mobr (version 3.0.0)

calc_beta_div: Calculate beta diversity from sites by species table.

Description

A wrapper for the function calc_comm_div that only returns scales = 'beta'

Usage

calc_beta_div(abund_mat, index, effort = NA, C_target_gamma = NA, ...)

Arguments

abund_mat

Abundance based site-by-species table. Species as columns

index

The calculated biodiversity indices. The options are

• N ... Number of individuals (total abundance)

• S ... Number of species

• S_n ... Rarefied or extrapolated number of species for n individuals

• S_C ... Estimate species richness of a given level of coverage by C_target_gamma

• S_asymp ... Estimated asymptotic species richness

• f_0 ... Estimated number of undetected species

• pct_rare ... The percent of rare species as defined by rare_thres

• PIE ... Hurlbert's PIE (Probability of Interspecific Encounter)

• S_PIE ... Effective number of species based on PIE

See Details for additional information on the biodiversity statistics.

effort

The standardized number of individuals used for the calculation of rarefied species richness. This can a be single integer or a vector of integers.

C_target_gamma

When computing coverage based richness (S_C) then this argument can be used to specify the coverage to be used for the gamma scale richness estimate. This defaults to NA in which case the target cover is computed by calc_C_target (i.e., the largest allowable sample size).

...

other arguments to pass to calc_comm_div

See Also

calc_comm_div

Examples

data(inv_comm)
beta_metrics = calc_beta_div(inv_comm, 'S_n', effort = c(5, 10))
beta_metrics