Description Usage Arguments Examples
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.
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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. |
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