xde_plot_X.SEIR
   - xde_lines_X_SEIR
-- title: Scaling Relationships
-  contents: ssMYZ
-- subtitle: Compute Scaling Relationships
-  contents:
-  - xde_scaling
-  - xde_scaling_Z
-  - xde_scaling_eir
-  - xde_scaling_lambda
-  - pr2Lambda
-- subtitle: Convert Scaling Relationships
+- title: Plot terms
   contents:
-  - xde_eir2ni
-  - xde_eir2pr
-  - xde_pr2eir
-  - xde_pr2ni
-  - xde_pr2m
-  - xde_pr2lambda
+  - plot_eirVpr
+  - lines_eirVpr
+  - plot_eirpr
+  - lines_eirpr

docs/pkgdown.yml

@@ -5,7 +5,7 @@ articles:
   MYZmod-RMG: MYZmod-RMG.html
   X-How_To_Add_Model: X-How_To_Add_Model.html
   Xmod-SIS: Xmod-SIS.html
-last_built: 2024-02-02T15:45Z
+last_built: 2024-02-02T16:06Z
 urls:
   reference: https://dd-harp.github.io/mobwork/reference
   article: https://dd-harp.github.io/mobwork/articles

vignettes/MYZmod-RMG.html

@@ -10,7 +10,7 @@
 
 
 
-<meta name="date" content="2024-02-01" />
+<meta name="date" content="2024-02-02" />
 
 <title>The adult mosquito model RMG</title>
 
@@ -375,7 +375,7 @@
 
 <h1 class="title toc-ignore">The adult mosquito model RMG</h1>
 <h3 class="subtitle">A Behavioral State Model</h3>
-<h4 class="date">February 01, 2024</h4>
+<h4 class="date">February 02, 2024</h4>
 
