fixed data files for knitting barnacles.Rmd after setting redo=T in…

… rocky.R and sourcing

fyi @mspector13 issue #7

data/oceano/.gitignore

@@ -0,0 +1 @@
+avg-sst_cinms.csv

deep-seafloor.html

@@ -22,8 +22,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
 <link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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-<link href="site_libs/font-awesome-5.3.1/css/v4-shims.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-5.13.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-5.13.0/css/v4-shims.min.css" rel="stylesheet" />
 
 <style type="text/css">code{white-space: pre;}</style>
 <style type="text/css">

modals/abalone.Rmd

@@ -2,7 +2,7 @@
 output:
    html_document:
       self_contained: false
-      keep_md: true
+      keep_md: false
 ---
 
 

modals/abalone.html

@@ -209,11 +209,11 @@ <h3>Red abalone (PISCO)</h3>
 </div>
 </div>
 <div class="figure">
-<img src="../img/cinms_cr/App.F.13.9.jpg" alt="A figure showing the average density of red abalone across the Northern Channel Islands from 2003 to 2016. Data source: PISCO; Figure credit: R. Freedman/NOAA." />
+<img src="../img/cinms_cr/App.F.13.9.jpg" alt="" />
 <p class="caption">A figure showing the average density of red abalone across the Northern Channel Islands from 2003 to 2016. Data source: PISCO; Figure credit: <a href='https://channelislands.noaa.gov/contact/freedman.html' target='_blank'>R. Freedman/NOAA</a>.</p>
 </div>
 <details>
-<summary>Click for Details</summary> Average density (+/- standard error) of red abalone (<em>Haliotis rufescens</em>) at 14 sites across four islands in Channel Islands National Marine Sanctuary monitored by the <a href='http://www.piscoweb.org/kelp-forest-sampling-protocols' target='_blank'>PISCO</a> kelp forest monitoring program from 2003-2016. Abalone are counted by SCUBA divers swimming along transect lines. Observed density was averaged across all monitoring sites at each island, including sites located inside and outside of marine reserves and conservation areas, to examine course-scale trends by island. Observed density was higher at San Miguel Island (blue). For more information, consult Figure App.F.13.9 in the <a href="https://nmssanctuaries.blob.core.windows.net/sanctuaries-prod/media/docs/2016-condition-report-channel-islands-nms.pdf" target="_blank"><span id="tooltip26" aria-describedby="tooltip26" tabindex="0" style="border-bottom: 1px dashed #000000; font-size:100%">CINMS</span> 2016 Condition Report</a>.
+<summary>Click for Details</summary> Average density (+/- standard error) of red abalone (<em>Haliotis rufescens</em>) at 14 sites across four islands in Channel Islands National Marine Sanctuary monitored by the <a href='http://www.piscoweb.org/kelp-forest-sampling-protocols' target='_blank'>PISCO</a> kelp forest monitoring program from 2003-2016. Abalone are counted by SCUBA divers swimming along transect lines. Observed density was averaged across all monitoring sites at each island, including sites located inside and outside of marine reserves and conservation areas, to examine course-scale trends by island. Observed density was higher at San Miguel Island (blue). For more information, consult Figure App.F.13.9 in the <a href="https://nmssanctuaries.blob.core.windows.net/sanctuaries-prod/media/docs/2016-condition-report-channel-islands-nms.pdf" target="_blank"><span id="tooltip27" aria-describedby="tooltip27" tabindex="0" style="border-bottom: 1px dashed #000000; font-size:100%">CINMS</span> 2016 Condition Report</a>.
 </details>
 </div>
 <div id="red-abalone-chis" class="section level3">
@@ -229,11 +229,11 @@ <h3>Red abalone (CHIS)</h3>
 </div>
 </div>
 <div class="figure">
-<img src="../img/cinms_cr/App.F.13.10a.Haliotis_rufescens_CINP.jpg" alt="A figure showing the average density of red abalone across the Northern Channel Islands from 1984 to 2016. Figure credit: Channel Islands National Park." />
+<img src="../img/cinms_cr/App.F.13.10a.Haliotis_rufescens_CINP.jpg" alt="" />
 <p class="caption">A figure showing the average density of red abalone across the Northern Channel Islands from 1984 to 2016. Figure credit: <a href='https://www.nps.gov/chis/index.htm' target='_blank'>Channel Islands National Park</a>.</p>
 </div>
 <details>
-<summary>Click for Details</summary> Average density of red abalone (<em>Haliotis rufescens</em>) at Channel Islands National Park kelp forest monitoring sites at the five islands in Channel Islands National Marine Sanctuary. Abundance of both species was greatly reduced by harvest at all islands prior to the fishery closure in 1997. A gradual increasing trend in abundance of red abalone has been observed since the fishery closure at San Miguel (blue) and more recently at Santa Rosa (red) islands. Abalone are counted by SCUBA divers and observed density was averaged across all monitoring sites at each island, including sites located inside and outside of marine reserves and conservation areas, to examine course-scale trends by island. For more information, consult Figure App.F.13.10a in the <a href="https://nmssanctuaries.blob.core.windows.net/sanctuaries-prod/media/docs/2016-condition-report-channel-islands-nms.pdf" target="_blank"><span id="tooltip26" aria-describedby="tooltip26" tabindex="0" style="border-bottom: 1px dashed #000000; font-size:100%">CINMS</span> 2016 Condition Report</a>.
