add 3.30.19 release html

docs/SS330_User_Manual_release.html

@@ -1642,209 +1642,204 @@ <h2 data-number="6.1" id="forecast-file-options-forecast.ss"><span class="header
 </tr>
 <tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
-<td style="text-align: left;">1 = do abbreviated U.S. West Coast rebuilder output; and</td>
+<td style="text-align: left;">1 = do abbreviated U.S. West Coast rebuilder output</td>
 <td style="text-align: left;"></td>
 </tr>
 <tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
-<td style="text-align: left;">2 = do extended U.S. West Coast rebuilder output.</td>
-<td style="text-align: left;"></td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">Rebuilder catch (Year Declared):</td>
 <td style="text-align: left;">Input line is required even if Rebuilder = 0, specified in the line above.</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">&gt;0 = year first catch should be set to zero; and</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">-1 = set to 1999.</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;">2004</td>
 <td style="text-align: left;">Rebuilder start year (Year Initial):</td>
 <td style="text-align: left;">Input line is required even if Rebuilder = 0, specified two line above.</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">&gt;0 = year for current age structure; and</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">-1 = set to end year +1.</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;">1</td>
 <td style="text-align: left;">Fleet Relative F:</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">1 = use first-last allocation year; and</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">2 = read season(row) x fleet (column) set below.</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;">2</td>
 <td style="text-align: left;">Basis for maximum forecast catch:</td>
 <td style="text-align: left;">The maximum basis for forecasted catch will be implemented for the for the &quot;First year for caps and allocations&quot; selected above. The maximum catch (biomass or numbers) by fleet is specified below on the &quot;Maximum total forecast catch by fleet&quot; line.</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">2 = total catch biomass;</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">3 = retained catch biomass;</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">5 = total catch numbers; and</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">6 = retained total numbers.</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;" colspan="3">COND 2: Conditional input for fleet relative F (Enter: Season, Fleet, Relative F)</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: right;">1 1 0.6</td>
 <td style="text-align: left;">Fleet allocation by relative F fraction.</td>
 <td style="text-align: left;">The fraction of the forecast F value. For a multiple area model user must define a fraction for each fleet and each area. The total fractions must sum to one over all fleets and areas.</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: right;">1 2 0.4</td>
 <td style="text-align: left;"></td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: right;">-9999 0 0</td>
 <td style="text-align: left;">Terminator line</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;">1 50</td>
 <td style="text-align: left;">Maximum total forecast catch by fleet (in units specified above total catch/numbers, retained catch/numbers)</td>
 <td style="text-align: left;">Enter fleet number and its maximum value. Last line of the entry must have fleet number = -9999.</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;">-9999 -1</td>
 <td style="text-align: left;"></td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;">-9999 -1</td>
 <td style="text-align: left;">Maximum total catch by area</td>
 <td style="text-align: left;">Enter area number and its max. Last line of the entry must have area number = -9999.</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">-1 = no maximum</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;">1 1</td>
 <td style="text-align: left;">Fleet assignment to allocation group</td>
 <td style="text-align: left;">Enter list of fleet number and its allocation group number if it is in a group. Last line of the entry must have fleet number = -9999.</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;">-9999 -1</td>
 <td style="text-align: left;"></td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;" colspan="2">COND: if N allocation groups is &gt;0</td>
 <td style="text-align: left;">Enter a year and the allocation fraction to each group for that year. SS3 will fill those values to the end of the forecast, then read another year from this list. Terminate with -9999 in year field. Annual values are rescaled to sum to 1.0.</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: right;">2002 1</td>
 <td style="text-align: left;">Allocation to each group for each year of the forecast</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: right;">-9999 1</td>
 <td style="text-align: left;"></td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;">-1</td>
 <td style="text-align: left;">Basis for forecast catch:</td>
 <td style="text-align: left;">The dead or retained value in the forecast catch inputs will be interpreted in terms of numbers or biomass based on the units of the input catch for each fleet.</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">-1 = Read basis with each observation, allows for a mixture of dead, retained, or F basis by different fleets for the fixed catches below;</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">2 = Dead catch (retained + discarded);</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">3 = Retained catch; and</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">99 = Input apical F (the apical F value for the model years can be found in the EXPLOITATION section in the Report file).</td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;">COND: == -1</td>
 <td style="text-align: left;" colspan="2">Forecasted catches - enter one line per number of fixed forecast year catch</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: right;">2012 1 1 1200 2</td>
 <td style="text-align: left;" colspan="2">Year &amp; Season &amp; Fleet &amp; Catch or F value &amp; Basis</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: right;">2013 1 1 1400 3</td>
 <td style="text-align: left;" colspan="2">Year &amp; Season &amp; Fleet &amp; Catch or F value &amp; Basis</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: right;">-9999 0 0 0 0</td>
 <td style="text-align: left;" colspan="2">Indicates end of inputted catches to read</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;"></td>
 <td style="text-align: left;"></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;">COND: &gt; 0</td>
 <td style="text-align: left;" colspan="2">Forecasted catches - enter one line per number of fixed forecast year catch</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: right;">2012 1 1 1200</td>
 <td style="text-align: left;" colspan="2">Year &amp; Season &amp; Fleet &amp; Catch or F value</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: right;">2013 1 1 1200</td>
 <td style="text-align: left;" colspan="2">Year &amp; Season &amp; Fleet &amp; Catch or F value</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: right;">-9999 0 0 0</td>
 <td style="text-align: left;" colspan="2">Indicates end of inputted catches to read</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;">999</td>
 <td style="text-align: left;">End of Input</td>
 <td style="text-align: left;"></td>
@@ -3822,7 +3817,9 @@ <h4 data-number="7.20.0.1" id="note-3"><span class="header-section-number">7.20.
