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Animal Populations

Monitor your simulation with these Animal Population tables. Make on-the-fly comparisons and keep tabs on intake and reproduction. Plenty of ways to extract your data, like ascii file dumps and graphs and grids.

Ouputs

The Animal Populations window provides data from your simulation for each animal type that you have in your model. The variables provided are; Animal Number, Animal Density, Births, Deaths, Neonates, Juveniles, Adult Males, Adult Females, Pregnant Females, Lactating Females, Foraging Area, Forage Biomass, Grazing Time, Total Distance, Potential Intake, Intake, Diet ratio, ME Potential, ME Intake, Digestibility, Maintenance, Yield by Height, Yield by Weight, Cells, Grid CV, Patchiness, G*, Tortuosity, Visual Acuity, GUD, Lethargy and Process. Details about these variables can be found in the Parameters section of this guide.

In addition to the detailed information for your animal types output to the main panel in the Animal Populations window, there are additional ways to get even more detailed information about each of the age classes used in your animal modules. This detailed information comes in the form of a series of ascii files. Each is a record of the animals within each age class (index, count and cumulative count), either in terms of their actual number, or in terms of their fat mass, a fundamental currency used in the modelling software for animal health. More information about these age classes can be found in Derry (1998). The animal number files tell you the frequency of individuals for each day elapsed since their introduction into the age class (i.e., their relative ages within the age class, 1 year + 1 day, 1 year + 2 days, and so on). The fat mass files give you the frequency of animals in fat mass classes, usually of 1 kg width, but you can change that using the Parameter View.

The currently active season (DRY or WET) is indicated in the Active Season panel
A season is activated according to your season start and end dates. Make your Climate settings in the Parameter View window.

Options

  • Use the Status bar information option to receive processing information from within your animal module in the status bar at the bottom of the window.
  • The Use Biomass (UB) Rule calculates animal consumption of plant material based on forage biomass rather than the typical method of using energy intake rate. You can read more about the UB Rule in the section on Ecological Architecture.

    These mechanisms work in parallel within the model software and are both active as a default. The light on the utilities panel is an indicator to tell you which mechanism is currently operating; red for energy intake rate and green for the UB Rule.

    If you want the UB Rule indicator to be updated for every cell added to your animal type's foraging path then click on the UB by cell option.

    You can control the workings of these mechanisms in the Parameter View window.

Utilities

The Animal Populations window also provides access to a suite of utilities for investigating each animal population.


At your disposal are

(1) The Commuting Grid
The Commuting Grid is a 2D plot specific to your animal population. Follow the daily foraging pathways for your animal type as they commute between feeding sites (commuting grid cells) plotted in the context of the spatial foraging decisions that their environment requires them to make to maintain sufficient food intake.

The environment

The environment (commuting grid cells) display the animals' forage resources in terms of,
  • energy intake rate (EIRO),
  • positive values of potential patch profitability (PPP) net the costs of travel (commuting plus foraging within cells),
  • positive values of PPP including other costs,

    or

  • positive and negative (costs are more than PPP) values of PPP including other costs.

    Alternatively, you can choose for the commuting grid to show

  • travel costs from the current cell to each other cell,

    or lastly,

  • the foraging "Process" for each cell which is a measure of forage abundance interpreted through an animal's encounter rate with its food items and how quick it can eat that food. In other words, the foraging process tells you what is delaying the animal while feeding; either how fast it can find food, or how fast it can eat it when found. To read more about foraging "Process" please see Spalinger & Hobbs (1992) and the section on Ecological Architecture.

    For your commuting grid you can select between mean and modal foraging Process.

Display

You can also display the gridlines in your commuting grid using the Lines option, and the values of whichever variable you have selected to display. The values are displayed when you select the Values option. The Water/Bomas option will mark with a blue grid cell the position of any water points and bomas that you have associated with your animal type in your model. You can set water points and bomas using the Water Locator and GIS Control.

Below these option tickboxes is a panel that displays the current commuting grid co-ordinates for the cells when you pass your mouse cursor over them. Also given are the dimensions of the area accessible to your animal type for foraging based on limitations to your site area defined by your Site Area Mask and restrictions on the foraging range of your animal type, e.g., herding practises and known barriers to animal habitat use and migration, defined with your GIS data and entered in to the GIS Control.

