# The primary function call for package TITAN

### Description

The primary wrapper function controlling operation of all subfunctions (txa.screen, env.part, getivz, ivzsums, obs.summ, boot.titan, small/big.boot, sumz.tab) apart from plotting functions within TITAN.

### Usage

1 2 3 |

### Arguments

`env` |
A vector of environmental values. |

`txa` |
A site by taxon matrix containing observed counts at each sampling location. |

`minSplt` |
The minimum split size to be used in partitioning. |

`numPerm` |
The number of replicates to be used during permutation. |

`boot` |
A logical indicating whether bootstrap resampling should be performed. |

`nBoot` |
The number of replicates to be used during bootstrap resampling. |

`imax` |
A logical indication whether taxon-specific change points should be determined using IndVal maxima or z-score maxima (as in Baker and King 2010, 2013). |

`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). |

`pur.cut` |
A proportion specifying the cutoff value for determining purity across all bootstrap replicates. |

`rel.cut` |
A proportion specifying the cutoff value for determining reliability across all bootstrap replicates. |

`ncpus` |
The number of processing cores to be used during processing. If greater than 1, TITAN will load and use the package 'snow' to perform parallel processing on each core. |

`memory` |
A logical indicating whether temporary files should be written to a scrath directory during bootstrap processing to preserve active memory. This fucntion is sometimes necessary for large data files (e.g., >400 sampling sites and >100 taxa). |

### Value

A list with 13 items:

sppmax Description of 'comp1'

sumz.cp Description of 'comp1'

env The vector of environmental values used in the TITAN function call

taxa The site-by-taxon matrix used in the TITAN function call

envlcs A vector of candidate partitions derived from subtracting 'minSplt' from 'env'

srtEnv A sorted version of environmental values

ivzScores A matrix containing group membership, z scores, IndVals, and p values for each taxon at every candidate partition in 'envcls'

ivz A 2-column matrix containing parallel vectors of sum(z-) and sum(z+ scores for every candidate partition in 'envcls')

ivz.f A 2-column matrix containing parallel vectors of sum(z-) and sum(z+ scores filtered by pure and reliable taxa for every candidate partition in 'envcls')

maxSumz A 2-column matrix of environmental values at sum(z-) and sum(z+) maxima across all bootstrap replicates

maxFsumz A 2-column matrix of environmental values at filtered sum(z-) and sum(z+) maxima across all bootstrap replicates

metricArray An array of group membership, env change points, z scores, and p values equivalent to 'ivzScores' for each bootstrap replicate

targs A vector of arguments used in the TITAN function call

### 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.

King, RS and ME Baker 2010. Considerations for identifying and interpreting ecological community thresholds. Journal of the North American Benthological Association 29(3):998-1008.

Baker ME and RS King. 2013. Of TITAN and straw men: an appeal for greater understanding of community data. Freshwater Science 32(2):489-506.

### Examples

1 2 3 4 5 6 7 8 9 10 11 | ```
## Not run: resampling is very slow
data(glades.env)
data(glades.taxa)
glades.titan <- titan(glades.env, glades.taxa, minSplt = 5,
numPerm = 250, boot = TRUE, nBoot = 500, imax = FALSE,
ivTot = FALSE, pur.cut = 0.95, rel.cut = 0.95, ncpus = 1, memory = FALSE
)
## End(Not run)
``` |