 <li><p>The transition matrix can depend upon weight-at-length which differs between sexes and can vary seasonally. Thus, the transition matrix is calculated internally for each sex and each season.</p></li>
 </ul>
 <h2 data-number="7.21" id="tag-recapture-data"><span class="header-section-number">7.21</span> Tag-Recapture Data</h2>
-<p>The ability to analyze tag-recapture data is available with SS3. Each released tag group is characterized by an area, time, sex and age at release. Each recapture event is characterized by a time and fleet. Fleets operate in only one area so it is not necessary to record the area of recapture. Fleets with tagging data needed to be specified as fishing fleets (e.g., fleet type 1 or 2)). Inside the model, the tagged cohort is apportioned across all growth patterns in a given area at a given time (with options to apportion to only one sex or to both). The tag cohort by growth pattern then behaves according to the movement and mortality of the growth pattern. The number of tagged fish is modeled as a negligible fraction of the total population. This means that a tagging event does not move fish from an untagged group to a tagged group. Instead, it acts as if the tags are seeded into the population with no impact at all on the total population abundance or mortality. The choice to require assignment of a predominant age at release for each tag group is a pragmatic coding and model efficiency choice. By assigning a tag group to a single age, rather than distributing it across all possible ages according to the size composition of the release group, it can be tracked as a single diagonal cohort through the age x time matrix with minimal overhead to the rest of the model. Tags are assumed to be released at the beginning of a season and recaptures follow the timing of the fleet that made the recapture.</p>
+<p>Each released tag group is characterized by an area, time, sex and age at release. Each recapture event is characterized by a time and fleet (since fleets operate in only one area, it is not necessary to specify the area of recapture). Fleets with tagging data must be fishing fleets (e.g., fleet type 1 or 2).</p>
+<p>Inside the model, the tagged cohort is apportioned across all growth patterns in a given area at a given time (with options to apportion to only one sex or to both). The tag cohort by growth pattern then behaves according to the movement and mortality of the growth pattern. The number of tagged fish is modeled as a negligible fraction of the total population, so a tagging event does not move fish from an untagged group to a tagged group. Instead, tagged fish are seeded into the population with no impact at all on the total population abundance or mortality.</p>
+<p>Predominant age at release for each tag group must be assigned; this requirement keeps SS3 efficient. By assigning a tag group to a single age rather than distributing it across all possible ages according to the size composition of the release group, the tag group can be tracked as a single cohort through the age by time matrix with minimal overhead to the rest of the model. Tags are released at the beginning of a season and recaptures follow the timing of the fleet that made the recapture.</p>
 <div class="center">
 <table>
 <thead>
@@ -3834,41 +3831,59 @@ <h2 data-number="7.21" id="tag-recapture-data"><span class="header-section-numbe
 <tr class="odd">
 <td style="text-align: left;white-space: nowrap;">1</td>
 <td style="text-align: left;"></td>
-<td style="text-align: left;" colspan="7">Do tags - if this value is 0, then omit all entries below.</td>
+<td style="text-align: left;" colspan="7">Do tags - 0/1/2. If this value is 0, then omit all entries below.</td>
 </tr>
 <tr class="even">
-<td style="text-align: left;" colspan="9">COND = 1 All subsequent tag-recapture entries must be omitted if &quot;Do Tags&quot; = 0</td>
+<td style="text-align: left;white-space: nowrap;"></td>
+<td style="text-align: left;"></td>
+<td style="text-align: left;" colspan="7">If value is 2, read 1 additional input.</td>
 </tr>
 <tr class="odd">
+<td style="text-align: left;" colspan="9">COND &gt; 0 All subsequent tag-recapture entries must be omitted if &quot;Do Tags&quot; = 0</td>
+</tr>
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">3</td>
