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02-sight.html
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<div id="sight" class="section level1">
<h1>Sightability</h1>
<p>Sightability models estimate abundance in a unit by combining the
number of animals that we have seen in aerial surveys with an estimated
number of animals that we have NOT seen using detection probability
models. These detection models consider ground vegetation, the animal’s
activity, snow cover, and the size of the group of animals to determine
the likelihood that an animal is seen with the interference of these
variables.</p>
<p><a href="#gl-stratum" style="color: #086e04;"><b>Stratum</b></a> are
used to organize habitat subunits by how well they would work as habitat
for the animal being surveyed. The “high” strata group represents
subunits that contain the best habitat, “low” is the group that has the
worst habitats, and “medium” falls in between. Subunits are determined
by previous observations from biologists and snow cover.</p>
<div id="sight-walk" class="section level2">
<h2>Walkthrough</h2>
<p>Using the Sightability tool can be split into two major processes:
preparing data and reviewing outputs.</p>
<div id="sight-prep" class="section level3">
<h3>Preparing Data</h3>
<p>To prepare the data, navigate to the Setup tab under the Sightability
dropdown.</p>
<center>
<img src="www/sight_walk1.png" />
</center>
<p>Within the setup section, the User Inputs window decides which survey
data you will load. Select your <a href="#gl-species"
style="color: #086e04;"><b>Species</b></a>, <a href="#gl-dau"
style="color: #086e04;"><b>DAU</b></a>, Survey Type (<a href="#gl-comp"
style="color: #086e04;"><b>Composition</b></a> or <a
href="#gl-sightabundance"
style="color: #086e04;"><b>Sightability-Abundance</b></a>), <a
href="#gl-year" style="color: #086e04;"><b>Year</b></a>, <a
href="#gl-anfocus" style="color: #086e04;"><b>Analysis Focus</b></a>,
and <a href="#gl-aircraft"
style="color: #086e04;"><b>Aircraft/Model</b></a>. The data preview on
the right side of the page will update as you adjust your settings.
Check it as you make your choices in the User Inputs window, but you do
not have to modify it any further.</p>
<center>
<img src="www/sight_walk2.png" />
</center>
<center>
<img src="www/sight_walk3.png" />
</center>
<p>Once you are satisfied with your choices in the User Input window, go
ahead and click <span style="color: #196eb0;"><b>Fit Model</b></span>.
You will get a dialog box letting you know when the tool ran
successfully.</p>
</div>
<div id="sight-look" class="section level3">
<h3>Reviewing Outputs</h3>
<p>Now that your data has been prepared you can go to the Tables tab,
which is where you can view the output of your model.</p>
<center>
<img src="www/sight_walk4.png" />
</center>
<p>Navigate with the tabs along the top of the screen to check your
estimates, survey design, detection, and covariates. You can also
download your detection and estimation results as .csv files with <span
style="color: #196eb0;"><b>Download</b></span> at the bottom of the
table.</p>
<center>
<img src="www/sight_walk5.png" />
</center>
<p>To get a more detailed report of your model that includes the
information in the Tables tab while keeping track of things like model
settings, click the Build Report tab under Sightability. A prompt will
appear asking you to download the report as an html file.</p>
<center>
<img src="www/sight_walk7.png" />
</center>
<center>
<img src="www/ipm_walk9.png" />
</center>
<p>If you would like to upload the results of your model to an IPM
database, you can click on the Admin tab.</p>
<center>
<img src="www/sight_walk6.png" />
</center>
<p><b>Edits here will change databases for everyone</b>. You can select
the database that you want to upload your data to, as well as review the
information that you will be uploading. Press <span
style="color: #196eb0;"><b>Update DB</b></span> to add your selected
results to a shared database.</p>
<center>
<img src="www/sight_walk8.png" />
</center>
</div>
</div>
<div id="sight-ref" class="section level2">
<h2>Reference</h2>
<div id="sight-setup" class="section level3">
<h3>Setup</h3>
<center>
<img src="www/sight_setup1.png" />
</center>
<p>The setup tab is used to select which <a href="#gl-dau"
style="color: #086e04;"><b>DAU</b></a> will be run through our
model.</p>
<p>Surveys will only appear in the preview window if they are a perfect
match to all of the dropdown menus, so make sure to double check that
you did not accidentally leave one of them as default if the survey you
are looking for refuses to appear in the preview window.</p>
<center>
<img src="www/sight_setup2.png" />
</center>
<p>The User Inputs tab on the left side of the screen allows you to
specify which data we will be analyzing. The species dropdown allows to
to choose whether you are selecting elk surveys or mule deer surveys.
