Calculates the species richness at a specified population size, taking an object of class DiveMaster as an input.
Usage
PopDiversity(dm, popsize, TopX=NULL)
Value
A list of objects:
estimate
point estimate of diversity (species richness)
upper_estimate
estimate upper bound
lower_estimate
estimate lower bound
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.
Author
Daniel J. Laydon, Aaron Sim, Charles R.M. Bangham, Becca Asquith
Details
CombDM combines multiple objects of class DiveMaster. Function used if DivE estimation has been split into multiple, separate calls to DiveMaster.
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