Improvements to enumerating trophic chains

[quicklizard99]

Two limitations relating to the way that Cheddar handles trophic chains:

1. TrophicChains() allocates a chunk of memory large enough to hold max.chains chains of length NumberOfChains() - this is very inefficient, requires the user to tweak max.chains and means that highly connected communities, such as SkiwithPond, cannot be enumerated on 32-bit operating systems
2. The only way to compute any statistics on trophic chains is to enumerate all of the chains using TrophicChains() and hold them in memory - very restrictive given point 1

[quicklizard99]

Fixed in 0.1-618:

1. TrophicChains() changed to allocate only the space that is needed. The following now works on 32-bit operating systems:

library(cheddar)
data(SkipwithPond)
chains <- TrophicChains(SkipwithPond)
dim(chains)    # 2538120 rows, 17 columns

1. Added a new function, TrophicChainsStats():

library(cheddar)
data(SkipwithPond)
stats <- TrophicChainsStats(SkipwithPond)
length(stats$chain.length)    # The length (i.e. number of links) of each of the 2538120 chains
mean(stats$chain.length)
summary(stats$chain.length)
# A matrix with a row for each node (37 for Skipwith Pond) and '1+max(stats$chain.lengths)' columns. 
# Elements are the number of chains in which a node appear in that position.
stats$node.pos.counts