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.
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]
This file is required for the model to run.
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
Back to alphabetical list of files
The population parameters file contains survival and reproductive probabilities for the killer whale population.
This file is required for the model to run.
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.csvThe 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.
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