CombDM {DivE}

CombDM

Description

Implements the DivE diversity estimator. Combines multiple objects of class DiveMaster.

Usage

CombDM(dmlist)

Arguments

dmlist

list of objects of class DiveMaster.

Details

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

Value

An object of class DiveMaster, i.e. a list of objects

model.score

a matrix of aggregated model scores

fmm

a list of fitsingMod objects corresponding to the list of fitted models

ssm

a matrix of scores of the fit of the models corresponding to the list of fitted models

estimate

the estimate of species richness (number of species/classes or diversity) at population size tot.pop. This is the geometric average of the models corresponding to the top-five model scores. This is recalculated based on the combined list of models

lower_estimate

as per estimate value, but the lowest prediction amongst the models having the top-five scores. This is recalculated based on the combined list of models

upper_estimate

as per estimate value, but the highest prediction amongst the models having the top-five scores. This is recalculated based on the combined list of models

models

list of original input models

m

number of topscoring models used for diversity estimate. This is set as the smallest m value of each of the DiveMaster objects in the list

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.