Calculates the species richness at a specified population size, taking an object of class DiversityMaster as an input.
Usage
popdiversity(dm, popsize, TopX=NULL)
Arguments
dm
list of objects of class DiversityMaster.
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
comb.dm combines multiple objects of class DiversityMaster. 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 Laydon, Aaron Sim, Charles Bangham, Becca Asquith
References
Laydon, D., 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