Docs: run Doxygen

docs/annotated.html

@@ -113,8 +113,8 @@
 <tr id="row_18_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classFleetInterfaceBase.html" target="_self">FleetInterfaceBase</a></td><td class="desc">Rcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherited and not called from R directly </td></tr>
 <tr id="row_19_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classGrowthInterfaceBase.html" target="_self">GrowthInterfaceBase</a></td><td class="desc">Rcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly </td></tr>
 <tr id="row_20_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classIndexDataInterface.html" target="_self">IndexDataInterface</a></td><td class="desc">Rcpp interface for data as an S4 object. To instantiate from R: fleet &lt;- new(fims$Index) </td></tr>
-<tr id="row_21_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classJsonParser.html" target="_self">JsonParser</a></td><td class="desc">Parses JSON strings and generates JSON values </td></tr>
-<tr id="row_22_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classJsonValue.html" target="_self">JsonValue</a></td><td class="desc">Represents a JSON value </td></tr>
+<tr id="row_21_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classJsonParser.html" target="_self">JsonParser</a></td><td class="desc"></td></tr>
+<tr id="row_22_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classJsonValue.html" target="_self">JsonValue</a></td><td class="desc"></td></tr>
 <tr id="row_23_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classLogisticMaturityInterface.html" target="_self">LogisticMaturityInterface</a></td><td class="desc">Rcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity &lt;- new(fims$logistic_maturity) </td></tr>
 <tr id="row_24_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classLogisticSelectivityInterface.html" target="_self">LogisticSelectivityInterface</a></td><td class="desc">Rcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity &lt;- new(fims$logistic_selectivity) </td></tr>
 <tr id="row_25_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classMaturityInterfaceBase.html" target="_self">MaturityInterfaceBase</a></td><td class="desc"><a class="el" href="classMaturityInterfaceBase.html" title="MaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible...">MaturityInterfaceBase</a> class should be inherited to define different Rcpp interfaces for each possible maturity function </td></tr>

docs/classBevertonHoltRecruitmentInterface-members.html

@@ -89,7 +89,7 @@
   <tr><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#aef43664185856d401935a02eef1ebbba">log_rzero</a></td><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html">BevertonHoltRecruitmentInterface</a></td><td class="entry"></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#ae9f46c25b71b73595850e6d24f91d1ea">log_sigma_recruit</a></td><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html">BevertonHoltRecruitmentInterface</a></td><td class="entry"></td></tr>
   <tr><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#a1d3c3a96a3ff9a872aeeb57e343e1073">logit_steep</a></td><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html">BevertonHoltRecruitmentInterface</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html#ad2cdb57b7cb0fa9bab4a3f036821872e">RecruitmentInterfaceBase</a>()</td><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>RecruitmentInterfaceBase</b>() (defined in <a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a>)</td><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>~BevertonHoltRecruitmentInterface</b>() (defined in <a class="el" href="classBevertonHoltRecruitmentInterface.html">BevertonHoltRecruitmentInterface</a>)</td><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html">BevertonHoltRecruitmentInterface</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~RecruitmentInterfaceBase</b>() (defined in <a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a>)</td><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
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docs/classBevertonHoltRecruitmentInterface.html

@@ -105,9 +105,6 @@
 <tr class="memitem:a0c22b325e9d6afa6d9d1ccf140a75ad1"><td class="memItemLeft" align="right" valign="top">virtual double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classBevertonHoltRecruitmentInterface.html#a0c22b325e9d6afa6d9d1ccf140a75ad1">evaluate_nll</a> ()</td></tr>
 <tr class="memdesc:a0c22b325e9d6afa6d9d1ccf140a75ad1"><td class="mdescLeft">&#160;</td><td class="mdescRight">evaluate recruitment nll  <a href="classBevertonHoltRecruitmentInterface.html#a0c22b325e9d6afa6d9d1ccf140a75ad1">More...</a><br /></td></tr>
 <tr class="separator:a0c22b325e9d6afa6d9d1ccf140a75ad1"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="inherit_header pub_methods_classRecruitmentInterfaceBase"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classRecruitmentInterfaceBase')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a></td></tr>
-<tr class="memitem:ad2cdb57b7cb0fa9bab4a3f036821872e inherit pub_methods_classRecruitmentInterfaceBase"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classRecruitmentInterfaceBase.html#ad2cdb57b7cb0fa9bab4a3f036821872e">RecruitmentInterfaceBase</a> ()</td></tr>
-<tr class="separator:ad2cdb57b7cb0fa9bab4a3f036821872e inherit pub_methods_classRecruitmentInterfaceBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="inherit_header pub_methods_classFIMSRcppInterfaceBase"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classFIMSRcppInterfaceBase')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classFIMSRcppInterfaceBase.html">FIMSRcppInterfaceBase</a></td></tr>
 <tr class="memitem:a9183d9379777d8be70ab66af1a07f94c inherit pub_methods_classFIMSRcppInterfaceBase"><td class="memItemLeft" align="right" valign="top"><a id="a9183d9379777d8be70ab66af1a07f94c"></a>
 virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classFIMSRcppInterfaceBase.html#a9183d9379777d8be70ab66af1a07f94c">add_to_fims_tmb</a> ()</td></tr>

