Set species interaction matrix
Usage
setInteraction(params, interaction = NULL)
interaction_matrix(params)
interaction_matrix(params) <- value
Value
setInteraction
: A MizerParams object with updated interaction
matrix
interaction_matrix()
: The interaction matrix (predator species x
prey species)
Setting interaction matrix
You do not need to specify an interaction matrix. If you do not, then the predator-prey interactions are purely determined by the size of predator and prey and totally independent of the species of predator and prey.
The interaction matrix
The interaction matrix is used when calculating the food encounter rate in
getEncounter()
and the predation mortality rate in getPredMort()
. Its
entries are dimensionless numbers. If all the values in the interaction
matrix are equal then predator-prey interactions are determined entirely by
size-preference.
This function checks that the supplied interaction matrix is valid and then
stores it in the interaction
slot of the params
object.
The order of the columns and rows of the interaction
argument should be
the same as the order in the species params data frame in the params
object. If you supply a named array then the function will check the order
and warn if it is different. One way of creating your own interaction
matrix is to enter the data using a spreadsheet program and saving it as a
.csv file. The data can then be read into R using the command read.csv()
.
The interaction of the species with the resource are set via a column
interaction_resource
in the species_params
data frame. By default this
column is set to all 1s.
See also
Other functions for setting parameters:
gear_params()
,
setExtEncounter()
,
setExtMort()
,
setFishing()
,
setInitialValues()
,
setMaxIntakeRate()
,
setMetabolicRate()
,
setParams()
,
setPredKernel()
,
setReproduction()
,
setSearchVolume()
,
species_params()
Examples
params <- newTraitParams(no_sp = 3)
inter <- getInteraction(params)
#> Warning: `getInteraction()` was deprecated in mizer 2.4.0.
#> ℹ Please use `interaction_matrix()` instead.
inter[1, 2:3] <- 0
params <- setInteraction(params, interaction = inter)
getInteraction(params)
#> prey
#> predator 1 2 3
#> 1 1 0 0
#> 2 1 1 1
#> 3 1 1 1