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<div id="ipm" class="section level1">
<h1>IPM</h1>
<p>An Integrated Population Model(IPM), jointly analyzes data on
population size and demographic parameters. Data collected in the field
inform the demographic parameters in the model and unifying the analyses
of multiple sources of data. Field data in the IPM database may come
from the outputs from survival models and sightability models run in the
PopR website, analysis done by a specific agencies, and/or agency
specific databases. The IPM analyzes populations at the <a
href="#gl-DAU" style="color: #086e04;"><b>DAU</b></a> level.</p>
<div id="ipm-model" class="section level2">
<h2>Walkthrough</h2>
<p>Using the IPM tool can be split into two major processes: preparing
data and reviewing outputs.</p>
<div id="ipm-load" class="section level3">
<h3>Preparing Data</h3>
<p>Click on the Setup tab, the first dropdown under the IPM tool
menu.</p>
<center>
<img src="www/ipm_walk1.png" />
</center>
<p>On the top left of the page should be a window labeled Overview, and
this is where you determine the data that you run through the IPM.
Select the database you want to retrieve the data from, then make sure
you choose your <a href="#gl-species"
style="color: #086e04;"><b>Species</b></a>, <a href="#gl-dau"
style="color: #086e04;"><b>DAU</b></a>, <a href="#gl-unit"
style="color: #086e04;"><b>Unit</b></a>, and Weather before you click
<span style="color: #196eb0;"><b>Fetch Harvest Data</b></span> on the
bottom right of the Overview window to retrieve the specific data you
requested.</p>
<center>
<img src="www/ipm_walk2.png" />
</center>
<p>Once the data is loaded, you should get a popup dialog letting you
know that the process was successful. It will also prompt you to proceed
to the Structure tab.</p>
<p>The Structure tab allows you to select the model structure used in
the analysis. For some agencies, the use of population reconstruction or
other structural components may be available as structural options. The
primary set-up options are to define whether your survival and
reproduction will vary annually or be constant. The defaults were chosen
to be well-suited to the specific species selected, so most of the time
clicking <span style="color: #196eb0;"><b>“Default Structure”</b></span>
is a good start for your analysis. The inputs that appear when the tool
is opened may not revert to the species specific defaults so clicking on
<span style="color: #196eb0;"><b>“Default Structure”</b></span>, will
make sure you have selected the defaults before you move on to
Harvest.</p>
<center>
<img src="www/ipm_walk4.png" />
</center>
<p>After you select your Structure, you can move on to the Harvest Tab.
Decide your effort variable and the years that you will be conducting
your analysis, then look at the given information for the years that
will be forecast. You can change the Harvest by double clicking the
numbers and typing in new entries.</p>
<center>
<img src="www/ipm_walk5.png" />
</center>
<p>Our next step is the Run tab, which again already has a decent set of
default values loaded. 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>. Decide
whether you would like to <a href="#gl-autoconv"
style="color: #086e04;"><b>Automate Convergence</b></a> (This may
increase the time it takes to run the model).</p>
<center>
<img src="www/ipm_walk6.png" />
</center>
<p>Once you are satisfied with all of the inputs outlined above, click
<span style="color: #196eb0;"><b>Fit Model</b></span> to begin analysis.
