bmpd: Beta mean pairwise distance (betaMPD)

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

Beta mean pairwise distance (betaMPD)

Description

Calculates mean pairwise distance separating taxa in each pair of communities in a given community matrix.

Usage

bmpd(comm, pd, abundance.weighted = TRUE, na.zero = TRUE,
     time.output = FALSE, unit.sum = NULL)

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.
na.zero	logic. when the sum of a row (a sample) is zero in community data matrix, the relative abundance will be NAN. Sometimes, to avoid some problem in following calculation, this kind of NAN value need be set as zero. Defalt is TRUE.
time.output	logic, whether to count calculation time, default is FALSE.
unit.sum	When a beta diversity index is calculated for a bin, the taxa abundances will be divided by unit.sum to calculate the relative abundances. usually, unit.sum can be set as the sequencing depth in each sample. Default setting is NULL, means not to do this special transformation.

Details

beta mean pairwise distance.

Value

Output is a distance object of pairwise betaMPD between samples.

Note

Version 3: 2020.8.16, add examples. Version 2: 2018.10.3, add unit.sum option. if unit.sum!=NULL, will calculate relative abundance according to unit.sum Version 1: 2015.8.21.

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

See Also

bNRIn.p

Examples

data("example.data")
comm=example.data$comm
pd=example.data$pd
bmpd.wt=bmpd(comm, pd, abundance.weighted = TRUE)

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