update style

_includes/pompstyle.css

@@ -10,7 +10,7 @@ body {
 
 code {
     font-family: monospace;
-    font-size: 1.125em;
+    font-size: 125%;
 }
 
 h1, h2, h3, h4 {
@@ -48,10 +48,12 @@ a:link, a:visited {
     color: #0000ff;
     text-decoration: none;
 }
+
 a:hover, a:active {
-    color: #cc3333; 
+    color: #cc3333;
     text-decoration: none;
 }
+
 a.activated {
     text-decoration: underline;
 }
@@ -81,20 +83,24 @@ dt {
 }
 
 .emph {
-    color: #cc3333; 
+    color: #cc3333;
     font-weight: bold;
 }
 
 .emph1 {
-    color: #3333ff; 
+    color: #3333ff;
     font-weight: bold;
 }
 
-.firstcharacter { 
-    float: left; 
-    color: #3333ff; 
+.firstcharacter {
+    float: left;
+    color: #3333ff;
     font-size: 2.5em;
     line-height: 0.8em;
     vertical-align: top;
     padding-right: 5px;
 }
+
+.sourceCode, .language-r, .language-c, .language-sh {
+    color: #000066;
+}

blog.html

@@ -1,6 +1,6 @@
 ---
 layout: pomp
-id: blog
+id: news
 title: pomp news blog
 ---
 <h1>News blog</h1>

install.md

@@ -6,43 +6,45 @@ layout: pomp
 
 # Installation instructions
 
-## From CRAN:
+### From CRAN:
 
 Source and binaries for the [CRAN version are available on CRAN](http://cran.r-project.org/package=pomp){:target="_blank"}.
 
 Install **pomp** from CRAN just like any other **R** package:
-```
+```r
 install.packages("pomp")
 ```
 
-## From Github:
+### From Github:
 
 The Github version is usually several weeks ahead of the version on CRAN.
 You can install it from the Github repository by executing the following in an **R** session:  
-```
+```r
 install.packages("pomp",repos="https://kingaa.github.io/")
 ```  
 On Windows and MacOS systems, this will cause a precompiled version of the latest release of **pomp** to be installed, if one is available, and will install from source if a binary is not available.
 
+### Download and install locally
+
 You can also [download the latest release](https://github.com/kingaa/pomp/releases/) and install it locally as you would any **R** package.
 
 ---------------------------
 
-## Testing your installation
+### Testing your installation
 
 To make use of **pomp**'s facilities for accelerated computation using compiled C code, and to compile the package from source, you will want the ability to compile C code and dynamically link it into an **R** session.
 To test this, run the following in an **R** session:
-```
+```r
 source("https://kingaa.github.io/scripts/helloC.R",echo=TRUE)
 ```
 This script attempts to compile a simple C program.
 Upon success, you'll see a "Hello!" message.
 
-If this fails, consult the instructions below, according to your operating system.
+<i>If this fails, consult the instructions below, according to your operating system.</i>
 
 --------------------------
 
-## Important note for Windows users
+### Important note for Windows users
 
 To use **pomp**'s compilation facility, you need to have the **Rtools** suite installed.
 This can be [downloaded from CRAN](http://cran.r-project.org/bin/windows/Rtools){:target="_blank"}.
@@ -51,36 +53,36 @@ This can be [downloaded from CRAN](http://cran.r-project.org/bin/windows/Rtools)
 A video tutorial on installing **Rtools** is [available here](https://youtu.be/lmIhiT_QsPE){:target="_blank"}.
 
 To test your **Rtools** installation, run the following in an **R** session:
-```
+```r
 source("https://kingaa.github.io/scripts/hello.R",echo=TRUE)
 ```
 On success, you will see two "Hello!" messages.
 
 ------------------------
 
-## Important note for Mac OS users
+### Important note for Mac OS users
 
 To use **pomp**'s compilation facility, you need to have the <code>Xcode</code> app installed.
 <code>Xcode</code> is free and can be installed according to [these instructions](https://mac.r-project.org/tools/){:target="_blank"}.
 
