PredationMatrixToLinks {cheddar}R Documentation

Predation matrix to trophic links

Description

A function that converts a predation matrix to a data.frame with the columns ‘resource’ and ‘consumer’.

Usage

PredationMatrixToLinks(pm, link.property=NULL)

Arguments

pm

a matrix or data.frame.

link.property

either NULL or a character.

Details

Returns a data.frame of trophic links contained within pm. Non-zero and non-NA values indicate a trophic link between a resource (row) and consumer (column). pm should have both row names and column names. The returned data.frame will contain the columns ‘resource’ and ‘consumer’. If pm contains quantitative information such as diet fractions or number of observations then you can set link.property to the name of the quantity and the returned data.frame will include a column with that name, that contains link strength values extracted from pm.

If you have existing food-web data in predation-matrix form then this function can help to import your data in to Cheddar.

Value

A data.frame

Author(s)

Lawrence Hudson

See Also

Community, PredationMatrix, TLPS

Examples

data(TL84)

links <- PredationMatrixToLinks(PredationMatrix(TL84))
identical(links, TLPS(TL84))    # TRUE

# Create a Cheddar community from an existing square predation matrix
node <- c('Leaf', 'Caterpillar', 'Bluetit')
pm <- matrix( c(0, 1, 0,
                0, 0, 1,
                0, 0, 0), 
             ncol=3, byrow=TRUE, dimnames=list(node, node))

community1 <- Community(nodes=data.frame(node=node),
                        trophic.links=PredationMatrixToLinks(pm),
                        properties=list(title='Test community'))
TLPS(community1)

# The same set of trophic links could be represented by a non-square predation 
# matrix
pm <- matrix( c(1, 0,
                0, 1), 
             ncol=2, byrow=TRUE, 
             dimnames=list(node[1:2], node[2:3]))

community2 <- Community(nodes=data.frame(node=node),
                        trophic.links=PredationMatrixToLinks(pm),
                        properties=list(title='Test community'))
TLPS(community2)

all.equal(community1, community2)    # TRUE

# Extract quantitative information
node <- c('Leaf 1', 'Leaf 2', 'Caterpillar 1', 'Caterpillar 2')
pm <- matrix( c(0, 0, 0.4, 0.8, 
                0, 0, 0.6, 0.2, 
                0, 0, 0,   0, 
                0, 0, 0,   0), 
             ncol=4, byrow=TRUE, dimnames=list(node, node))

# A data.frame that has a column called diet.fraction
PredationMatrixToLinks(pm, link.property='diet.fraction')

[Package cheddar version 0.1-636 Index]