stdEffects obtains the standardized effect of each species on each function
stdEffects(cmat, adf, vars, species)Matrix of coefficients of species effects on functions from getRedundancy with output="coef".
Data frame with plot level data for species and functions.
Names of columns with data for functions in adf.
Names of columns with data for species in adf.
Returns a matrix of standardized coefficients.
stdEffects takes a matrix of coefficients for relationships between species and functions, the data frame used to generate those coefficients and the names of species and function, and then it calculates standardized coefficients using std coef = b *sx/sy
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)
#########
# A function that uses the coefficient matrix and information from the
# data to calculate standardized effects of species using the method
# std coef = b *sx/sy
#########