RemoveNodes: Remove nodes

In cheddar: Analysis and Visualisation of Ecological Communities

Remove nodes

Description

Remove one or more nodes.

Usage

RemoveNodes(community, remove, title, 
                   method=c('direct','secondary','cascade'))

Arguments

community	an object of class Community.
remove	a vector of either names, integer indices or logicals indicating nodes to be removed.
title	a title for the new community.
method	how species removals are propogated through the food web.

Details

Returns a new Community with nodes in remove removed. An error is raised if remove refers to nodes not in the community of if remove refers to all nodes in the community.

If method is ‘direct’, only the nodes in remove are removed. If method is ‘secondary’, secondarily extinct nodes - those that directly consume one or more nodes in ‘remove’ and that no longer have any resources (except themselves) after the removal - are also removed. If method is ‘cascade’, a multistep version of ‘secondary’ is applied. This has the effect of propogating extinctions though the community - all consumers that are ultimately dependent upon all species in ‘remove’, and upon no other nodes (except themselves), will be removed.

Value

A new object of class Community.

Author(s)

Lawrence Hudson

See Also

Community, BasalNodes, IsolatedNodes, NumberOfNodes

Examples

data(TL84)

# Three different ways of removing node 56 (Umbra limi)
a <- RemoveNodes(TL84, 56)
b <- RemoveNodes(TL84, 'Umbra limi')
c <- RemoveNodes(TL84, c(rep(FALSE,55), TRUE))

identical(a,b)  # TRUE
identical(a,c)  # TRUE

# The behaviours of the different methods
NumberOfNodes(TL84)         # 56 nodes in total
length(BasalNodes(TL84))    # 25 basal nodes
length(IsolatedNodes(TL84)) #  6 isolated nodes

RemoveNodes(TL84, BasalNodes(TL84)) # 56 - 25 = 31 nodes remain
RemoveNodes(TL84, BasalNodes(TL84), method='secondary') # 14 nodes remain
RemoveNodes(TL84, BasalNodes(TL84), method='cascade')   # 6 isolated nodes remain

# Results in an error
## Not run: RemoveNodes(TL84, 1:NumberOfNodes(TL84))

cheddar documentation built on Sept. 11, 2024, 5:16 p.m.