dot-move: One move of the limiting similarity algorithm

In emilio-berti/assembly: Simulate Community Assembly

One move of the limiting similarity algorithm

Description

One move of the limiting similarity algorithm

Usage

.move(
  sp.names,
  metaweb,
  t = 0,
  method = "jaccard",
  stat = "mean",
  mode = "all",
  return.similarity = FALSE
)

Arguments

sp.names	vector, names of the species in the meta-community.
metaweb	adjacency matrix of the meta food web (metaweb).
t	is the 'temperature' of the system.
method	character, same as in similarity (igraph). Options are 'jaccard', 'dice', and 'invlogweighted'.
stat	character, statistic used to summarize similarity. Currently available are c("mean", "sum", "max").
mode	character, which edges are used to compute similarity. Currently available are c("all", "in", "out").
return.similarity	logical, if to return the difference in similarity score.

Details

Similarities are calculated using igraph as matrices. To summarize these into species-level metrics, the argument "stat" is needed. When stat = "mean", probability of removal of species is proportional to the average of their similarities, etc. Global similarities, i.e. of the whole food web, are also summarized depending on the "stat" argument in a similar way.

When mode = 'in', similarity is computed using only 'in' links, i.e. species are considered similar if they share similar resources, but not necessarily have similar consumers. The opposite is treu when mode = 'out'. When mode = 'all' (default) all edges are considered.

Value

A vector with the species names.

emilio-berti/assembly documentation built on Aug. 16, 2022, 9:50 p.m.