CommunityFactory: Community factory
In quicklizard99/Basingstoke: Food-web structural models

Description Usage Arguments Details Value Author(s) See Also Examples

Community factory.

CommunityFactory(S, nodes, generator, n=1, 
                 accept=NULL, energetically.feasible=TRUE, 
                 trace.progress=FALSE, validate=TRUE,
                 properties=NULL, ...)

`S`	number of nodes in the generated communities.
`nodes`	either a vector of node names or a `data.frame` of node properties that satisfies the conditions nodes of Community.
`generator`	function used to generate sets of trophic links.
`n`	number of communities to generate.
`accept`	either `NULL` or a function that takes a community as its only argument and returns a `logical`.
`energetically.feasible`	if `TRUE`, communities that are not energetically feasible according to Cheddar's `PreyAveragedTrophicLevel` function are discarded.
`trace.progress`	if `TRUE` then feedback is printed as the function runs.
`validate`	if 'TRUE', created communities are validated using the checks provided by Cheddar's `Community` function.
`properties`	either `NULL` or a `list` of community-level properties.
`...`	.

Either ‘S’ or ‘nodes’ should be provided - no need to provide both.

A list of ‘n’ Community objects.

Lawrence Hudson

Community, PreyAveragedTrophicLevel IsIsolatedNode, IsolatedNodes IsBasalNode, BasalNodes

# Example 1
# Use the niche model to create 12 communities containing 25 species with a
# directed connectance close to 0.15. 
communities <- CommunityFactory(S=25, n=12, generator=NicheModelLinks, C=0.15)

# Communities are named 'Artificial community 1'..'Artificial community n'
names(communities)

# Each has 25 nodes
sapply(communities, NumberOfNodes)

# Each has a C close to 0.15
sapply(communities, DirectedConnectance)
hist(sapply(communities, DirectedConnectance))

# Plot nodes stacked vertically by trophic level
plot(communities, ncol=4)

# At least one community will have a non-zero number of isolated nodes
sapply(communities, function(c) return(length(IsolatedNodes(c))))


# Example 2
# Use the accept argument to ensure that the communities have no isolated
# nodes, using Cheddar' IsIsolatedNode function
communities <- CommunityFactory(S=25,
                                n=12,
                                generator=NicheModelLinks,
                                C=0.15,
                                accept=function(c) 0==sum(IsIsolatedNode(c)))

# All zero
sapply(communities, function(c) return(length(IsolatedNodes(c))))


# Example 3
# Guarantee that communities have no isolated nodes and exactly 5 basal nodes -
# use Cheddar's IsBasalNode function for this; also get CommunityFactory to
# trace its progress.
communities <- CommunityFactory(S=25,
                                n=12,
                                generator=NicheModelLinks,
                                C=0.15,
                                accept=function(c) 0==sum(IsIsolatedNode(c)) &&
                                                   5==sum(IsBasalNode(c)),
                                trace.progress=TRUE)

# No community has isolated nodes
all(0==sapply(communities, function(c) return(length(IsolatedNodes(c)))))

# All communities have five basal nodes
all(5==sapply(communities, function(c) return(length(BasalNodes(c)))))