iCAMP (version 1.8.6)

bmpd.big: Beta mean pairwise distance (betaMPD) for big data

Description

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

Usage

bmpd.big(comm, pd.desc = "pd.desc", pd.spname, pd.wd,
         spname.check = FALSE, abundance.weighted = TRUE,
         na.zero = TRUE, unit.sum = NULL)

Value

Output is a distance object of pairwise betaMPD between samples.

Arguments

comm

matrix or data.frame, community data matrix, rownames are sample names, colnames are taxa ids.

pd.desc

character, the name to describe bigmemory file of phylogenetic distance matrix, default is "pd.desc".

pd.spname

vector, the OTU ids (species names) in exactly the same order as the phylogenetic matrix rows or columns

pd.wd

the path of the folder saving the phylogenetic distance matrix.

spname.check

logic, whether to check the OTU ids (species names) in community matrix and phylogenetic distance matrix are the same.

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.

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.

Author

Daliang Ning

Details

beta mean pairwise distance.

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

bNRI.big.cm

Examples

data("example.data")
comm=example.data$comm
tree=example.data$tree

# since it needs to save some file to a certain folder,
# the following code is set as 'not test'.
# but you may test the code on your computer
# after change the folder path for 'save.wd'.
# \donttest{
wd0=getwd()
save.wd=paste0(tempdir(),"/pdbig.bmpd.big")
# you may change save.wd to the folder you want to save the pd.big output.
nworker=2 # parallel computing thread number
pd.big=pdist.big(tree = tree, wd=save.wd, nworker = nworker)
bmpd.wt=bmpd.big(comm=comm, pd.desc = pd.big$pd.file,
                 pd.spname = pd.big$tip.label, pd.wd = pd.big$pd.wd,
                 abundance.weighted = TRUE)
setwd(wd0)
# }