mntdn {iCAMP} | R Documentation |
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
Examples
data("example.data")
comm=example.data$comm
pd=example.data$pd
mntd=mntdn(comm=comm,pd=pd,abundance.weighted = TRUE)