getOverlap {multifunc} | R Documentation |
getOverlap
Description
getOverlap
goes through all m-wise combinations of species
and returns the amount of overlap between species in functions they perform
for each combination
Usage
getOverlap(
overData,
m = 2,
type = "positive",
index = "sorensen",
denom = "set"
)
Arguments
overData |
Matrix of functions and which species affect them from |
m |
Number of functions. Defaults to 2. |
type |
Are the kinds of effects we're looking at "positive", "negative" or "all". |
index |
Type of overlap index to be used. Defaults to "sorenson" but currently incorporates "mountford" and "jaccard" as well. |
denom |
Should the denominator be "all" species or just the "set" of species with the types of interactions being considered? Defaults to "set". |
Details
getOverlap takes a matrix of 1s and -1s, and depending on whether we're interested in positive, negative, or both types of interactions looks for the m-wise overlap between species and returns the overlap index for each combination
Value
Returns a vector of overlap indices.
Author(s)
Jarrett Byrnes.
Examples
data(all_biodepth)
allVars <- qw(biomassY3, root3, N.g.m2, light3, N.Soil, wood3, cotton3)
germany <- subset(all_biodepth, all_biodepth$location == "Germany")
vars <- whichVars(germany, allVars)
species <- relevantSp(germany, 26:ncol(germany))
# re-normalize N.Soil so that everything is on the
# same sign-scale (e.g. the maximum level of a function is the "best" function)
germany$N.Soil <- -1 * germany$N.Soil + max(germany$N.Soil, na.rm = TRUE)
res.list <- lapply(vars, function(x) sAICfun(x, species, germany))
names(res.list) <- vars
redund <- getRedundancy(vars, species, germany)
getOverlap(redund, m = 2)
getOverlap(redund, m = 2, index = "jaccard")
getOverlap(redund, m = 2, index = "mountford")
#########
# getOverlap takes a matrix of 1s and -1s, and depending on whether we're
# interested in positive, negative, or both types of interactions looks for the
# m-wise overlap
#########