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@ChristineStawitz-NOAA
ChristineStawitz-NOAA committed Dec 9, 2024
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36 changes: 15 additions & 21 deletions docs/annotated.html
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9 changes: 3 additions & 6 deletions docs/classAgeCompDataInterface-members.html
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<tr><td class="entry"><a class="el" href="classAgeCompDataInterface.html#ab4bea155960215f368f55fc226d11020">amax</a></td><td class="entry"><a class="el" href="classAgeCompDataInterface.html">AgeCompDataInterface</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classDataInterfaceBase.html#a440fbc882d52e8239332127f1ec041d3">DataInterfaceBase</a>()</td><td class="entry"><a class="el" href="classDataInterfaceBase.html">DataInterfaceBase</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
<tr><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html#a27f6c0a9860f56c17951872fe26b1515">fims_interface_objects</a></td><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html">FIMSRcppInterfaceBase</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html#abdfb6b47bd4ea86042f84590236036d7">finalize</a>()</td><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html">FIMSRcppInterfaceBase</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
<tr><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html#a44e4e3b1dd18103bf79ccb30a76f5933">finalized</a></td><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html">FIMSRcppInterfaceBase</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classAgeCompDataInterface.html#a958c311a4133ca6866cb1b0622665948">get_id</a>()</td><td class="entry"><a class="el" href="classAgeCompDataInterface.html">AgeCompDataInterface</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
<tr><td class="entry"><a class="el" href="classDataInterfaceBase.html#a88e19c1bbcc54def5095ce57143ad484">id</a></td><td class="entry"><a class="el" href="classDataInterfaceBase.html">DataInterfaceBase</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classDataInterfaceBase.html#a66892533bbb1380c43244b07c7308b9e">id_g</a></td><td class="entry"><a class="el" href="classDataInterfaceBase.html">DataInterfaceBase</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
<tr><td class="entry"><a class="el" href="classDataInterfaceBase.html#a193b46f3002eda7eaef25e2106104fbf">live_objects</a></td><td class="entry"><a class="el" href="classDataInterfaceBase.html">DataInterfaceBase</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classDataInterfaceBase.html#af9ee39d3918b797fd8f5b59b73865530">observed_data</a></td><td class="entry"><a class="el" href="classDataInterfaceBase.html">DataInterfaceBase</a></td><td class="entry"></td></tr>
<tr><td class="entry"><a class="el" href="classAgeCompDataInterface.html#a2ff550b84e84b05fac80726c92944ba6">to_json</a>()</td><td class="entry"><a class="el" href="classAgeCompDataInterface.html">AgeCompDataInterface</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classAgeCompDataInterface.html#a065981c4d8dd880ce7f3892502e8b8fe">ymax</a></td><td class="entry"><a class="el" href="classAgeCompDataInterface.html">AgeCompDataInterface</a></td><td class="entry"></td></tr>
<tr><td class="entry"><a class="el" href="classAgeCompDataInterface.html#a166f71a43a8c71e567bf8acb1d426d13">~AgeCompDataInterface</a>()</td><td class="entry"><a class="el" href="classAgeCompDataInterface.html">AgeCompDataInterface</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classDataInterfaceBase.html#a3bf54a43965ae51e7a881f359fa0019b">~DataInterfaceBase</a>()</td><td class="entry"><a class="el" href="classDataInterfaceBase.html">DataInterfaceBase</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
<tr><td class="entry"><a class="el" href="classAgeCompDataInterface.html#a065981c4d8dd880ce7f3892502e8b8fe">ymax</a></td><td class="entry"><a class="el" href="classAgeCompDataInterface.html">AgeCompDataInterface</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classAgeCompDataInterface.html#a166f71a43a8c71e567bf8acb1d426d13">~AgeCompDataInterface</a>()</td><td class="entry"><a class="el" href="classAgeCompDataInterface.html">AgeCompDataInterface</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
<tr><td class="entry"><a class="el" href="classDataInterfaceBase.html#a3bf54a43965ae51e7a881f359fa0019b">~DataInterfaceBase</a>()</td><td class="entry"><a class="el" href="classDataInterfaceBase.html">DataInterfaceBase</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
</table></div><!-- contents -->
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virtual uint32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classAgeCompDataInterface.html#a958c311a4133ca6866cb1b0622665948">get_id</a> ()</td></tr>
<tr class="memdesc:a958c311a4133ca6866cb1b0622665948"><td class="mdescLeft">&#160;</td><td class="mdescRight">get the ID of the interface base object <br /></td></tr>
<tr class="separator:a958c311a4133ca6866cb1b0622665948"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a2ff550b84e84b05fac80726c92944ba6"><td class="memItemLeft" align="right" valign="top"><a id="a2ff550b84e84b05fac80726c92944ba6"></a>
virtual std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classAgeCompDataInterface.html#a2ff550b84e84b05fac80726c92944ba6">to_json</a> ()</td></tr>
<tr class="memdesc:a2ff550b84e84b05fac80726c92944ba6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Convert the data to json representation for the output. <br /></td></tr>
<tr class="separator:a2ff550b84e84b05fac80726c92944ba6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_methods_classDataInterfaceBase"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classDataInterfaceBase')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classDataInterfaceBase.html">DataInterfaceBase</a></td></tr>
<tr class="memitem:a440fbc882d52e8239332127f1ec041d3 inherit pub_methods_classDataInterfaceBase"><td class="memItemLeft" align="right" valign="top"><a id="a440fbc882d52e8239332127f1ec041d3"></a>
&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classDataInterfaceBase.html#a440fbc882d52e8239332127f1ec041d3">DataInterfaceBase</a> ()</td></tr>
