mpdn: Mean pairwise distance (MPD)

In iCAMP: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

Mean pairwise distance (MPD)

Description

Calculate mean pairwise distance (MPD) in each community in a given community matrix.

Usage

mpdn(comm, pd, abundance.weighted = TRUE, time.output = FALSE)

Arguments

comm	matrix or data.frame, community data matrix, rownames are sample names, colnames are OTU ids.
pd	matrix, pairwise phylogenetic distance matrix.
abundance.weighted	logic, whether weighted by species abundance, default is TRUE, means weighted.
time.output	logic, whether to count calculation time, default is FALSE.

Details

mean pairwise distance (MPD) in each community, which is the same index as 'mpd' in package 'picante', but calculated by matrix multiplication.

Value

result is a numeric vector with sample names

Note

Version 2: 2020.8.19, update help document, add example. Version 1: 2017.3.13

Author(s)

Daliang Ning

References

Webb C, Ackerly D, McPeek M, and Donoghue M. (2002). Phylogenies and community ecology. Annual Review of Ecology and Systematics 33:475-505.

Kembel, S.W., Cowan, P.D., Helmus, M.R., Cornwell, W.K., Morlon, H., Ackerly, D.D. et al. (2010). Picante: R tools for integrating phylogenies and ecology. Bioinformatics, 26, 1463-1464.

See Also

NRI.p

Examples

data("example.data")
comm=example.data$comm
pd=example.data$pd
mpd=mpdn(comm = comm, pd = pd, abundance.weighted = TRUE)

iCAMP documentation built on June 1, 2022, 9:08 a.m.