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03-surv.html
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<div id="surv" class="section level1">
<h1>Survival</h1>
<p>Survival is something often calculated in a classroom setting, but
the practicalities of calculating it in the real world can make things
very tricky. Small sample sizes that can be found in collar studies can
present a few problems, even if everything goes to plan. For example, if
a collar study is composed of 4 animals, 3 of them may die (maybe it was
deer opener). However, our Kaplan Meier model is telling us that 75% of
our deer are dead! Is survival for that year really 0.25? Unless you
know of some catastrophe this is very unlikely. Our five deer study
poses another problem, which is that the hypothetical 0.2 we produced
earlier is one of only 5 possible survival rates that can come from this
population!(0, 0.25, 0.5 ,0.75, 1) If true survival is 0.66, then we
have a problem because there is no possible way to get that output from
our model. All of this is assuming that things go to plan, things
like:<br />
</p>
<p>All deer were collared at the same time<br />
All dead deer were found with their collar<br />
All collars worked for the duration of the study<br />
</p>
<p>Things often do not go to plan, and so more complicated models need
to be created to account for for the reality of survival studies. Our
models can consider mortality and survival data from the entire
state/province as well as information from your particular DAU of
interest. If there is sufficient data for your target DAU the model will
use that information, but in the case that there isn’t enough, the model
can dip into a state-wide database that includes all capture and
mortality data for the month in order to fill in gaps. Keep this in mind
when your data is scarce, as the less data you have the closer your
estimate will come to the state average.</p>
<div id="surv-walk" class="section level2">
<h2>Walkthrough</h2>
<p>Using the Survival tool can be split into three major processes:
preparing data, reviewing outputs, and uploading data.</p>
<div id="surv-prep" class="section level3">
<h3>Preparing Data</h3>
<p>The first step is to obtain your data. Click Setup under the Survival
dropdown.</p>
<center>
<img src="www/surv_walk1.png" />
</center>
<p>You will notice a window at the top left of the page labeled
Overview, and this is where you will decide the <a href="#gl-species"
style="color: #086e04;"><b>species</b></a> and <a href="#gl-dau"
style="color: #086e04;"><b>DAU</b></a> that we will be analyzing. Once
you have made your selections, click <span
style="color: #196eb0;"><b>Download Data</b></span> at the bottom of the
window.</p>
<center>
<img src="www/surv_walk2.png" />
</center>
<p>Now that your data is loaded, feel free to look it over using the
windows to the right of and below the Overview window.</p>
<center>
<img src="www/surv_walk3.png" />
</center>
<center>
<img src="www/surv_walk4.png" />
</center>
<p>Once you have looked over your data, we can move on to the next step
by navigating to the Subset tab next to the Overview one. Select the sex
and age of the animals you will be analyzing, as well as the years your
analysis will take place.</p>
<center>
<img src="www/surv_walk5.png" />
</center>
<p>We will next move on to the Structure window, where we will determine
our model type, as well as our variances for sex, time, and space. We
can also choose to censor harvest mortalities.</p>
<center>
<img src="www/surv_walk6.png" />
</center>
<p>Once you have made your choices, you can move on to the Run tab.
Under the run tab, decide your <a href="#gl-burnin"
style="color: #086e04;"><b>Burnin Length</b></a>, <a href="#gl-mcmciter"
style="color: #086e04;"><b>MCMC Iterations</b></a>, and <a
href="#gl-thin" style="color: #086e04;"><b>Thinning Rate</b></a>, then
decide whether or not you would like to <a href="#gl-autoconv"
style="color: #086e04;"><b>Automate Convergence</b></a>. We have
provided a set of defaults that are well suited for a variety of
situations, but feel free to modify the values to better fit your
situation.</p>
<center>
<img src="www/surv_walk7.png" />
</center>
<p>When you are done, click <span style="color: #196eb0;"><b>Fit
Model</b></span> to run the analysis. You will get a dialog box when the
process is done.</p>
</div>
<div id="surv-look" class="section level3">
<h3>Reviewing Outputs</h3>
<p>Once your model is finished running, you can view the results in the
Tables tab.</p>
<center>
<img src="www/surv_walk8.png" />
</center>
<p>Note that the first ten entries that appear when you open this page
are only a small fraction of the total. Use the page list on the bottom
right to see more pages of data or use <span
style="color: #196eb0;"><b>Show (10) Entries</b></span> on the top left
to make more entries appear on each page.</p>
<center>
<img src="www/surv_walk9.png" />
</center>
</div>
<div id="surv-upload" class="section level3">
<h3>Uploading Data</h3>
<p>If you’re feeling confident about your results, you can add them to
an IPM database using the Admin tab, but understand that <b>edits you
make here will edit the database for everyone</b>, which is why we ask
that you’re confident about your results before you add them.</p>
<center>
<img src="www/surv_walk10.png" />
</center>
<p>The IPM Data window allows you to select which database will receive
your data, and the Estimates tab allows you to review the data that you
will be adding to the database. <span style="color: #196eb0;"><b>Update
DB</b></span> will upload your data when you are ready.</p>
<center>
<img src="www/surv_walk11.png" />
</center>
</div>
</div>
<div id="surv-ref" class="section level2">
<h2>Reference</h2>
<div id="surv-setup" class="section level3">
<h3>Setup</h3>
<center>
<img src="www/surv_setup1.png" />
</center>
<p>The window on the top left determines how your model is going to be
run.</p>
<center>
<img src="www/surv_setup2.png" />
</center>
<p>The Overview tab is where you select and download the data that you
will be modeling for survival by <a href="#gl-species"
style="color: #086e04;"><b>species</b></a> of animal and <a
href="#gl-dau" style="color: #086e04;"><b>DAU</b></a> that the data was
collected in. The only way to preview the data before modeling is to
download it, and you will have to redownload if you want to change the
species or DAU before you run the model. If data is pulled from your
agencies database via an API, the data must be modified at the source.
