multidiv: Calculate multifunctionality

In allanecology/multiFunBetadivLuiGDM: Testing effects of multitrophic beta-diversity and land-use intensity (LUI) on ecosystem multifunctionality

Calculate multifunctionality

Description

created by Eric Allan

Usage

multidiv(
  x,
  threshold = FALSE,
  sc = "max",
  mx = 1,
  cent = FALSE,
  by = FALSE,
  weights = 1
)

Arguments

x	Input data frame or matrix. Rows are different diversities/ functions for multifun/div calculation. Columns are replicates, e.g. plots.
threshold	can be a proportion of the maximum e.g. 0.5 or can be the median or mean. It can also be a vector of the same length as the number of diversities to allow different thresholds for different diversities. threshold = FALSE calculates the mean of the scaled diversities or functions
sc	scaling can be by any function specified in "sc", i.e. max, mean, sd etc., max is the default. If the maximum should be a mean of the top n values specify sc = "maxx", mx = n
mx	only if sc = "maxx", when the maximum should be a mean of the top n values, mx = n.
cent	centering by the mean is possible with cent = TRUE, to take z-scores of the diversities/processes, use sc="sd" and cent = TRUE
by	specifies a vector of the same length as nrow(x) to be used to split the data and use different thresholds for the groups in "by"
weights	allows different weightings for the different diversities/functions and should be a vector of the same length as the number of diversities/functions (shorter vectors will be recycled) to weight a diversity as 0 and drop it from the calculation, code the weight as "NA" the default is weights = 1: all diversities weighted the same

Value

matrix with 2 columns, the first column is the multidiversity/ -functionality of each plot, the second being the number of measured (non NA) functions per plot.

Examples

# create fantasy dataset with 3 functions f1, f2 and f3 and 30 plots.
set.seed(2)
fundataset <- data.table::data.table(f1 = runif(30, min=0, max=100), f2 = runif(30, min=0, max=1), f3 = runif(30, min=0, max=10))
# calculate multifunctionality of this dataset, being the proportion of functions per plot which exceed the threshold of 0.5
# of the mean of maximum 5 functions.
multidiv(fundataset, threshold = 0.5, sc = "maxx", mx = 5, cent=FALSE, weights = 1)

allanecology/multiFunBetadivLuiGDM documentation built on Nov. 12, 2023, 6:16 a.m.