filterCoefData: filterCoefData

In jebyrnes/multifunc: Analysis of Ecological Drivers on Ecosystem Multifunctionality

filterCoefData

Description

filterCoefData filters contributions of species to function by sign.

Usage

filterCoefData(coefData, type = "positive")

Arguments

coefData	Matrix of functions and coefficients for which species affect them from getRedundancy.
type	Are the kinds of effects we're looking at "positive", "negative" or "all".

Details

Takes a matrix of functions and coefficients for species and filters out only the sign of contributions desired. Typically used by other functions in the package.

Value

Returns a filtered matrix.

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

coefs <- getRedundancy(vars, species, germany, output = "coef")
stdCoefs <- stdEffects(coefs, germany, vars, species)

filterCoefData(stdCoefs)


#########
# filterCoefData takes a matrix of coefficients
# and filters it so that only the positive, negative, or both contributions
# are present
#########

jebyrnes/multifunc documentation built on May 25, 2022, 9:43 p.m.