Update documentation

03_model_habitat_linear.html

@@ -96,13 +96,13 @@
 </ul>
 <p>Per species threshold values for stream gradient and discharge/channel width are noted (and can be adjusted) in the file <a class="reference external" href="https://github.com/smnorris/bcfishpass/blob/main/parameters/example_testing/parameters_habitat_thresholds.csv">parameters_habitat_thresholds.csv</a>.</p>
 <p>Sources (via literature and analysis) for these values for Pacific salmon and steelhead are documented in Table 1 of <a class="reference external" href="https://cwf-fcf.org/en/resources/research-papers/BC_report_formatted_final.pdf">Rebelatto et al (2024)</a>.</p>
-<p>Output model data is augmented with observed spawning locations from <a class="reference external" href="https://catalogue.data.gov.bc.ca/dataset/known-bc-fish-observations-and-bc-fish-distributions">FISS</a> via <a class="reference external" href="https://github.com/smnorris/bcfishobs">bcfishobs</a>, PSF’s <a class="reference external" href="https://www.salmonexplorer.ca">Pacific Salmon Explorer</a>, and CWF <a class="reference external" href="https://www.globalconservationsolutions.com/wp-content/uploads/2022/03/CWF-WCRP-Guide.pdf">WCRP</a> stakeholder inputs.</p>
+<p>Streams with observed spawning or rearing (from <a class="reference external" href="https://catalogue.data.gov.bc.ca/dataset/known-bc-fish-observations-and-bc-fish-distributions">FISS</a> via <a class="reference external" href="https://github.com/smnorris/bcfishobs">bcfishobs</a>, PSF’s <a class="reference external" href="https://www.salmonexplorer.ca">Pacific Salmon Explorer</a>, and CWF <a class="reference external" href="https://www.globalconservationsolutions.com/wp-content/uploads/2022/03/CWF-WCRP-Guide.pdf">WCRP</a> stakeholder inputs) are automatically classified as spawning or rearing regardless of stream characteristics.</p>
 <section id="gradient">
 <h2>Gradient<a class="headerlink" href="#gradient" title="Link to this heading"></a></h2>
 <p>Per species spawning/rearing gradient thresholds were taken from the literature and, where unavailable in the literature, derived from known fish spawning locations.</p>
-<p>Gradient of each stream segment is calculated as rise over run. Rise is taken from the Z value of the endpoints of the stream segments. Run is the length of the steam segments.</p>
-<p>Stream segments are BC Freshwater Atlas stream network features, further subdivided by other stream-referenced features used in the model (streams are split at barriers and observations when processing the access model).</p>
-<p>Note that stream lengths and resulting gradient will change if a new observation or barrier is added to the database, breaking an existing segment into smaller segments. This results in small inconsistencies to modelled spawning/rearing outputs for a given area over time, a known limitation of the current model.</p>
+<p>Gradient of each stream segment is calculated as rise over run. Rise is taken from the Z value (elevation) of the endpoints of the stream segments. Run is the length of the steam segments.<br />
+Stream segments are BC Freshwater Atlas stream network features, further subdivided by other stream-referenced features used in the model (when processing the access model, streams are split at natural barriers, anthropogenic crossings, and at locations of FISS observations of species listed <a class="reference external" href="https://github.com/smnorris/bcfishpass/blob/main/model/01_access/sql/load_observations.sql">here</a> - currently <code class="docutils literal notranslate"><span class="pre">BT</span></code>,<code class="docutils literal notranslate"><span class="pre">CH</span></code>,<code class="docutils literal notranslate"><span class="pre">CM</span></code>,<code class="docutils literal notranslate"><span class="pre">CO</span></code>,<code class="docutils literal notranslate"><span class="pre">CT</span></code>,<code class="docutils literal notranslate"><span class="pre">DV</span></code>,<code class="docutils literal notranslate"><span class="pre">GR</span></code>,<code class="docutils literal notranslate"><span class="pre">PK</span></code>,<code class="docutils literal notranslate"><span class="pre">RB</span></code>,<code class="docutils literal notranslate"><span class="pre">SK</span></code>,<code class="docutils literal notranslate"><span class="pre">ST</span></code>,<code class="docutils literal notranslate"><span class="pre">WCT</span></code>).</p>
+<p>Note that stream lengths and resulting gradient will change if a new natural barrier, anthropogenic crossing, or observation is added to the database - breaking an existing segment into smaller segments. These changes to gradient can result in small inconsistencies to modelled spawning/rearing outputs for a given area over time.</p>
 </section>
 <section id="discharge-channel-width">
 <h2>Discharge / channel width<a class="headerlink" href="#discharge-channel-width" title="Link to this heading"></a></h2>