docs/classGrowthInterfaceBase.html

@@ -126,6 +126,7 @@
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Rcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly. </p>
+<p>Growth Rcpp interface * </p>
 </div><h2 class="groupheader">Member Data Documentation</h2>
 <a id="aedcf584aed8f0401ebb0b2bb99c3394a"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#aedcf584aed8f0401ebb0b2bb99c3394a">&#9670;&nbsp;</a></span>id</h2>

docs/classJsonParser.html

@@ -76,21 +76,15 @@
 </div><!--header-->
 <div class="contents">
 
-<p>Parses JSON strings and generates JSON values.  
- <a href="classJsonParser.html#details">More...</a></p>
-
 <p><code>#include &lt;<a class="el" href="fims__json_8hpp_source.html">fims_json.hpp</a>&gt;</code></p>
 <table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
 Public Member Functions</h2></td></tr>
 <tr class="memitem:a1235f9548b6424f04fe7071c5d04a425"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classJsonValue.html">JsonValue</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classJsonParser.html#a1235f9548b6424f04fe7071c5d04a425">Parse</a> (const std::string &amp;json)</td></tr>
-<tr class="memdesc:a1235f9548b6424f04fe7071c5d04a425"><td class="mdescLeft">&#160;</td><td class="mdescRight">Parse a JSON string and return the corresponding JSON value.  <a href="classJsonParser.html#a1235f9548b6424f04fe7071c5d04a425">More...</a><br /></td></tr>
 <tr class="separator:a1235f9548b6424f04fe7071c5d04a425"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:ad8ffc15c33b35e9efea97829fadbb5cb"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classJsonParser.html#ad8ffc15c33b35e9efea97829fadbb5cb">WriteToFile</a> (const std::string &amp;filename, <a class="el" href="classJsonValue.html">JsonValue</a> jsonValue)</td></tr>
-<tr class="memdesc:ad8ffc15c33b35e9efea97829fadbb5cb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Write a JSON value to a file.  <a href="classJsonParser.html#ad8ffc15c33b35e9efea97829fadbb5cb">More...</a><br /></td></tr>
 <tr class="separator:ad8ffc15c33b35e9efea97829fadbb5cb"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:acccfd891551f614d40d7320dd6ae943e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classJsonParser.html#acccfd891551f614d40d7320dd6ae943e">Show</a> (<a class="el" href="classJsonValue.html">JsonValue</a> jsonValue)</td></tr>
-<tr class="memdesc:acccfd891551f614d40d7320dd6ae943e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Display a JSON value to the standard output.  <a href="classJsonParser.html#acccfd891551f614d40d7320dd6ae943e">More...</a><br /></td></tr>
 <tr class="separator:acccfd891551f614d40d7320dd6ae943e"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
@@ -111,8 +105,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a1235f9548b6424f04fe7071c
         </tr>
       </table>
 </div><div class="memdoc">
-
-<p>Parse a JSON string and return the corresponding JSON value. </p>
+<p>Parse a JSON string and return the corresponding JSON value.</p>
 <p>Parse a JSON string and return the corresponding JSON value. </p><dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
     <tr><td class="paramname">json</td><td>The JSON string to parse. </td></tr>
@@ -138,8 +131,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#acccfd891551f614d40d7320d
         </tr>
       </table>
 </div><div class="memdoc">
-
-<p>Display a JSON value to the standard output. </p>
+<p>Display a JSON value to the standard output.</p>
 <p>Display a JSON value to the standard output. </p><dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
     <tr><td class="paramname">jsonValue</td><td>The JSON value to display. </td></tr>
@@ -174,15 +166,15 @@ <h2 class="memtitle"><span class="permalink"><a href="#ad8ffc15c33b35e9efea97829
         </tr>
       </table>
 </div><div class="memdoc">
-
-<p>Write a JSON value to a file. </p>
+<p>Write a JSON value to a file.</p>
 <p>Write a JSON value to an output file. </p><dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
     <tr><td class="paramname">filename</td><td>The name of the output file. </td></tr>
     <tr><td class="paramname">jsonValue</td><td>The JSON value to write. </td></tr>
   </table>
   </dd>
 </dl>
+<p>Call a private helper function to write JSON values recursively</p>
 
 </div>
 </div>