create.tw.dat: Creates 'tw.dat' file with parameters of TWINSPAN analysis

In zdealveindy/twinspanR: TWo-way INdicator SPecies ANalysis (and its modified version) in R

Description

Internal function used to generate file tw.dat file with parameters entering twinspan.exe. Contains all TWINSPAN parameters which could be modified (also via the function twinspan).

Usage

create.tw.dat(
  input.file = "tw.cc!",
  omit.samples = -1,
  no.cut.levels = length(cut.levels),
  cut.levels = c(0, 2, 5, 10, 20),
  min.group.size = 5,
  max.no.ind = 7,
  max.no.sp.table = 100,
  levels = 6,
  long.output = 1,
  diagram = 0,
  machine.readable.output = 1,
  pseudosp.weights = -1,
  indicator.potential = -1,
  ommited.species = -1,
  samples.weights = -1,
  species.weights = -1
)

Arguments

input.file	Input file with data (default = "tw.cc!", should not be changed).
omit.samples	Which samples should be omitted from analysis? (default = -1, meaning no samples omitted)
no.cut.levels	How many pseudospecies cut levels? (default = length (cut.levels), should not be changed)
cut.levels	Pseudospecies cut levels (default = c(0,2,5,10,20)). Should not exceed 9 cut levels.
min.group.size	Minimum size of the group, which should not be further divided (default = 5).
max.no.ind	Maximum number of indicator species (default = 7, should be between 0 and 15).
max.no.sp.table	Maximum number of species in the output table stored in tw.TWI file (default = 100, should be between 0 and 1000).
levels	Number of hierarchical levels of divisions (default = 6, should be between 0 and 15).
long.output	Should the long output be produced? (default = 1, means yes)
diagram	Should the diagram be appended in output? (default = 0, means no)
machine.readable.output	Should the machine readable output be created? (default = 1, means yes, and should not be changed, othewise the result cannot be read back to R)
pseudosp.weights	Weights for pseudospecies.
indicator.potential	Indicator potential for cut levels.
ommited.species	Numbers (not names) of species which should be omitted from the list of potential indicators.
samples.weights	Weights of samples.
species.weights	Weights of species.

Value

Creates file tw.dat in the subdirectory exec of the twinspan library folder. This file contains all parameters needed to setup the TWINSPAN algorithm, and is loaded into twinspan.exe together with the community data (reformated into condensed format and stored in tw.cc!).

Author(s)

David Zeleny ([e-mail])

zdealveindy/twinspanR documentation built on March 13, 2021, 8:35 a.m.