PopDiversity {DivE}

PopDiversity

Description

Calculates the species richness at a specified population size, taking an object of class DiveMaster as an input.

Usage

PopDiversity(dm, popsize, TopX=NULL)

Arguments

dm

list of objects of class DiveMaster.

popsize

positive real number. Population size.

TopX

a positive integer, less than the number of models contained in dm, representing the number of best-performing models used for the aggregated estimate of the population diversity. If NULL (default), then dm$m models are aggregated. If TopX is larger than the the number of models fitted, then min(5, length(dm$fmm)) models are aggregated.

Details

CombDM combines multiple objects of class DiveMaster. Function used if DivE estimation has been split into multiple, separate calls to DiveMaster.

Value

A list of objects:

estimate

point estimate of diversity (species richness)

upper_estimate

estimate upper bound

lower_estimate

estimate lower bound

Author(s)

Daniel J. Laydon, Aaron Sim, Charles R.M. Bangham, Becca Asquith

References

Laydon, D. J., Melamed, A., Sim, A., Gillet, N. A., Sim, K., Darko, S., Kroll, S., Douek, D. C., Price, D., Bangham, C. R. M., Asquith, B., Quantification of HTLV-1 clonality and TCR diversity, PLOS Comput. Biol. 2014

See Also

DiveMaster

Examples

# See DiveMaster documentation for examples.