bmntd.big: beta mean nearest taxon distance (betaMNTD) from big data

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

beta mean nearest taxon distance (betaMNTD) from big data

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, using bigmemory (Kane et al 2013) to deal with too large dataset.

Usage

bmntd.big(comm, pd.desc = "pd.desc", pd.spname, pd.wd,
          spname.check = FALSE, abundance.weighted = TRUE,
          exclude.conspecifics = FALSE, time.output = FALSE)

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.
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.

Details

beta mean nearest taxon distance for taxa in each pair of communities. Improved from 'comdistnt' in package 'picante'(Kembel et al 2010). This function adds bigmemory part (Kane et al 2013) to deal with large dataset.

Value

result is a distance object.

Note

Version 4: 2020.12.5, copy from package NST to iCAMP to improve the function qpen. Version 3: 2020.9.9, remove setwd; change dontrun to donttest and revise save.wd in help doc. Version 2: 2020.8.22, add to NST package, update help document. Version 1: 2017.3.13

Author(s)

Daliang Ning ([e-mail])

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.

Kane, M.J., Emerson, J., Weston, S. (2013). Scalable Strategies for Computing with Massive Data. Journal of Statistical Software, 55(14), 1-19. URL http://www.jstatsoft.org/v55/i14/.

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'.

wd0=getwd()
save.wd=paste0(tempdir(),"/pdbig.bmntd.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)
bmntd.wt=bmntd.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)

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