 In addition, some users report problems installing **pomp** from source due to lack of an appropriate **gfortran** installation, which is not included by default in all versions of **Xcode**.
 If you have this problem, see [these instructions](https://mac.r-project.org/tools/){:target="_blank"}.
 To test your <code>Xcode</code> and Fortran installations, run the following in an **R** session:
-```
+```r
 source("https://kingaa.github.io/scripts/hello.R",echo=TRUE)
 ```
 On success, you will see two "Hello!" messages.
 
 ------------------------
 
-## Important note for Linux users
+### Important note for Linux users
 
 To install **pomp** from source, you will need the `gfortran` compiler on your machine and will therefore may need to install it.
 To do so on a Debian-based system (e.g., Ubuntu), for example, run:
-```
+```sh
 sudo apt install gfortran
 ```
 On an RPM-based system, run:
-```
+```sh
 sudo yum install gcc-gfortran
 ```

vignettes/C_API.Rmd

@@ -3,27 +3,13 @@ title: 'pomp C API'
 output: 
   html_document:
     theme: null
-    highlight: kate
+    highlight: haddock
     toc: yes
     toc_depth: 3
 params:
   prefix: "c_api"
 ---
 
-```{css echo=FALSE}
-a:link, a:visited {
-  color: #0000ff;
-  text-decoration: none;
-}
-a:hover, a:active {
-  color: #cc3333;
-  text-decoration: none;
-}
-code {
-  font-size: 110%;
-}
-```
-
 ```{r knitr-opts,include=FALSE,purl=FALSE,cache=FALSE}
 source("setup.R", local = knitr::knit_global())
 ```
@@ -189,16 +175,16 @@ void to_log_barycentric(double *xt, const double *x, int n);
 void from_log_barycentric(double *xt, const double *x, int n);
 ```
 
-The log-barycentric transformation takes a vector $X_i\in\mathbb{R}^n_+$, $i=1,\dots,n$, to a vector $Y_i\in\mathbb{R}^n$, where 
+The log-barycentric transformation takes a vector $X\in\mathbb{R}^n_+$ to a vector $Y\in\mathbb{R}^n$, where 
 $$Y_i = \log\frac{X_i}{\sum_j\!X_j}.$$
-The log-barycentric transformation takes every simplex defined by $\sum_i\!X_i = c$, $c$ constant, to $n$-dimensional Euclidean space $\mathbb{R}^n$.
+For every $c>0$, this transformation maps the simplex $\{X\in\mathbb{R}^n_+\;\vert\;\sum_i\!X_i = c\}$ bijectively onto $\mathbb{R}^n$.
 
 The pseudo-inverse transformation takes $\mathbb{R}^n$ to the unit simplex $S=\{X\in\mathbb{R}^n_+\;\vert\;\sum_i\!X_i=1\}$.
 Specifically,
 $$X_i = \frac{e^{Y_i}}{\sum_j\!e^{Y_j}}.$$
 
 Note that if $T:\mathbb{R}^n_+\to\mathbb{R}^n$ is the log-barycentric transformation so defined, $U$ is the pseudo-inverse, and $Id$ denotes the identity map, then $T\circ U=Id:\mathbb{R}^n\to\mathbb{R}^n$ but $U\circ T\ne Id$.
-However, if $T$ is restricted to the unit simplex, then $U\circ T=Id:S\to S$.
+However, if $T$ is restricted to the unit simplex S, then $U\circ{T\vert_{S}}=Id:S\to S$.
 
 Input:
 

vignettes/C_API.html

@@ -89,46 +89,38 @@
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     -ms-user-select: none; user-select: none;
     padding: 0 4px; width: 4em;
-    background-color: #ffffff;
-    color: #a0a0a0;
+    color: #aaaaaa;
   }
-pre.numberSource { margin-left: 3em; border-left: 1px solid #a0a0a0;  padding-left: 4px; }
+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
 div.sourceCode
-  { color: #1f1c1b; background-color: #ffffff; }
+  {   }
 @media screen {
 pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
 }
-code span { color: #1f1c1b; } /* Normal */
-code span.al { color: #bf0303; background-color: #f7e6e6; font-weight: bold; } /* Alert */
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+code span.vs { color: #008080; } /* VerbatimString */
+code span.wa { color: #008000; font-weight: bold; } /* Warning */
 
 </style>
 <script>
@@ -218,19 +210,6 @@ <h1 class="title toc-ignore">pomp C API</h1>
 </ul>
 </div>
 