With the following options:
  • Redraw - plot every time a cell is added to the daily foraging path.
  • Start - display the starting terminus of the daily foraging path.
  • Path - display the daily foraging path.
  • End - display the end terminus of the daily foraging path.
  • Scan - display the cells assessed for forage resources by the spatial foraging module.
  • Seen - display the cells assessed for forage resources by the spatial foraging module divided into directional quadrants.
  • Direction - show the direction in which the spatial foraging module has decided to move your animal type.
  • Remembered - display the memory scores for each cell instead of the commuting grid's Display settings (EIRO, PPP, Travel, etc.).

Extras

At any point use the snapshot button to cature a bitmap image of your Commuting Grid window. This image is automatically stored to the target folder given for commuting grid outputs. Change this location in the Parameter View window where you can also set this image export to be automatic. The default location is the same as your export folder for other Grid windows which you can modify under the Grid tab in your Preferences window.

Finally, click the Colour Key button to access the colour key for a description of the colour coding used in your commuting grid.


(2) The Resource Matching Plot
Ideal Free theory predicts that herbivore densities should reflect resource distribution in a heterogeneous environment, assuming that animals have perfect ("ideal") knowledge of resource profitability and are "free" to move between resource sites. Causes of deviation from the Ideal Free Distribution (IFD) arise from limitations in resource perception (not "ideal") and resource utilisation. Alternatively, unbalanced inter-patch emigration and disproportionate survival costs incurred during travel also cause deviation from the IFD (not "free"). IFD theory predicts perfect matching of animal distribution to the distribution of their resource, i.e., IFD is the distribution at which animal populations are in equilibrium with their resource. Overmatching is the utilisation of available resources at a rate above the ideal. More commonplace in the real world, however, is undermatching, the failure to meet the IFD because of real world constraints on resource accessibility and animal perception. It is worth noting that as the IFD applies to all resource locations within an environment, undermatching involves negative deviation from IFD predictions at highly profitable resource sites balanced by an equal amount of positive deviation from low profitability sites.

This Resource Matching Plot is a graph of resource utilization (consumption of forage) plotted against resource availability (forage abundance). If a regression of the resulting plot can be described using the equation for a straight line y=mx through the origin (0,0), then overmatching occurs for m>1 and undermatching for m<1. Exact matching is when m=1 and x=y.

  • Use the On / Off switch to activate your plot.
  • Use the XY option to select between an XY scatter plot and a histogram.
  • A histogram shows you classes of utilization efficiency (use versus availability). This one shows a typical right-skewed distribution of impacts
  • Set the number of bins to divide these classes in the #Bins box.
  • Use the Regress option to carry out a regresssion of your XY scatter plot. The regression equation is displayed in the status bar at the bottom of the window. You can save the regression statistics in ascii output files associated with your animal module.
  • Use the X=Y option to display the line x=y (exact matching) for comparison with your plot. Here the animals are not doing too well (compare the solid regression line with the dotted x=y line) and undermatching their resource distribution
  • Exclude zeros from your plot using the 0's option.
  • Choose your x-axis to be in terms of potential energy intake rate (EIRO) or actual forage biomass using the X=EIRO and X=Forage Biomass switch.
  • Choose your y-axis from the dropdown list. You can choose from
    • Distribution - simple frequencies
    • Encounters - total visits scored
    • Total Biomass Consumption - plant material intake
    • Mean Energy Consumption - energy intake
    • Slope b - regression slope parameter
    • Intercept a - regression intercept parameter
    • Memory history - stored encounters
  • Left truncate your x-axis so that it starts at the minimum value rather than zero using the 0-->X option.
  • Use the close button to close the window.


(3) Commuting Grid Details
Use this window to annotate your Commuting Grid display. It provides additional information at a glance about your animal type and their foraging decisions, e.g., current location of herd, directional scores for forage availability, foraging distance, cells visited and pathway tortuosity.


(4) Commuting Grid Cell Details
Use this window to query individual cells in your Commuting Grid. Click on the cell and supplementary information will appear in this window, e.g., potential energy intake rate, biomass consumed and current memory status.


(5) The Piosphere Plot


The concentration of impacts when animals congregate at water points gives rise to a gradient called the piosphere.

This plot does not provide a formula to describe piospheres resulting from your model, but it does allow you to visually monitor piosphere generation and also provides a way to export the results for post-simulation analysis in other software. Click on the Output to file option and select the frequency for file out, daily, monthly or annual. The sequence of files containing the plot data as xy pairs will be saved to your main simulation output folder set in your Preferences. For information about analysis techniques, please see the Analysis section in this guide.

You can also access a thesis dedicated to piospheres and gradient analyses in Derry (2004).
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