beta_diversity: Calculate beta diveristies of S_cov, S_N and S_PIE

In T-Engel/hammeRs:

Description

Beta diversities quantify spatial species turnover of samples belonging to the sama gamma scale/ group. beta_S_PIE characterises spatial turnover of dominant species (i.e. the base of the individual based rarefaction curve). Beta diversities of S_N and S_cov reflect spatial turnover of rare species.

Usage

beta_diversity(mob_in, group_var, effort_samples = NULL,
  stand_cov = NULL, extrapolate = c(N = TRUE, cov = TRUE), na.rm = T)

Arguments

mob_in	A mob_in object that contains the commnity matrix and the env dataframe eith a grouping variable specified in group_var.
group_var	A character string referring to the column in mob_in$env that groups the alpha-scale samples into gammas.
effort_samples	The number of individuals N used for beta_S_N. If not specified, it will automatically use the recommended sample size. That is the number of individuals in the smallest sample if extrapolate = FALSE or twice as many if extrapolate = TRUE.
stand_cov	The coverage used for coverage based rarefaction. If not specified, it will automatically use the recommended sample coverage. That is the lowest coverage value of the alpha samples if extrapolate = FALSE or the expected coverage of that sample if it was extrapolated to 2N. See recommended_C() for details.
extrapolate	A boolean vecotor of length 1 or 2 specifing whether extrapolation should be used for individial- and coverage-based richness standardisation. The first value in the vector corresponds to individual-based standardisation, the second to coverage-based standardisation. If a single value is supplied, it is adopted for both.
na.rm	Boolean. Passed on to the function that aggregates the alpha diversities to a mean.

Examples

library(mobr)
data("inv_comm")
data("inv_plot_attr")
inv_mob_in<-make_mob_in(inv_comm, inv_plot_attr)
betas<-beta

T-Engel/hammeRs documentation built on May 22, 2019, 2:16 p.m.