-<style type="text/css">
-a:link, a:visited {
-  color: #0000ff;
-  text-decoration: none;
-}
-a:hover, a:active {
-  color: #cc3333;
-  text-decoration: none;
-}
-code {
-  font-size: 110%;
-}
-</style>
 <hr />
 <div id="overview" class="section level2">
 <h2>Overview</h2>
@@ -337,9 +316,9 @@ <h3>Logit transformation</h3>
 <h3>Log-barycentric transformation</h3>
 <div class="sourceCode" id="cb8"><pre class="sourceCode c"><code class="sourceCode c"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true"></a><span class="dt">void</span> to_log_barycentric(<span class="dt">double</span> *xt, <span class="dt">const</span> <span class="dt">double</span> *x, <span class="dt">int</span> n);</span>
 <span id="cb8-2"><a href="#cb8-2" aria-hidden="true"></a><span class="dt">void</span> from_log_barycentric(<span class="dt">double</span> *xt, <span class="dt">const</span> <span class="dt">double</span> *x, <span class="dt">int</span> n);</span></code></pre></div>
-<p>The log-barycentric transformation takes a vector <span class="math inline">\(X_i\in\mathbb{R}^n_+\)</span>, <span class="math inline">\(i=1,\dots,n\)</span>, to a vector <span class="math inline">\(Y_i\in\mathbb{R}^n\)</span>, where <span class="math display">\[Y_i = \log\frac{X_i}{\sum_j\!X_j}.\]</span> The log-barycentric transformation takes every simplex defined by <span class="math inline">\(\sum_i\!X_i = c\)</span>, <span class="math inline">\(c\)</span> constant, to <span class="math inline">\(n\)</span>-dimensional Euclidean space <span class="math inline">\(\mathbb{R}^n\)</span>.</p>
+<p>The log-barycentric transformation takes a vector <span class="math inline">\(X\in\mathbb{R}^n_+\)</span> to a vector <span class="math inline">\(Y\in\mathbb{R}^n\)</span>, where <span class="math display">\[Y_i = \log\frac{X_i}{\sum_j\!X_j}.\]</span> For every <span class="math inline">\(c&gt;0\)</span>, this transformation maps the simplex <span class="math inline">\(\{X\in\mathbb{R}^n_+\;\vert\;\sum_i\!X_i = c\}\)</span> bijectively onto <span class="math inline">\(\mathbb{R}^n\)</span>.</p>
 <p>The pseudo-inverse transformation takes <span class="math inline">\(\mathbb{R}^n\)</span> to the unit simplex <span class="math inline">\(S=\{X\in\mathbb{R}^n_+\;\vert\;\sum_i\!X_i=1\}\)</span>. Specifically, <span class="math display">\[X_i = \frac{e^{Y_i}}{\sum_j\!e^{Y_j}}.\]</span></p>
-<p>Note that if <span class="math inline">\(T:\mathbb{R}^n_+\to\mathbb{R}^n\)</span> is the log-barycentric transformation so defined, <span class="math inline">\(U\)</span> is the pseudo-inverse, and <span class="math inline">\(Id\)</span> denotes the identity map, then <span class="math inline">\(T\circ U=Id:\mathbb{R}^n\to\mathbb{R}^n\)</span> but <span class="math inline">\(U\circ T\ne Id\)</span>. However, if <span class="math inline">\(T\)</span> is restricted to the unit simplex, then <span class="math inline">\(U\circ T=Id:S\to S\)</span>.</p>
+<p>Note that if <span class="math inline">\(T:\mathbb{R}^n_+\to\mathbb{R}^n\)</span> is the log-barycentric transformation so defined, <span class="math inline">\(U\)</span> is the pseudo-inverse, and <span class="math inline">\(Id\)</span> denotes the identity map, then <span class="math inline">\(T\circ U=Id:\mathbb{R}^n\to\mathbb{R}^n\)</span> but <span class="math inline">\(U\circ T\ne Id\)</span>. However, if <span class="math inline">\(T\)</span> is restricted to the unit simplex S, then <span class="math inline">\(U\circ{T\vert_{S}}=Id:S\to S\)</span>.</p>
 <p>Input:</p>
 <ul>
 <li><code>x</code> is a pointer to vector of parameters to be tranformed either to or from log barycentric coordinates.</li>