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consolidate figures and headers
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mkapur-noaa committed Oct 23, 2024
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159 changes: 120 additions & 39 deletions docs/2024_BSAI_FHS_Nov.html
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Expand Up @@ -445,12 +445,14 @@ <h2>Fishery Age Comps</h2>
}</style></aside>

<img data-src="2024/model_plots/comp_agefit_flt1mkt0.png" width="975" class="r-stretch"></section>
<section id="fishery-length-comps-early-years" class="slide level2">
<h2>Fishery Length Comps (early years)</h2>
<section id="fishery-age-comp-residuals-pearson" class="slide level2">
<h2>Fishery Age Comp Residuals (Pearson)</h2>

<img data-src="2024/model_plots/comp_lenfit__multi-fleet_comparison.png" width="975" class="r-stretch"></section>
<section id="fishery-age-comp-residuals-osa" class="slide level2">
<h2>Fishery Age Comp Residuals (OSA)</h2>
<aside class="notes">
<p>these are not perfect; not weighted highly in model and didn’t update ISS</p>
<p>large pearson residual in 1983 might be a data artifact</p>
<p>misfits in 20-30cm range largely driven pre 1983</p>
<p>the glaring issue in 1983 goes away</p>
<style type="text/css">
span.MJX_Assistive_MathML {
position:absolute!important;
Expand All @@ -462,11 +464,30 @@ <h2>Fishery Length Comps (early years)</h2>
overflow: hidden!important;
display:block!important;
}</style></aside>

<img data-src="2024/model_plots/comp_lenfit_flt1mkt0_page1.png" width="975" class="r-stretch"></section>
<section id="fishery-length-comps-recent-years-1" class="slide level2">
<h2>Fishery Length Comps (recent years)</h2>
<div class="columns">
<div class="column" style="width:45%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/osa_fishery_length_females_diagnostics.png" width="350" height="500"></p>
</div>
</div>
</div><div class="column" style="width:5%;">
<!-- empty column to create gap -->
</div><div class="column" style="width:45%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/osa_fishery_length_males_diagnostics.png" width="350" height="500"></p>
</div>
</div>
</div>
</div>
</section>
<section id="fishery-length-comps" class="slide level2">
<h2>Fishery Length Comps</h2>
<aside class="notes">
<p>these are not perfect; not weighted highly in model and didn’t update ISS</p>
<p>large pearson residual in 1983 might be a data artifact</p>
<p>misfits in 20-30cm range largely driven pre 1983</p>
<p>low sampling in 70s clean up with survey timeblock some over est in recent years have recdevs set to mean in 2020 which would be informing the 25-40 length bin also don’t have age data and these are weighted really low aggregate fig shows ugly gap, this was present in previous models, structural not misspec</p>
<style type="text/css">
span.MJX_Assistive_MathML {
Expand All @@ -479,14 +500,28 @@ <h2>Fishery Length Comps (recent years)</h2>
overflow: hidden!important;
display:block!important;
}</style></aside>

<img data-src="2024/model_plots/comp_lenfit_flt1mkt0_page2.png" width="975" class="r-stretch"></section>
<section id="length-comp-residuals-pearson" class="slide level2">
<h2>Length Comp Residuals: Pearson</h2>
<div class="columns">
<div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/comp_lenfit_flt1mkt0_page1.png" width="975"></p>
</div>
</div>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/comp_lenfit_flt1mkt0_page2.png" width="975"></p>
</div>
</div>
</div>
</div>
</section>
<section id="fishery-length-comp-residuals-pearson" class="slide level2">
<h2>Fishery Length Comp Residuals (Pearson)</h2>

<img data-src="2024/model_plots/comp_lenfit__multi-fleet_comparison.png" width="975" class="r-stretch"></section>
<section id="length-comp-residuals-osa-fishery" class="slide level2">
<h2>Length Comp Residuals: OSA (Fishery)</h2>
<section id="fishery-length-comp-residuals-osa" class="slide level2">
<h2>Fishery Length Comp Residuals (OSA)</h2>
<aside class="notes">
<p>the glaring issue in 1983 goes away</p>
<style type="text/css">
Expand All @@ -501,15 +536,13 @@ <h2>Length Comp Residuals: OSA (Fishery)</h2>
display:block!important;
}</style></aside>
<div class="columns">
<div class="column" style="width:45%;">
<div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/osa_fishery_length_females_diagnostics.png" width="350" height="500"></p>
</div>
</div>
</div><div class="column" style="width:5%;">
<!-- empty column to create gap -->
</div><div class="column" style="width:45%;">
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/osa_fishery_length_males_diagnostics.png" width="350" height="500"></p>
Expand All @@ -522,8 +555,8 @@ <h2>Length Comp Residuals: OSA (Fishery)</h2>
<h2>Survey Biomass</h2>

