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NOAA-FIMS · Oct 24, 2023 · 856e788 · 856e788
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diff --git a/docs/fleet_8hpp_source.html b/docs/fleet_8hpp_source.html
@@ -204,13 +204,13 @@
 <div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;        expected_acomp.resize(this-&gt;nages);</div>
 <div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;        Type sum = 0.0;</div>
 <div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> a = 0; a &lt; this-&gt;<a class="code" href="structfims_1_1Fleet.html#a8a81de06e87320303de61a48cf7c6ce1">nages</a>; a++) {</div>
-<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;          <span class="keywordtype">size_t</span> index_ya = y * this-&gt;nages + a;</div>
-<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;          sum += this-&gt;catch_numbers_at_age[index_ya];</div>
+<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;          <span class="keywordtype">size_t</span> i_age_year = y * this-&gt;nages + a;</div>
+<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;          sum += this-&gt;catch_numbers_at_age[i_age_year];</div>
 <div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;        }</div>
 <div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160; </div>
 <div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> a = 0; a &lt; this-&gt;<a class="code" href="structfims_1_1Fleet.html#a8a81de06e87320303de61a48cf7c6ce1">nages</a>; a++) {</div>
-<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;          <span class="keywordtype">size_t</span> index_ya = y * this-&gt;nages + a;</div>
-<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;          expected_acomp[a] = this-&gt;catch_numbers_at_age[index_ya] /</div>
+<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;          <span class="keywordtype">size_t</span> i_age_year = y * this-&gt;nages + a;</div>
+<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;          expected_acomp[a] = this-&gt;catch_numbers_at_age[i_age_year] /</div>
 <div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;                              sum;  <span class="comment">// probabilities for ages</span></div>
 <div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160; </div>
 <div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;          observed_acomp[a] = this-&gt;<a class="code" href="structfims_1_1Fleet.html#a1fcf95f3fbe97fbad3e79032d03cb63a">observed_agecomp_data</a>-&gt;at(y, a);</div>

diff --git a/docs/functions_c.html b/docs/functions_c.html
@@ -72,49 +72,49 @@
 
 <h3><a id="index_c"></a>- c -</h3><ul>
 <li>CalculateBiomass()
-: <a class="el" href="structfims_1_1Population.html#aa99d3a12832981bde02ec6209b8bb8f3">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#acb272698aa52b3300e5f59543e8d6c69">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateCatch()
 : <a class="el" href="structfims_1_1Population.html#a42ae74167edbd0c33c3631dd53a098bf">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateCatchNumbersAA()
-: <a class="el" href="structfims_1_1Population.html#a52659a5dd17dd5e4037baf8d5a2c3b03">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a246521e79a706259e889bd3c6c98d997">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateCatchWeightAA()
 : <a class="el" href="structfims_1_1Population.html#a0c1dbf679cd29f6feaa086ffc05d5448">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateIndex()
-: <a class="el" href="structfims_1_1Population.html#a51ecf9f79d9c1dc1f518429e1f9428cd">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a1c8f27b40986041c8d5763aced0b0e8b">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateInitialNumbersAA()
-: <a class="el" href="structfims_1_1Population.html#a03ccdec7810da08b0f2ab01f83e24b21">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a8c178c4605bad2716c2fcc1589780119">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateMaturityAA()
-: <a class="el" href="structfims_1_1Population.html#a76fdbc84a14ec45b45b3c0dcc4181dca">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a9d2dcc253a1943c34ba1f4f398cc09a9">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateMortality()
-: <a class="el" href="structfims_1_1Population.html#aeb128a695221f8dedb2e03bca4e02cd3">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#ae9b14d81d9ab060ce90c61845f3267f7">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateNumbersAA()
-: <a class="el" href="structfims_1_1Population.html#aef69a0ce476738d9d8d7bf67ca080478">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a0d1570631e36c111589328bf95ceb5b6">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateRecruitment()
-: <a class="el" href="structfims_1_1Population.html#aed32c40be2379d05825dcb659b6c6bbc">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a5d8acb1c398f7e1598d5c276de870c2f">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateSBPR0()
 : <a class="el" href="structfims_1_1Population.html#aec0f5f622bf1504b7a16f0f33731b966">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateSpawningBiomass()
-: <a class="el" href="structfims_1_1Population.html#a0dfd20d074e80ec9538df0c3cd9087d5">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#ad96495905afefcebfee2bdfb78f656e5">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateUnfishedBiomass()
-: <a class="el" href="structfims_1_1Population.html#a2c5bc92d6a9a2ae8eff2a8c9d14e0c35">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#af2c3a279222631987832bb8cd5ac2823">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateUnfishedNumbersAA()
-: <a class="el" href="structfims_1_1Population.html#af8c7871660e49a568d5a3592ed798efa">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a00d940dd02cd06495f73fef142840956">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateUnfishedSpawningBiomass()
-: <a class="el" href="structfims_1_1Population.html#a9372f8eb17ddfdce1456fdd368b3c1d6">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#aafa7d7a11bd86b3a9b72e1b82a1cf9f2">fims::Population&lt; Type &gt;</a>
 </li>
 <li>catch_at_age
 : <a class="el" href="structfims_1_1Fleet.html#a35e648c97bb303d6c57bac942c7a8c41">fims::Fleet&lt; Type &gt;</a>

