iCAMP (version 1.5.12)

bmntd: beta mean nearest taxon distance (betaMNTD)

Description

Calculates beta MNTD (beta mean nearest taxon distance, Webb et al 2008) for taxa in each pair of communities in a givern community matrix.

Usage

bmntd(comm, pd, abundance.weighted = TRUE,
      exclude.conspecifics = FALSE,time.output=FALSE,
      unit.sum=NULL, spname.check = TRUE, silent = TRUE)

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.

exclude.conspecifics

logic, whether conspecific taxa in different communities be exclude from beta MNTD calculations, default is FALSE.

time.output

logic, whether to count calculation time, default is FALSE.

unit.sum

NULL or a number or a nemeric vector. When unit.sum is not NULL and 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.

spname.check

logic, whether to check the species names in comm and pd.

silent

logic, if FALSE, some messages will be showed if any mismatch in spcies names.

Value

result is a distance object of pairwise beta MNTD between samples.

Details

beta mean nearest taxon distance for taxa in each pair of communities. Modified from 'comdistnt' in package 'picante'(Kembel et al 2010), this function includes matrix multiplication to be efficient for medium size dataset.

References

Webb, C.O., Ackerly, D.D. & Kembel, S.W. (2008). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24, 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

bNTIn.p

Examples

# NOT RUN {
data("example.data")
comm=example.data$comm
pd=example.data$pd
bmntd.wt=bmntd(comm, pd, abundance.weighted = TRUE,
               exclude.conspecifics = FALSE)
# }