<img data-src="2024/model_plots/index2_cpuefit_Survey.png" width="975" class="r-stretch"></section>
<section id="survey-length-comp" class="slide level2">
<h2>Survey Length Comp</h2>
<section id="survey-length-comps" class="slide level2">
<h2>Survey Length Comps</h2>
<aside class="notes">
<p>misfit 20-30 cm; seen this since 2012 previous authors tried flexible selectivity patterns, a four-parameter growth curve, more complexity in CV in length at age, alternative and data weighting schemes</p>
<p>it’s possible that we aren’t sampling length-at-age well</p>
Expand All @@ -538,14 +571,28 @@ <h2>Survey Length Comp</h2>
overflow: hidden!important;
display:block!important;
}</style></aside>

<img data-src="2024/model_plots/comp_lenfit_flt2mkt0_page2.png" width="975" class="r-stretch"></section>
<section id="length-comp-residuals-pearson-1" class="slide level2">
<h2>Length Comp Residuals: Pearson</h2>
<div class="columns">
<div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/comp_lenfit_flt2mkt0_page1.png" width="975"></p>
</div>
</div>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/comp_lenfit_flt2mkt0_page2.png" width="975"></p>
</div>
</div>
</div>
</div>
</section>
<section id="survey-length-comp-residuals-pearson" class="slide level2">
<h2>Survey Length Comp Residuals (Pearson)</h2>

<img data-src="2024/model_plots/comp_lenfit__multi-fleet_comparison.png" width="975" class="r-stretch"></section>
<section id="length-comp-residuals-osa-survey" class="slide level2">
<h2>Length Comp Residuals: OSA (Survey)</h2>
<section id="survey-length-comp-residuals-osa" class="slide level2">
<h2>Survey Length Comp Residuals (OSA)</h2>
<div class="columns">
<div class="column" style="width:45%;">
<div class="cell">
Expand All @@ -564,8 +611,8 @@ <h2>Length Comp Residuals: OSA (Survey)</h2>
</div>
</div>
</section>
<section id="survey-caal-fits-recent-years-i" class="slide level2">
<h2>Survey CAAL Fits (recent years) I</h2>
<section id="survey-caal-fits-recent-years" class="slide level2">
<h2>Survey CAAL Fits (recent years)</h2>
<aside class="notes">
<p>if we had stuck with the n_otoliths approach we would have overstated the sample size by a factor of ~2, hence the doubling of the francis weights</p>
<style type="text/css">
Expand All @@ -579,28 +626,62 @@ <h2>Survey CAAL Fits (recent years) I</h2>
overflow: hidden!important;
display:block!important;
}</style></aside>
<div class="columns">
<div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/comp_condAALfit_Andre_plotsflt2mkt0_page7.png" width="975"></p>
</div>
</div>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/comp_condAALfit_Andre_plotsflt2mkt0_page7.png" width="600" height="600"></p>
<p><img data-src="2024/model_plots/comp_condAALfit_Andre_plotsflt2mkt0_page8.png" width="975"></p>
</div>
</div>
</div>
</div>
</section>
<section id="survey-caal-fits-recent-years-ii" class="slide level2">
<h2>Survey CAAL Fits (recent years) II</h2>

<img data-src="2024/model_plots/comp_condAALfit_Andre_plotsflt2mkt0_page8.png" width="750" class="r-stretch"></section>
<section id="bioselex-curves" class="slide level2">
<h2>Bio/Selex Curves</h2>

<img data-src="2024/model_plots/growth_selex_maturity.png" width="1260" class="r-stretch"></section>
<section id="time-series-ssb-total-biomass" class="slide level2">
<h2>Time Series: SSB &amp; Total Biomass</h2>

<img data-src="2024/model_plots/compare1_spawnbio.png" width="975" class="r-stretch"></section>
<div class="columns">
<div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/compare1_spawnbio.png" width="975"></p>
</div>
</div>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/compare18_totalbiomass.png" width="1300"></p>
</div>
</div>
</div>
</div>
</section>
<section id="time-series-recruitment" class="slide level2">
<h2>Time Series: Recruitment</h2>

<img data-src="2024/model_plots/compare10_recruits_uncertainty.png" width="975" class="r-stretch"></section>
<div class="columns">
<div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/compare10_recruits_uncertainty.png" width="975"></p>
</div>
</div>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="2024/model_plots/compare12_recdevs_uncertainty.png" width="975"></p>
</div>
</div>
</div>
</div>
</section>
<section id="time-series-fishing-mortality" class="slide level2">
<h2>Time Series: Fishing Mortality</h2>

Expand Down Expand Up @@ -648,7 +729,7 @@ <h1>Extra Material</h1>
<div class="cell">
<div class="cell-output-display">