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virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classDataInterfaceBase.html#a330a22bd2b5488b310024342338933c5">add_to_fims_tmb</a> ()</td></tr>
<tr class="memdesc:a330a22bd2b5488b310024342338933c5 inherit pub_methods_classDataInterfaceBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">add_to_fims_tmb dummy method <br /></td></tr>
<tr class="separator:a330a22bd2b5488b310024342338933c5 inherit pub_methods_classDataInterfaceBase"><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:abdfb6b47bd4ea86042f84590236036d7 inherit pub_methods_classFIMSRcppInterfaceBase"><td class="memItemLeft" align="right" valign="top"><a id="abdfb6b47bd4ea86042f84590236036d7"></a>
virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classFIMSRcppInterfaceBase.html#abdfb6b47bd4ea86042f84590236036d7">finalize</a> ()</td></tr>
<tr class="memdesc:abdfb6b47bd4ea86042f84590236036d7 inherit pub_methods_classFIMSRcppInterfaceBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object. <br /></td></tr>
<tr class="separator:abdfb6b47bd4ea86042f84590236036d7 inherit pub_methods_classFIMSRcppInterfaceBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a>
Public Attributes</h2></td></tr>
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<tr class="separator:af9ee39d3918b797fd8f5b59b73865530 inherit pub_attribs_classDataInterfaceBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a88e19c1bbcc54def5095ce57143ad484 inherit pub_attribs_classDataInterfaceBase"><td class="memItemLeft" align="right" valign="top">uint32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classDataInterfaceBase.html#a88e19c1bbcc54def5095ce57143ad484">id</a></td></tr>
<tr class="separator:a88e19c1bbcc54def5095ce57143ad484 inherit pub_attribs_classDataInterfaceBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_attribs_classFIMSRcppInterfaceBase"><td colspan="2" onclick="javascript:toggleInherit('pub_attribs_classFIMSRcppInterfaceBase')"><img src="closed.png" alt="-"/>&#160;Public Attributes inherited from <a class="el" href="classFIMSRcppInterfaceBase.html">FIMSRcppInterfaceBase</a></td></tr>
<tr class="memitem:a44e4e3b1dd18103bf79ccb30a76f5933 inherit pub_attribs_classFIMSRcppInterfaceBase"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classFIMSRcppInterfaceBase.html#a44e4e3b1dd18103bf79ccb30a76f5933">finalized</a> = false</td></tr>
<tr class="separator:a44e4e3b1dd18103bf79ccb30a76f5933 inherit pub_attribs_classFIMSRcppInterfaceBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html#a9183d9379777d8be70ab66af1a07f94c">add_to_fims_tmb</a>()</td><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html">FIMSRcppInterfaceBase</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</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></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#afe2980ec7c59a65a74d9d94ff47a6d41">estimate_log_devs</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#a8180838808f9c5d9f6840e7694218b07">estimated_log_devs</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#a785f95507532e23b39bb9a2f10258e5c">estimated_log_rzero</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#a4a34dc749e25e4466829e567a4495243">estimated_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="classBevertonHoltRecruitmentInterface.html#a769423d2ff84105da200df7ccdb12593">evaluate</a>(double spawners, double ssbzero)</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><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#a769423d2ff84105da200df7ccdb12593">evaluate</a>(double spawners, double ssbzero)</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 class="even"><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#a0c22b325e9d6afa6d9d1ccf140a75ad1">evaluate_nll</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><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html#a27f6c0a9860f56c17951872fe26b1515">fims_interface_objects</a></td><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html">FIMSRcppInterfaceBase</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#a4e183cccdd0aac1162b621b663b2848a">finalize</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><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html#a44e4e3b1dd18103bf79ccb30a76f5933">finalized</a></td><td class="entry"><a class="el" href="classFIMSRcppInterfaceBase.html">FIMSRcppInterfaceBase</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#aca73a10cce5316257a27744622cd4e13">get_id</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><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html#a3edf8070f5555b4868b429f7ef1b41be">id</a></td><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html#add97b934e6c02e4c768d71d2d50bc2fd">id_g</a></td><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
<tr><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html#a37028a265deac1c36cdc879d5d6ac18a">live_objects</a></td><td class="entry"><a class="el" href="classRecruitmentInterfaceBase.html">RecruitmentInterfaceBase</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#a17e12fbcc067297e0c04e0c0b06c0226">log_devs</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#a926b4044a3612a96d7d4a8ad482a0a14">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#a3bed47b44fe4d76bd83cbe5ab656d5c3">logit_steep</a></td><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html">BevertonHoltRecruitmentInterface</a></td><td class="entry"></td></tr>
<tr bgcolor="#f0f0f0"><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 class="even"><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#a3fe268ea362772d045c4fe7618bcf8fc">to_json</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 class="even"><td class="entry"><a class="el" href="classBevertonHoltRecruitmentInterface.html#a82ef977b840ba6c2881eee57178861cd">log_devs</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#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 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>
</table></div><!-- contents -->
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