R: Controls the allocation of bootstrap replicates

boot.titan {TITAN2}

R Documentation

Controls the allocation of bootstrap replicates

Description

A wrapper function for controlling the implementation of bootstrap replicates using the function 'tboot' by sequential or parallel processing.

Usage

boot.titan(
  env,
  taxa,
  ivTot = ivTot,
  boot = boot,
  ncpus = ncpus,
  nBoot = nBoot,
  minSplt = minSplt,
  nPerm = 250,
  memory = memory,
  imax = imax,
  numUnit = numUnit
)

Arguments

`env`	A vector of values for each sampling location along the environmental gradient.
`taxa`	A site-by-taxon matrix of taxa counts at each sampling location.
`ivTot`	A logical indicating whether IndVal scores should be calculated using total relative abundance or the mean relative abundace originally proposed by Dufrene and Legendre (1997). The default is to pass on the argument from the original TITAN funtion call.
`boot`	A logical specifying whether or not to implement TITAN's' boostrap procedure. The default is to use the value specified in the original TITAN function call.
`ncpus`	An argument specifying the number of processing cores used by the TITAN function call. If ncpus>1 then parallel processing is implemented. The default is to use the value specified in the original TITAN function call.
`nBoot`	An argument specifying the number of bootstrap replicates. The default is to use the value specified in the original TITAN function call.
`minSplt`	An argument specifying minimum split size for partitioning along the environmental gradient. The default is to use the value specified in the original TITAN function call.
`nPerm`	The number of replicates used by the permutation procedure (not to be confused with the number of bootstrap replicates).
`memory`	A logical indicating whether scratch files should be used to store temporary data in order to conserve active memory during bootstrapping of large data sets. The default is to pass on the argument from the original TITAN funtion call.
`imax`	A logical indicating whether taxon-specific change points should be determined by IndVal maxima or z-score maxima (as in TITAN v1.0). The default is to pass on the argument from the original TITAN funtion call.
`numUnit`	An argument specifying the number of values along the environmental gradient.

Details

If 'ncpus'>1 evaluates to TRUE, the function employs the package 'snow' to implement parallel processing on multicore processors common in modern desktop computers. With some minor modification it is possible to configure this code to allocate processes to cores on a high-performance computing cluster (i.e., a supercomputer). If 'ncpus'>1 evaluates to FALSE, the function uses 'lapply' to run 'tboot' in sequence 1:nBoot times.

Value

A list of two items:

bSeq: An index of the sequence of bootstrap replicates. The structure of bSeq will differ for sequential or parallel processing.
ivz.bt.list: Itself a list of four items comprising output passed on from function tboot()

Author(s)

M. Baker and R. King

References

Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37.