<div class="tabwid"><style>.cl-f5dabfe6{}.cl-f5cff8ae{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-f5cff8b8{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-f5d3aa8a{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-f5d3aa9e{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-f5d3ca92{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-f5d3ca9c{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-f5d3cab0{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-f5d3caba{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-f5d3cabb{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-f5d3cabc{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-f5dabfe6"><thead><tr style="overflow-wrap:break-word;"><th class="cl-f5d3ca92"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Fleet</span></p></th><th class="cl-f5d3ca92"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Type</span></p></th><th class="cl-f5d3ca9c"><p class="cl-f5d3aa9e"><span class="cl-f5cff8ae">ISS_from_Nhauls</span></p></th><th class="cl-f5d3ca9c"><p class="cl-f5d3aa9e"><span class="cl-f5cff8ae">ISS_from_Package</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-f5d3cab0"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Fishery</span></p></td><td class="cl-f5d3cab0"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Length</span></p></td><td class="cl-f5d3caba"><p class="cl-f5d3aa9e"><span class="cl-f5cff8ae">0.079732</span></p></td><td class="cl-f5d3caba"><p class="cl-f5d3aa9e"><span class="cl-f5cff8ae">0.079018</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-f5d3cab0"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Survey</span></p></td><td class="cl-f5d3cab0"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Length</span></p></td><td class="cl-f5d3caba"><p class="cl-f5d3aa9e"><span class="cl-f5cff8ae">0.359831</span></p></td><td class="cl-f5d3caba"><p class="cl-f5d3aa9e"><span class="cl-f5cff8b8">0.062439</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-f5d3cab0"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Fishery</span></p></td><td class="cl-f5d3cab0"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Age</span></p></td><td class="cl-f5d3caba"><p class="cl-f5d3aa9e"><span class="cl-f5cff8ae">0.086647</span></p></td><td class="cl-f5d3caba"><p class="cl-f5d3aa9e"><span class="cl-f5cff8ae">0.085811</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-f5d3cabb"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">Survey</span></p></td><td class="cl-f5d3cabb"><p class="cl-f5d3aa8a"><span class="cl-f5cff8ae">CAAL</span></p></td><td class="cl-f5d3cabc"><p class="cl-f5d3aa9e"><span class="cl-f5cff8ae">0.272054</span></p></td><td class="cl-f5d3cabc"><p class="cl-f5d3aa9e"><span class="cl-f5cff8b8">0.481957</span></p></td></tr></tbody></table></div>
<div class="tabwid"><style>.cl-60cfc5ce{}.cl-60c5199e{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-60c519b2{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-60c96b02{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-60c96b0c{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-60c98cfe{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-60c98d08{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-60c98d09{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-60c98d12{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-60c98d13{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-60c98d14{width:0.75in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-60cfc5ce"><thead><tr style="overflow-wrap:break-word;"><th class="cl-60c98cfe"><p class="cl-60c96b02"><span class="cl-60c5199e">Fleet</span></p></th><th class="cl-60c98cfe"><p class="cl-60c96b02"><span class="cl-60c5199e">Type</span></p></th><th class="cl-60c98d08"><p class="cl-60c96b0c"><span class="cl-60c5199e">ISS_from_Nhauls</span></p></th><th class="cl-60c98d08"><p class="cl-60c96b0c"><span class="cl-60c5199e">ISS_from_Package</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-60c98d09"><p class="cl-60c96b02"><span class="cl-60c5199e">Fishery</span></p></td><td class="cl-60c98d09"><p class="cl-60c96b02"><span class="cl-60c5199e">Length</span></p></td><td class="cl-60c98d12"><p class="cl-60c96b0c"><span class="cl-60c5199e">0.079732</span></p></td><td class="cl-60c98d12"><p class="cl-60c96b0c"><span class="cl-60c5199e">0.079018</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-60c98d09"><p class="cl-60c96b02"><span class="cl-60c5199e">Survey</span></p></td><td class="cl-60c98d09"><p class="cl-60c96b02"><span class="cl-60c5199e">Length</span></p></td><td class="cl-60c98d12"><p class="cl-60c96b0c"><span class="cl-60c5199e">0.359831</span></p></td><td class="cl-60c98d12"><p class="cl-60c96b0c"><span class="cl-60c519b2">0.062439</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-60c98d09"><p class="cl-60c96b02"><span class="cl-60c5199e">Fishery</span></p></td><td class="cl-60c98d09"><p class="cl-60c96b02"><span class="cl-60c5199e">Age</span></p></td><td class="cl-60c98d12"><p class="cl-60c96b0c"><span class="cl-60c5199e">0.086647</span></p></td><td class="cl-60c98d12"><p class="cl-60c96b0c"><span class="cl-60c5199e">0.085811</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-60c98d13"><p class="cl-60c96b02"><span class="cl-60c5199e">Survey</span></p></td><td class="cl-60c98d13"><p class="cl-60c96b02"><span class="cl-60c5199e">CAAL</span></p></td><td class="cl-60c98d14"><p class="cl-60c96b0c"><span class="cl-60c5199e">0.272054</span></p></td><td class="cl-60c98d14"><p class="cl-60c96b0c"><span class="cl-60c519b2">0.481957</span></p></td></tr></tbody></table></div>
</div>
</div>
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