maxbigm: Find maximum value in a big matrix
In iCAMP: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

maxbigm

R Documentation

Find maximum value in a big matrix

Description

Return the maxium value and its (their) location(s) in a big matrix.

Usage

maxbigm(m.desc, m.wd, nworker = 1, rm.na = TRUE, size.limit = 10000 * 10000)

Arguments

`m.desc`	the name of the file to hold the backingfile description of the big matrix.
`m.wd`	the path of the folder holding the big matrix file.
`nworker`	integer, for parallel computing. Either a character vector of host names on which to run the worker copies of R, or a positive integer (in which case that number of copies is run on localhost). default is 4, means 4 threads will be run.
`rm.na`	logic, whether to remove NA. Default is TRUE.
`size.limit`	the matrix size which your current computer memory can easily handle at each time.

Details

A tool to figure out the maximum value in the big phylogenetic distance matrix.

Value

Output is a list of two elements.

`max.value`	Numeric, the maximum value.
`row.col`	Matrix, the row(s) and column(s), i.e. the location(s), of the maximum value in the big matrix.

Note

Version 3: 2020.9.1, remove setwd; change dontrun to donttest and revise save.wd in help doc. Version 2: 2020.8.19, add example. Version 1: 2015.12.16

Author(s)

Daliang Ning

References

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

Examples

# this example shows how to find maximum value
# in a big phylogenetic distance matrix.
data("example.data")
tree=example.data$tree
# since pdist.big need to save output 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.maxbigm")
  # please change 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)
  
  maxb=maxbigm(m.desc = pd.big$pd.file, m.wd = pd.big$pd.wd,
               nworker = nworker, rm.na = TRUE)
  setwd(wd0)

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