 </div>
 
@@ -385,10 +385,9 @@ <h4 class="date">February 01, 2024</h4>
 or infected and infectious. A few models have been developed that track
 also track <em>parity.</em> A different class of models tracks the
 behavioral / physiological state of mosquitoes, so we call them
-<em>behavioral state models.</em> In this model, mosquitoes are either
-<em>blood feeding</em> or <em>egg laying,</em> following Le Menach,
-<em>et al.</em> (2005)<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a>. The model also has <em>infection
-states.</em></p>
+<em>behavioral state models.</em> A model with both <em>infection
+states</em> and <em>behavioral states</em> was first published by Le
+Menach, <em>et al.</em> (2005)<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a>.</p>
 <div id="the-model" class="section level2">
 <h2>The Model</h2>
 <p>This is a patch-based model with <span class="math inline">\(p\)</span> patches, and we assume that all the
@@ -412,6 +411,7 @@ <h3>Variables</h3>
 </div>
 <div id="terms" class="section level3">
 <h3>Terms</h3>
+<p>Two terms are passed from another component of the model.</p>
 <ul>
 <li><p><span class="math inline">\(\Lambda\)</span> - the emergence rate
 of adult mosquitoes from aquatic habitats in each patch</p></li>
@@ -422,6 +422,8 @@ <h3>Terms</h3>
 </div>
 <div id="parameters" class="section level3">
 <h3>Parameters</h3>
+<p><strong>Bionomics</strong> - Each one of the following parameters can
+take on a unique value in each patch.</p>
 <ul>
 <li><p><span class="math inline">\(f\)</span> - the blood feeding
 rate</p></li>
@@ -437,28 +439,45 @@ <h3>Parameters</h3>
 emigration rate for blood-feeding mosquitoes</p></li>
 <li><p><span class="math inline">\(\sigma_q\)</span> - the patch
 emigration rate for egg-laying mosquitoes</p></li>
+</ul>
+<p><strong>Dipsersal Matrices</strong> - Each one of the following
+parameters can take on a unique value in each patch.</p>
+<ul>
 <li><p><span class="math inline">\({\cal K}_b\)</span> - the dispersal
-matrix for blood-feeding mosquitoes</p></li>
+matrix for blood-feeding mosquitoes, which has the form: <span class="math display">\[{\cal K} = \left[
+\begin{array}{ccccl}
+0 &amp; k_{1,2} &amp; k_{1,3} &amp; \ldots &amp; k_{1,p} \\
+k_{2,1} &amp; 0 &amp; k_{2,3} &amp;  \ldots &amp; k_{2,p} \\
+k_{3,1} &amp; k_{3,2} &amp; 0 &amp;  \ldots &amp; k_{3,p} \\
+\vdots&amp; \vdots &amp;\vdots &amp; \ddots &amp; k_{p-1, p} \\
+k_{p,1} &amp; k_{p,2} &amp; k_{p,3} &amp;  \ldots &amp; 0 \\
+\end{array}
+\right].\]</span> The diagonal elements are all <span class="math inline">\(0\)</span>, and other elements, <span class="math inline">\(k_{i,j} \in {\cal K}\)</span>, are the fraction of
+blood feeding mosquitoes leaving patch <span class="math inline">\(j\)</span> that end up in patch <span class="math inline">\(i\)</span>; the notation should be read as <span class="math inline">\(i \leftarrow j\)</span>, or <em>to <span class="math inline">\(i\)</span> from <span class="math inline">\(j\)</span></em>. Notably, the form of <span class="math inline">\(\cal K\)</span> is constrained such that <span class="math display">\[\sum_i k_{i,j} = 1.\]</span></p></li>
 <li><p><span class="math inline">\({\cal K}_q\)</span> - the dispersal
-matrix for egg-laying mosquitoes</p></li>
+matrix for egg-laying mosquitoes, which has the same form as <span class="math inline">\({\cal K}_b\)</span></p></li>
+</ul>
+<p><strong>The Demographic Matrices</strong></p>
+<ul>
 <li><p><span class="math inline">\(\Omega_b\)</span> - the demographic
 matrix for blood feeding mosquitoes; letting <span class="math inline">\(I\)</span> denote the identity matrix, <span class="math display">\[\Omega_b = \mbox{diag}\left(g\right) -
 \mbox{diag}\left(\sigma_b\right) \left(I - \cal K_b
 \right)\]</span></p></li>
 <li><p><span class="math inline">\(\Omega_q\)</span> - the demographic
-matrix for egg laying mosquitoes; letting <span class="math inline">\(I\)</span> denote the identity matrix,<br />
-<span class="math display">\[\mbox{diag} \left(g\right) - \mbox{diag}
-\left(\sigma_q\right) \left(I - \cal K_q \right)\]</span></p></li>
+matrix for egg laying mosquitoes; which has the same form as <span class="math inline">\(\Omega_b\)</span>.</p></li>
 </ul>
 </div>
-<div id="equations" class="section level3">
-<h3>Equations</h3>
+<div id="dynamics" class="section level3">
+<h3>Dynamics</h3>
+<p>The following equations track adult mosquito behavioral and infection
+dynamics. A key assumption is that a fraction <span class="math inline">\(q\kappa\)</span> of blood feeding, uninfected
+mosquitoes become infected, thus transition from <span class="math inline">\(U_b\)</span> to <span class="math inline">\(Y_g.\)</span></p>
 <p><span class="math display">\[
 \begin{array}{rl}
 \dfrac{dU_b}{dt} &amp;= \Lambda  + \nu U_g - f U_b - \Omega_b \cdot U_b
 \\
-\dfrac{dU_g}{dt} &amp;= f (1- f q \kappa) U_b - \nu U_g  - \Omega_g
-\cdot U_g \\
+\dfrac{dU_g}{dt} &amp;= f (1- q \kappa) U_b - \nu U_g  - \Omega_g \cdot
+U_g \\
 \dfrac{dY_b}{dt} &amp;= \nu Y_g + \phi Y_g - (f+\varphi) Y_g - \Omega_b
 \cdot Y_b \\
 \dfrac{dY_g}{dt} &amp;= f q \kappa U_b + f Y_b - (\nu + \varphi) Y_g -