+<summary>Click for Details</summary> Average density of red abalone (<em>Haliotis rufescens</em>) at Channel Islands National Park kelp forest monitoring sites at the five islands in Channel Islands National Marine Sanctuary. Abundance of both species was greatly reduced by harvest at all islands prior to the fishery closure in 1997. A gradual increasing trend in abundance of red abalone has been observed since the fishery closure at San Miguel (blue) and more recently at Santa Rosa (red) islands. Abalone are counted by SCUBA divers and observed density was averaged across all monitoring sites at each island, including sites located inside and outside of marine reserves and conservation areas, to examine course-scale trends by island. For more information, consult Figure App.F.13.10a in the <a href="https://nmssanctuaries.blob.core.windows.net/sanctuaries-prod/media/docs/2016-condition-report-channel-islands-nms.pdf" target="_blank"><span id="tooltip27" aria-describedby="tooltip27" tabindex="0" style="border-bottom: 1px dashed #000000; font-size:100%">CINMS</span> 2016 Condition Report</a>.
 </details>
 </div>
 <div id="pink-abalone-chis" class="section level3">
@@ -249,15 +249,15 @@ <h3>Pink abalone (CHIS)</h3>
 </div>
 </div>
 <div class="figure">
-<img src="../img/cinms_cr/App.F.13.10b.Haliotis_corrugata_CINP.jpg" alt="A figure showing the average density of pink abalone across the Northern Channel Islands from 1984 to 2016. Figure credit: Channel Islands National Park." />
+<img src="../img/cinms_cr/App.F.13.10b.Haliotis_corrugata_CINP.jpg" alt="" />
 <p class="caption">A figure showing the average density of pink abalone across the Northern Channel Islands from 1984 to 2016. Figure credit: <a href='https://www.nps.gov/chis/index.htm' target='_blank'>Channel Islands National Park</a>.</p>
 </div>
 <details>
-<summary>Click for Details</summary> Average density of pink abalone (<em>H. corrugata</em>) at Channel Islands National Park kelp forest monitoring sites at the five islands in Channel Islands National Marine Sanctuary. Abundance of both species was greatly reduced by harvest at all islands prior to the fishery closure in 1997. A gradual increasing trend in abundance of red abalone has been observed since the fishery closure at San Miguel (blue) and more recently at Santa Rosa (red) islands. Abalone are counted by SCUBA divers and observed density was averaged across all monitoring sites at each island, including sites located inside and outside of marine reserves and conservation areas, to examine course-scale trends by island. For more information, consult Figure App.F.13.10b in the <a href="https://nmssanctuaries.blob.core.windows.net/sanctuaries-prod/media/docs/2016-condition-report-channel-islands-nms.pdf" target="_blank"><span id="tooltip26" aria-describedby="tooltip26" tabindex="0" style="border-bottom: 1px dashed #000000; font-size:100%">CINMS</span> 2016 Condition Report</a>.
+<summary>Click for Details</summary> Average density of pink abalone (<em>H. corrugata</em>) at Channel Islands National Park kelp forest monitoring sites at the five islands in Channel Islands National Marine Sanctuary. Abundance of both species was greatly reduced by harvest at all islands prior to the fishery closure in 1997. A gradual increasing trend in abundance of red abalone has been observed since the fishery closure at San Miguel (blue) and more recently at Santa Rosa (red) islands. Abalone are counted by SCUBA divers and observed density was averaged across all monitoring sites at each island, including sites located inside and outside of marine reserves and conservation areas, to examine course-scale trends by island. For more information, consult Figure App.F.13.10b in the <a href="https://nmssanctuaries.blob.core.windows.net/sanctuaries-prod/media/docs/2016-condition-report-channel-islands-nms.pdf" target="_blank"><span id="tooltip27" aria-describedby="tooltip27" tabindex="0" style="border-bottom: 1px dashed #000000; font-size:100%">CINMS</span> 2016 Condition Report</a>.
 </details>
 <script src="https://unpkg.com/@popperjs/core@2"></script>
 <script src="https://unpkg.com/tippy.js@6"></script>
-<script>tippy ("#tooltip26",{content: "Channel Islands National Marine Sanctuary"});</script>
+<script>tippy ("#tooltip27",{content: "Channel Islands National Marine Sanctuary"});</script>
 </div>
 </div>