Documentation and Reference

User's Manuals

Quick Start Tutorial - walkthrough of the process of running a simulation.
SplitOutput User's Guide - documentation on the use of the SplitOutput program.

Alphabetical List of Files

Formula List - specifies user-defined formulae to be included in the output file.
Population - contains information for a starting population of killer whales.
Population Parameters - survival and reproductive rates for the killer whale population.
Prey Adjustments - lists adjustments to be made to the prey base, currently harvests or regime shifts.
Prey Parameters - contains information describing one or more prey species for use by the model.

Formula List

Description

The formula list file specifies user-defined formulae to be included as columns in the output file. A formula consists of a name in square brackets, an equal sign, and an expression that may contain variables or constants. A formula's name may contain the string '_Prey' (capitalization does not matter), making it a "prey formula", which will be output for each prey type, with '_Prey' replaced by the name of the prey type.

There are two types of variables that can be used to build formulae - external and internal. External variables correspond to columns in the output file, and are represented by the name of the column surrounded by square brackets, e.g. [Alive A]. Because a formula creates a new output column, it also creates a new external variable that may be used by other formulae. Internal variables are not normally included in the output, but they are available for building formulae. Internal variables should only be used in "prey formulae".

Here is a list of all available internal variables:

This file is optional.

Structure

This file is a list of formulae, one formula per line. The first non-whitespace character of a formula line must be '['; any line beginning with any other character is ignored. Tabs are strictly illegal - any line containing a tab is ignored.

Example of formula:
[Total Alive] = [Alive 0] + [Alive 1] + [Alive 2] + [Alive J] + [Alive A]

Sample file: formula_list.txt
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Population

Description

This file is required for the model to run.

Structure

The initial population is a CSV file. The first column is a unique ID for each whale. The second is "F" or "M" to indicate gender. The third column is the age of the whale. The fourth column is the ID of the whale's mother. The fifth column is "A" or "D" for alive or deceased whales.
Sample file: population50.csv
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Population Parameters

Description

The population parameters file contains survival and reproductive probabilities for the killer whale population.

This file is required for the model to run.

Structure

The population parameters file is a basic CSV file. The first line is a header identifying the columns, and the following lines contain the data. There are four columns: age, female survival probability, male survival probability, and reproductive probability.

Sample file: popparms.csv
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Prey Adjustments

Description

The prey adjustments file is used to specify adjustments to be made to the prey population during the course of a run. Each adjustment will affect a specified prey on a specified year and day. Currently there are two types of adjustments: harvests and regime shifts.

A harvest adjustment removes up to a specified number of individuals from the prey population. A percentage of the population may be designated as non-harvestable. It is possible to inject individuals into the population by specifying a negative number to harvest.

A regime shift adjustment changes the Ricker parameters for the prey species.

This file is optional.

Structure

Blank lines are skipped; lines starting with ';' are comments. Entries need not be sorted, but they will be handled more efficiently if they are.

Harvests are specified by the keyword "harvest", followed by the year and day of the harvest, then the name of the prey, the number to harvest, and the minimum percent of the prey that may not be harvested.

Example of harvest:
harvest, 2, 1, porpoise, 500000, 5

Regime shifts are specified by the keyword "regime", followed by the year and day of the shift, then the name of the prey, then the Ricker parameters: survA, survB, birthA, birthB.

Example of regime shift:
regime, 8, 1, porpoise, .99e-20, 3.5, 7e-26, 3

Sample file: prey_adjustments.txt
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