The Analysis DAU dropdown selects which data analysis unit we will be
analyzing. All <a href="#gl-dau" style="color: #086e04;"><b>DAU</b></a>
are included as options for a survey, but this does not necessarily mean
that surveys from all of them have been uploaded to the speedgoat
database. If nothing appears in the preview window on the right side of
the screen when you select a <a href="#gl-dau"
style="color: #086e04;"><b>DAU</b></a>, then it means there is no data
available. The Survey Type dropdown includes both <a href="#gl-comp"
style="color: #086e04;"><b>composition</b></a> and <a
href="#gl-sightabundance"
style="color: #086e04;"><b>sightability-abundance</b></a> surveys. The
<a href="#gl-year" style="color: #086e04;"><b>year</b></a> tab refers to
which biological year the survey was carried out on. The <a
href="#gl-anfocus" style="color: #086e04;"><b>Analysis Focus</b></a>
dropdown determines what scale the analysis will be carried out within
the DAU you selected. It works best if the analysis is carried out at
the same scale that data is collected. <a href="#gl-aircraft"
style="color: #086e04;"><b>Aircraft/Model</b></a> is more helpful with
elk studies than mule deer studies, but it is helpful to know which
aircraft flew your surveys no matter what.</p>
<center>
<img src="www/sight_setup3.png" />
</center>
</div>
<div id="sight-table" class="section level3">
<h3>Tables</h3>
<center>
<img src="www/sight_table1.png" />
</center>
<p>The Tables tab allows you to look at the output of your model run
from Setup. The Estimates tab displays model outputs based on your
survey information, including abundance estimates for all age and sex
demographics as well as Male:Female and Young:Female ratio. You can
search each row with the blank box at the top. The Survey Design tab
gives model settings for reference, as well as the proportion of
subunits sampled and the abundance estimate for the area that you
selected in Setup. The Detection tab gives raw survey info that the
model used for its estimates. Notice that the page of data being
displayed is only one of many pages which you can navigate with the page
list on the bottom right of the window. Use the download button at the
bottom of the Estimates and Detections tabs to download those results as
a .csv. The covariates tab gives you a glimpse into how our models work
by showing the covariate options, their <a href="#gl-modelv"
style="color: #086e04;"><b>model values</b></a>, and their <a
href="#gl-beta" style="color: #086e04;"><b>beta</b></a>. This is not a
table of outputs, but rather an insight as to how our model interprets
the data you put into it. For example, while it would be tempting to
spend precious time on a survey flight determining a specific snowcover
percentage, a look at the covariates tab will tell you that snowcover is
actually a categorical variable. Specifically, snowcover has three
categories (1%-20%, 21%-79%, 80%-100%), which means that finding an
exact percentage is a waste of time, since all values within the
discrete categories will be treated the same. The reason you cannot see
the 80-100% category on the covariates page is because of how our model
interprets snowfall. Instead of three separate categories, all
categories are in terms of the 80%-100% one. Our model does not think of
the 1%-20% and 21-79% categories as independent, but as (80%-100%
category) - (some value). 80%-100% is the default category, and default
values are not displayed in the table.</p>
</div>
<div id="sight-report" class="section level3">
<h3>Build Report</h3>
<center>
<img src="www/sight_report1.png" />
</center>
<p>The Build Report tab prints your model outputs from the tables tab
and saves model settings. Clicking the Build Report button will open a
popup menu, click the download button to download the file to your
machine as an HTML file.</p>
</div>
<div id="sight-admin" class="section level3">
<h3>Admin</h3>
<center>
<img src="www/sight_admin1.png" />
</center>
The Admin tab is used to upload the results of your model to your
database of choice. The bottom window can be used to preview the data
that you plan to upload, so make sure you are comfortable with your
results before you upload them to the public database. Data you upload
will be incorporated into everyone else’s model runs.
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