ens: ens Effective Number of Species

Description Usage Arguments Author(s) References Examples

View source: R/divo.R

Description

Calculates diversity profile (DP) using the effective number of species (ENS) based on inverting the Renyi entropy. For any monotone diversity index (see, Rempala and Seweryn 2013) the ENS is defined as the size of a uniform population with the same index value as the current population. The ENS may be considered as a measure of population diversity expressed in the units of species counts. The ENS profile is calculated against the Renyi entropy index, which allows for a direct comparison with the diversity profile (as in dp). The option of performing the Horvitz-Thompson correction is available in the function ens.ht. For more details on ENS, see Rempala and Seweryn (2013) or Jost (2006).

Usage

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ens(x, alpha = seq(0.1, 2, 0.1), CI = 0.95, resample = 100, 
single_graph = FALSE, pooled_graph = FALSE, csv_output = FALSE, 
PlugIn = FALSE, size = 1, CVG = FALSE, saveBootstrap = FALSE)

Arguments

x

a matrix containing input populations

alpha

a vector containing alpha values, default = seq(0.1, 2, 0.1)

CVG

a list containing alpha values multiplied by coverage; default = FALSE

CI

Confidence Interval default = 0.95, range (0, 1)

resample

set number of repetitions, default = 100

single_graph

default = FALSE, plot of the Diversity Profile for each population; single_graph = 'fileName' user-defined output file name

pooled_graph

default = FALSE, plot of the Diversity Profile for all populations; pooled_graph = 'fileName' user-defined output file name

csv_output

save the result of the analysis as .CSV file, default = FALSE; csv_output = 'fileName' user-defined output file name

PlugIn

standard plug-in estimator, default = FALSE

size

resampled fraction of the population, default = 1 (actual size of populations). The value should not be smaller than 10% of population (size = 0.1)

saveBootstrap

Saves bootstrap result to a file. Use saveBootstrap = TRUE to save bootstrap results to a Bootstrap folder in current directory; saveBootstrap = 'FolderName' - saves bootstrap results to user-named folder

Author(s)

Christoph Sadee, Maciej Pietrzak, Michal Seweryn, Cankun Wang, Grzegorz Rempala
Maintainer: Maciej Pietrzak pietrzak.20@osu.edu

References

Jost L. (2006) Entropy and diversity. Oikos 113:363-75

Rempala G.A., Seweryn M. Methods for diversity and overlap analysis in T-cell receptor populations. (2013) J Math Biol 67:1339-68

Examples

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data(TCR.Data)
result <- ens(x, PlugIn = TRUE)

divo documentation built on Dec. 18, 2019, 1:51 a.m.