| TrophicChains {cheddar} | R Documentation |
Trophic chains
Description
Enumerates every trophic chain in a food web.
Usage
TrophicChains(community, node.properties = NULL, chain.properties = NULL)
Arguments
community |
an object of class |
node.properties |
the names of the node properties to return. Should
meet the criteria of the |
chain.properties |
the names of chain properties to return. |
Details
Enumerates every trophic chain in the food-web and returns a
data.frame containing any requested node and trophic-link columns.
Some network properties and analyses require knowledge of every unique path
- ‘trophic chain’ - through the food-web. A trophic chain starts at a basal
node (BasalNodes) and ends when it is not possible to
add nodes that are not already in the chain, so loops and cannibalism are
ignored. For communities that have one or more top-level nodes
(TopLevelNodes) each trophic chain will end with a top-level node.
If your analysis requires only simple statistics about trophic chains, the
TrophicChainsStats function is more suitable as it is much faster and
requires less memory than TrophicChains. This is particularly true
for communities that contain a large number of trophic chains, such as the
SkipwithPond dataset, which has more than $10^5$ unique chains.
It will not be possible to compute, within reasonable time and available system
memory, trophic chains for food webs with a large number of nodes and/or
trophic links. TrophicChains will raises an error 'Unable to compute
paths' for these food webs. The ‘Large numbers of trophic chains’ section of
the ‘Community’ vignette explains this in more detail.
Value
A data.frame.
Author(s)
Lawrence Hudson
See Also
BasalNodes, TopLevelNodes,
TLPS, ThreeNodeChains,
TrophicChainsStats, SkipwithPond
Examples
data(TL84)
tc <- TrophicChains(TL84)
# Every chain starts with a basal node
BasalNodes(TL84)
first <- tc[,1]
all(IsBasalNode(TL84)[unique(first)])
# TL84 has a single top-level consumer - every trophic chain ends with this
# consumer
TopLevelNodes(TL84)
# Get the last node in each chain
last <- apply(tc, 1, function(row) row[max(which(""!=row))])
unique(last)
# M of nodes
head(TrophicChains(TL84, node.properties='M'))
# M and N of nodes
head(TrophicChains(TL84, node.properties=c('M','N')))
# Skipwith Pond has more than 10e5 unique chains
data(SkipwithPond)
# Not all systems will be able to allocate the memory required to hold the
# chains
## Not run: dim(TrophicChains(SkipwithPond))