mntdn: Mean nearest taxon distance (MNTD)

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

Mean nearest taxon distance (MNTD)

Description

Calculate mean nearest taxon distance (MNTD) in each community in a given community matrix.

Usage

mntdn(comm, pd, abundance.weighted = TRUE,
      check.name = TRUE, memory.G = 50, time.count = 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.
check.name	logic, whether to check the OTU ids (species names) in community matrix and phylogenetic distance matrix are the same.
memory.G	numeric, to set the memory size as you need, so that calculation of large tree will not be limited by physical memory. unit is Gb. default is 50Gb
time.count	logic, whether to count calculation time, default is FALSE.

Details

mean nearest taxon distance (MNTD) in each community, using the same algrithm as the function 'mntd' in package 'picante'.

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 CO, Ackerly DD, and Kembel SW. (2008). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 18:2098-2100

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

NTI.p

Examples

data("example.data")
comm=example.data$comm
pd=example.data$pd
mntd=mntdn(comm=comm,pd=pd,abundance.weighted = TRUE)

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