_sources/03_model_habitat_linear.md.txt

@@ -15,17 +15,16 @@ https://github.com/smnorris/bcfishpass/blob/main/parameters/example_testing/para
 
 Sources (via literature and analysis) for these values for Pacific salmon and steelhead are documented in Table 1 of [Rebelatto et al (2024)](https://cwf-fcf.org/en/resources/research-papers/BC_report_formatted_final.pdf).
 
-Output model data is augmented with observed spawning locations from [FISS](https://catalogue.data.gov.bc.ca/dataset/known-bc-fish-observations-and-bc-fish-distributions) via [bcfishobs](https://github.com/smnorris/bcfishobs), PSF's [Pacific Salmon Explorer](https://www.salmonexplorer.ca), and CWF [WCRP](https://www.globalconservationsolutions.com/wp-content/uploads/2022/03/CWF-WCRP-Guide.pdf) stakeholder inputs.
+Streams with observed spawning or rearing (from [FISS](https://catalogue.data.gov.bc.ca/dataset/known-bc-fish-observations-and-bc-fish-distributions) via [bcfishobs](https://github.com/smnorris/bcfishobs), PSF's [Pacific Salmon Explorer](https://www.salmonexplorer.ca), and CWF [WCRP](https://www.globalconservationsolutions.com/wp-content/uploads/2022/03/CWF-WCRP-Guide.pdf) stakeholder inputs) are automatically classified as spawning or rearing regardless of stream characteristics.
 
 ## Gradient
 
 Per species spawning/rearing gradient thresholds were taken from the literature and, where unavailable in the literature, derived from known fish spawning locations.
 
-Gradient of each stream segment is calculated as rise over run. Rise is taken from the Z value of the endpoints of the stream segments. Run is the length of the steam segments.  
+Gradient of each stream segment is calculated as rise over run. Rise is taken from the Z value (elevation) of the endpoints of the stream segments. Run is the length of the steam segments.  
+Stream segments are BC Freshwater Atlas stream network features, further subdivided by other stream-referenced features used in the model (when processing the access model, streams are split at natural barriers, anthropogenic crossings, and at locations of FISS observations of species listed [here](https://github.com/smnorris/bcfishpass/blob/main/model/01_access/sql/load_observations.sql) - currently `BT`,`CH`,`CM`,`CO`,`CT`,`DV`,`GR`,`PK`,`RB`,`SK`,`ST`,`WCT`).  
 
-Stream segments are BC Freshwater Atlas stream network features, further subdivided by other stream-referenced features used in the model (streams are split at barriers and observations when processing the access model).  
-
-Note that stream lengths and resulting gradient will change if a new observation or barrier is added to the database, breaking an existing segment into smaller segments. This results in small inconsistencies to modelled spawning/rearing outputs for a given area over time, a known limitation of the current model.
+Note that stream lengths and resulting gradient will change if a new natural barrier, anthropogenic crossing, or observation is added to the database - breaking an existing segment into smaller segments. These changes to gradient can result in small inconsistencies to modelled spawning/rearing outputs for a given area over time.