This should take some time, but you will get a dialog box letting you
know when the process is complete</p>
</div>
<div id="ipm-look" class="section level3">
<h3>Reviewing Outputs</h3>
<p><b>(NOTE: This section will only work if you completed the steps
above to prepare your data and fit your model beforehand.</b>)</p>
<p>To look at the model output, wait until the model that you initiated
in the setup tab has finished running, then go ahead and click the Plots
tab on the IPM dropdown menu to check the results. Hovering your mouse
over a point on a plot will give you the parameter, year, age, sex,
control limits, and mean associated with the dataset that created the
data point. These plots also contain the analogous data from the IPM
inputs, so you can compare the model output with the data that was
provided as inputs to the model.</p>
<center>
<img src="www/ipm_walk7.png" />
</center>
<p>You can also check the model output by clicking the Tables tab right
below the Plots one on the IPM dropdown. Rhat values greater than 1.1
are highlighted in red, which means the model may not have converged and
should be run again after modifying the settings on the Run tab in the
Setup tool. The first ten entries that appear when you open the table
tab are not the only outputs of the model. You will notice that you may
navigate the pages with the list to the bottom right, or you may
increase the number of entries visible at the top left of the page,
using the <span style="color: #196eb0;"><b>Show (10) Entries</b></span>
dropdown.</p>
<center>
<img src="www/ipm_walk8.png" />
</center>
<p>As a final step to get more diagnostic information, use the Build
Report tool.</p>
<center>
<img src="www/ipm_walk10.png" />
</center>
<p>Simply click on the tool and then click the download prompt on the
popup window. The resulting document contains interactive plots as well
as model specifications and fit.</p>
<center>
<img src="www/ipm_walk9.png" />
</center>
</div>
</div>
<div id="ipm-ref" class="section level2">
<h2>Reference</h2>
<div id="ipm-setup" class="section level3">
<h3>Setup</h3>
<center>
<img src="www/ipm_walk1.png" />
</center>
<p>The main purpose of the Setup tab is to load and preview data that
will be used for later analysis, and we will spend more time describing
each element in detail. The window on the top left of the page has
several tabs related to data preparation labeled Overview, Structure,
Harvest, and Run.</p>
<center>
<img src="www/ipm_setup1.png" />
</center>
<p>The Overview tab helps you find the data you will be loading for your
IPM. Make sure that you are pulling from the correct database! Also, the
Future Weather dropdown allows you to consider weather in your IPM
analysis. Average assumes mean observed weather conditions, Good assumes
upper 95% quantile of observed weather, and Bad assumes lower 5%
quantile of observed weather. You may also choose not to include weather
in your analysis. All of these values were developed from the
dissertation of Mark Hurley.</p>
<p>The Structure tab gives our model some information about assumptions.
Population reconstruction is the process of estimating past abundance
using a combination of known harvest data and estimated natural
mortality rates. If you know when an animal died AND how old it was when
it died, then you also know when it was alive. Using this
“back-tracking” can create an abundance estimate for past years even if
one was not carried out.</p>
<p>The Harvest tab gives our model some important context on harvest
metrics. The slider at the top tells our model which years are being
analyzed. The effort variable allows us to choose whether effort is
determined by the number of days in the field or the number of hunters
themselves. It also gives more context to our harvest numbers and helps
us tease apart the relationship that hunter effectiveness and raw number
of hunters had on the harvest that year. You may also give hypothetical
harvest numbers for our model to consider so you may estimate the
effects of management decisions on rates like survival and
abundance.</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>The window on the top right of the page is for previewing and
exploring the data that will create your analysis. Keep in mind that at
this stage you are looking at the model input rather than the output,
which is located in Plots and Tables. You can view <a
href="#gl-abundance" style="color: #086e04;"><b>Abundance</b></a>, <a
href="#gl-surv" style="color: #086e04;"><b>Survival</b></a>, <a
href="#gl-sexratio" style="color: #086e04;"><b>Sex Ratios</b></a>,
Harvest numbers, and <a href="#gl-huntereffort"
style="color: #086e04;"><b>Hunter Effort</b></a>, as well as our Prior
distribution for population parameters. A priors distribution gives a
range of possible values for each of the factors that are considered by
the IPM such as recruitment, survival, and mortality and then the
likelihood of each value. This allows the model to consider historical
data, but does not give too much power to outlier values. Just because a
deer population lost 90% of their population in one year historically
does not necessarily mean that it is likely to happen again in future
years, but it should not be completely ignored either.</p>
<center>
<img src="www/ipm_setup6.png" />
</center>
<p>You can explore your graphs in this section with the pan and two zoom
features on the side of each graph. Click the reset button to return to
the original view. If any of these tabs are blank, it means that the
dataset you picked does not have the relevant data to populate it.</p>
<p>The table at the bottom of the page gives another way to preview the
data you loaded in the Overview tab. Use the blank column headers to
look through your data with their keyword search function. You can page
