iCAMP (version 1.5.12)

maxbigm: 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.

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.

Details

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

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/.

See Also

midpoint.root.big

Examples

# NOT RUN {
# 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'.
# }
# NOT RUN {
  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)
# }