PopR only loads the data temporarily using an API, and so cannot modify
it. The Subset tab lets you decide which sections of your elk or mule
deer population will be included in your output, and over what period of
time. The default inputs are Sex:All, Age:A.</p>
<p>In the Structure tab, we get to make some decisions about our model.
The Default inputs work well for a variety of situations and you should
keep them if you plan on putting the results of this model into an IPM
dataset. They are: Model Type: Known Fate, Covariates: None, Censor
Fate(s): None, Model sexes as: Same, Model time as: Constant, Model
space as: Constant. Use the known fate model if you know when every
animal died in your study, but the multi-state model can make estimates
even if you censored animals. You can also select which covariates will
be included in your analysis here. Censor fate allows you to remove
animals from your analysis who were harvested by hunters. Simply click
the Harvest option. Model Sexes can get survival metrics of both males
and females separately by setting it to Different. You can model both
time and space as both constant and monthly.</p>
<p>The Run tab gives direction to our actual modeling process. The given
settings control how we deal with the many thousands of times the model
must run to calibrate itself. Adjust your <a href="#gl-burnin"
style="color: #086e04;"><b>Burnin Length</b></a>, <a href="#gl-mcmciter"
style="color: #086e04;"><b>MCMC Iterations</b></a> and <a
href="#gl-thin" style="color: #086e04;"><b>Thinning Rate</b></a>. The
bottom of the window gives an option for <a href="#gl-autoconv"
style="color: #086e04;"><b>Automating Convergence</b></a> as well. You
may adjust any of these factors, but the defaults are appropriate for a
wide variety of situations.</p>
<p>Use the window at the top right of the page to check for data issues.
The window to the top right is very useful for troubleshooting. The
capture tab displays the ID of an animal that that has bad or no XY data
in the capture tab at the bottom of the page. The Mortalities tab
displays Mortality data whose XY data needs fixing as well. To get a
better idea of which points are causing a problem, points can be clicked
on the map to get their IDs as well.</p>
<center>
<img src="www/surv_setup3.png" />
</center>
<p>The window at the bottom of the page works as a preview for data that
is gathered by the download data button. All of the tables can be
downloaded with the corresponding button, but only data that is
displayed will be downloaded, so make sure <span
style="color: #196eb0;"><b>Show (10) Entries</b></span> is changed to
“All” if you would like to get your entire output in one .csv. All of
the tables can be searched using the empty slots at the top of each
column. Searching the ID column can be very helpful for finding data
that is also displayed in the window that shows entries with damaged xy
data.</p>
<center>
<img src="www/surv_setup4.png" />
</center>
</div>
<div id="surv-admin" class="section level3">
<h3>Admin</h3>
<center>
<img src="www/surv_admin1.png" />
</center>
<p>The Admin tab is a straightforward page 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, so be careful.</p>
<center>
<img src="www/surv_admin2.png" />
</center>
</div>
<div id="surv-tables" class="section level3">
<h3>Tables</h3>
<center>
<img src="www/surv_tables1.png" />
</center>
<p>Once your model is finished running, you can view the results in the
Tables tab. Note that the first ten entries that appear when you open
this page are only a small fraction of the total. Use the page list on
the bottom right to see more pages of data or use the dropdown menu on
the top left to make more entries appear on each page.</p>
</div>
<div id="surv-indiv" class="section level3">
<h3>Individuals</h3>
<center>
<img src="www/surv_indiv1.png" />
</center>
<p>If the window in the setup tab shows that there may be problems with
XY data in capture and mortalities, this is the place to go. After
selecting your individual of interest at the top of the page, the bottom
two windows show all data available about that particular animal.</p>
<center>
<img src="www/surv_indiv2.png" />
</center>
<p>Raw data, is on the left. The two tabs in this window are Raw and Raw
minimized, which removes some of the columns from the Raw tab to make it
easier to navigate. The empty box at the top of each column is a keyword
search.</p>
<center>
<img src="www/surv_indiv3.png" />
</center>
<p>Data formatted by speedgoat for our model is on the right. There are
many columns, so make sure to scroll horizontally to make sure you see
them all. The empty text box at the top of each column allows you to do
a keyword search.</p>
<center>
<img src="www/surv_indiv4.png" />
</center>
</div>
</div>
</div>
</div>
</div>
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