diff --git a/docs/functions_func.html b/docs/functions_func.html
@@ -86,49 +86,49 @@ <h3><a id="index_a"></a>- a -</h3><ul>
 
 <h3><a id="index_c"></a>- c -</h3><ul>
 <li>CalculateBiomass()
-: <a class="el" href="structfims_1_1Population.html#aa99d3a12832981bde02ec6209b8bb8f3">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#acb272698aa52b3300e5f59543e8d6c69">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateCatch()
 : <a class="el" href="structfims_1_1Population.html#a42ae74167edbd0c33c3631dd53a098bf">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateCatchNumbersAA()
-: <a class="el" href="structfims_1_1Population.html#a52659a5dd17dd5e4037baf8d5a2c3b03">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a246521e79a706259e889bd3c6c98d997">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateCatchWeightAA()
 : <a class="el" href="structfims_1_1Population.html#a0c1dbf679cd29f6feaa086ffc05d5448">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateIndex()
-: <a class="el" href="structfims_1_1Population.html#a51ecf9f79d9c1dc1f518429e1f9428cd">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a1c8f27b40986041c8d5763aced0b0e8b">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateInitialNumbersAA()
-: <a class="el" href="structfims_1_1Population.html#a03ccdec7810da08b0f2ab01f83e24b21">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a8c178c4605bad2716c2fcc1589780119">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateMaturityAA()
-: <a class="el" href="structfims_1_1Population.html#a76fdbc84a14ec45b45b3c0dcc4181dca">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a9d2dcc253a1943c34ba1f4f398cc09a9">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateMortality()
-: <a class="el" href="structfims_1_1Population.html#aeb128a695221f8dedb2e03bca4e02cd3">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#ae9b14d81d9ab060ce90c61845f3267f7">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateNumbersAA()
-: <a class="el" href="structfims_1_1Population.html#aef69a0ce476738d9d8d7bf67ca080478">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a0d1570631e36c111589328bf95ceb5b6">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateRecruitment()
-: <a class="el" href="structfims_1_1Population.html#aed32c40be2379d05825dcb659b6c6bbc">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a5d8acb1c398f7e1598d5c276de870c2f">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateSBPR0()
 : <a class="el" href="structfims_1_1Population.html#aec0f5f622bf1504b7a16f0f33731b966">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateSpawningBiomass()
-: <a class="el" href="structfims_1_1Population.html#a0dfd20d074e80ec9538df0c3cd9087d5">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#ad96495905afefcebfee2bdfb78f656e5">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateUnfishedBiomass()
-: <a class="el" href="structfims_1_1Population.html#a2c5bc92d6a9a2ae8eff2a8c9d14e0c35">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#af2c3a279222631987832bb8cd5ac2823">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateUnfishedNumbersAA()
-: <a class="el" href="structfims_1_1Population.html#af8c7871660e49a568d5a3592ed798efa">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#a00d940dd02cd06495f73fef142840956">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CalculateUnfishedSpawningBiomass()
-: <a class="el" href="structfims_1_1Population.html#a9372f8eb17ddfdce1456fdd368b3c1d6">fims::Population&lt; Type &gt;</a>
+: <a class="el" href="structfims_1_1Population.html#aafa7d7a11bd86b3a9b72e1b82a1cf9f2">fims::Population&lt; Type &gt;</a>
 </li>
 <li>CreateModel()
 : <a class="el" href="classfims_1_1Information.html#a736ba30994a8c2b3a3c5093f3e692d49">fims::Information&lt; T &gt;</a>