through your data with the previous and next buttons at the bottom of
the page.</p>
<center>
<img src="www/ipm_setup7.png" />
</center>
</div>
<div id="ipm-dbmgmt" class="section level3">
<h3>Database Management</h3>
<center>
<img src="www/ipm_db1.png" />
</center>
<p>The DB Mgmt tab creates, deletes and edits databases.The tools may be
minimized, but to open them for use just click on the plus sign on the
right side of the box containing the tool. Press it again to minimize
it. Note that because databases are shared between users, edits here
will change databases for EVERYONE. Data losses and changes will be
permanent if you do not back up your data. You can also use the Create
window to make a new database. NOTE: for some users this feature is only
available for administrators and you may need to contact your
administrator to create a new database or delete or edit an existing
entry.</p>
<p>When using the Create window you can paste data from a spreadsheet
app like Excel. You can also start off with data from any existing
database, which you can select under the Historic Data box. once the
data is loaded, you can filter the entries by usinf the blank box at the
top of each column as a keyword search bar. Make sure to give your new
database a name, and then click the create database button to add a
database to the Speedgoat server! You can also use the download tool to
get the data you have loaded into our servers as a .csv.</p>
<center>
<img src="www/ipm_db2.png" />
</center>
<p>The Delete DB tool will delete the database you select from the
server. Deleting it here will delete it for everyone, so make sure that
your data is backed up and that nobody is still working on a database
before you delete it.</p>
<center>
<img src="www/ipm_db3.png" />
</center>
<p>The Edit tool allows you to add and delete rows of data from the
database selected in the menu at the top of the tool. None of the edits
you make will be applied until the Save Changes button is clicked, but
once that button is clicked changes will be applied for everyone that
uses that database.</p>
<center>
<img src="www/ipm_db4.png" />
</center>
</div>
<div id="ipm-plot" class="section level3">
<h3>Plots</h3>
<center>
<img src="www/ipm_plot2.png" />
</center>
<p>The plots page displays the outputs of the IPM. Use the zoom and pan
tools to change your view of the graph, and use the reset button to
return to your original view.</p>
<p>Though there are only four windows to display data, each of these
windows can be changed by selecting the options across the top. Pictured
are the options given for the Abundance window, which allows us to
explore <a href="#gl-abundance"
style="color: #086e04;"><b>abundance</b></a> during different times of
year, as well as separating measurements by sex.</p>
<center>
<img src="www/ipm_plot1.png" />
</center>
<p>The ratios window allows us to break down the demographics that make
up our study population, either by <a href="#gl-ageratio"
style="color: #086e04;"><b>age</b></a>. or <a href="#gl-sexratio"
style="color: #086e04;"><b>sex</b></a>. This tab may also contain an age
distribution plot that breaks down either proportion of the population
or counts of the population by age. This plot is generated based on the
expectation that the current population is broken down into ages based
on the current survival rate of the specified age and sex class and may
not be an accurate representation of the population age structure.</p>
<center>
<img src="www/ipm_plot3.png" />
</center>
<p>The survival window displays survival through the years for both
males and females. Within each sex’s tab, you can also select the age
group of the animal to compare rates between adults and juveniles.</p>
<center>
<img src="www/ipm_plot4.png" />
</center>
<p>The Misc window contains many rates that are useful for understanding
a population. Growth rate tracks how a population grows as a proportion
of the population of the year before. For example, if a population of
100 animals grows by 50 in one year, the growth rate would be 0.5. MSY
allows you to select which vital rate will be displayed on your y-axis.
Lambda measures growth year by year, recruitment measures population
growth, but specifically how many juveniles became adults in a
population and how many adults immigrate into a population. Harvest and
Harvest rate are often confused, but mean slightly different things.
Harvest is the number of animals whose cause of death would be
hunter-related, where harvest rate is the proportion of the population
that was harvested. Effort measures how hunters put pressure on a
population, and is either measured by the number of hunters on the
landscape or how many cumulative days that hunters spent in the field.
Note: these plots may be customized depending on your agencies needs, so
the plots you see may not be the same as the ones pictured here.</p>
<center>
<img src="www/ipm_plot5.png" />
</center>
</div>
<div id="ipm-table" class="section level3">
<h3>Tables</h3>
<center>
<img src="www/ipm_tables1.png" />
</center>
<p>On the Tables page you can download and edit the data you are using
for analysis. You can download your data here as well, but note that you
will only download the data being displayed to you. By default, the
table only shows the first ten entries of your dataset, so if you would
like to download your data here make sure you change the dropdown at the
top of the window from Show 10 entries to Show All entries.</p>
</div>
<div id="ipm-report" class="section level3">
<h3>Build Report</h3>
<center>
<img src="www/ipm_report1.png" />
</center>
<p>The Build Report tool gives a summary of the analysis conducted,
while keeping relevant information like model settings for future
comparisons.</p>
</div>
</div>
</div>
</div>
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