 <td style="text-align: left;" colspan="7">Number of tag groups</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">7</td>
 <td style="text-align: left;" colspan="7">Number of recapture events</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">2</td>
-<td style="text-align: left;" colspan="7">Mixing latency period: N periods to delay before comparing</td>
+<td style="text-align: left;" colspan="7">Mixing latency period: N periods to delay before comparing observed</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;"></td>
-<td style="text-align: left;" colspan="7">observed to expected recoveries (0 = release period)</td>
+<td style="text-align: left;" colspan="7">to expected recoveries (0 = release period).</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;">10</td>
 <td style="text-align: left;" colspan="7">Max periods (seasons) to track recoveries, after which tags enter</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;"></td>
 <td style="text-align: left;" colspan="7">accumulator</td>
 </tr>
+<tr class="even">
+<td style="text-align: left;" colspan="9">COND = 2</td>
+</tr>
+<tr class="odd">
+<td style="text-align: left;white-space: nowrap;"></td>
+<td style="text-align: left;">2</td>
+<td style="text-align: left;" colspan="7">Minimum recaptures. The number of recaptures &gt;= mixperiod must be</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;white-space: nowrap;"></td>
+<td style="text-align: left;"></td>
+<td style="text-align: left;" colspan="7">&gt;= min tags recaptured specified to include tag group in log likelihood</td>
+</tr>
 <tr class="odd">
 <td style="text-align: left;white-space: nowrap;"></td>
 <td style="text-align: left;" colspan="8">Release Data</td>
@@ -4018,7 +4033,8 @@ <h4 data-number="7.21.0.1" id="note-4"><span class="header-section-number">7.21.
 <ul>
 <li><p>The release data must be entered in tag group order.</p></li>
 <li><p>&lt;tfill&gt; values are place holders and are replaced by program generated values for model time.</p></li>
-<li><p>Analysis of the tag-recapture data has one negative log likelihood component for the distribution of recaptures across areas and another negative log likelihood component for the decay of tag recaptures from a group over time, hence informative about mortality. More on this is in the control file.</p></li>
+<li><p>Analysis of the tag-recapture data has one negative log likelihood component for the distribution of recaptures across areas and another negative log likelihood component for the decay of tag recaptures from a group over time. Note the decay of tag recaptures from a group over time suggests information about mortality is available in the tag-recapture data. More on this is in the <a href="#tagrecapture">control file documentation</a>.</p></li>
+<li><p>Do tags option 2 adds an additional input compared to do tags option 1, minimum recaptures. Minimum recaptures allows the user to exclude tag groups that have few recaptures after the mixing period from the likelihood. This may be useful when few tags from a group have been recaptured as an alternative to manually removing the groups with these low numbers of recaptured tags from the tagging data.</p></li>
 <li><p>Warning for earlier versions of SS3: A shortcoming in the recapture calculations when also using Pope’s F approach was identified and corrected in version 3.30.14.</p></li>
 </ul>
 <h2 data-number="7.22" id="stock-morph-composition-data"><span class="header-section-number">7.22</span> Stock (Morph) Composition Data</h2>
@@ -8747,6 +8763,9 @@ <h3 data-number="8.9.9" id="two-dimensional-auto-regressive-selectivity-semi-par
 <li><p>Before Range: How should selectivity be modeled in the years prior to Ymin? Available options are (0) apply no deviations, (1) use deviations from the first year with deviations (Ymin), and (3) use average across all years with deviations (Ymin to Ymax).</p></li>
 <li><p>After Range: Similar to Before Range but defines how selectivity should be modeled after Ymax.</p></li>
 </ul>
+<div id="tagrecapture">
+
+</div>
 <h2 data-number="8.10" id="tag-recapture-parameters"><span class="header-section-number">8.10</span> Tag Recapture Parameters</h2>
 <p>Specify if tagging data are being used:</p>
 <table>