partition {SyNet}R Documentation

Test of Adequacy

Description

Tests the capability of a sympatry network to contain units of co-occurrence.

Usage

  partition(iptsymp, replica = 1)

Arguments

iptsymp Matrix object. It must be binary (1/0) and symmetric.
replica Number of random matrices to be produced.

Details

The input argument iptsymp corresponds to any adjacency matrix that reflects the incidence (1) or not (0) of a sympatric link between pairs of species.

Random matrices are generated according to a Bernoulli model. A random number between 0 and 1 is generated for each pair of species or cell. If this number is lower than the density of the network associated to the observed matrix, a 1 score is assigned.

The statisitc corresponds to the Partition Index (PI). The test counts the number of random matrices that yields a PI value higher or equal to the observed one.

Value

If replica > 1, a list is generated with the following components:

$Input Sympatry matrix observed.
$ProbTie Density of network associated to.
$NodeNr Number of nodes considered.
$PIobserved Observed Partition Index.
$PIrandomized Statistical summary of randomized Partition Index.
$ProbTie Fraction of replica where the randomized Partition Index is >= the observed one.


If replica = 1, the Partition Index of the observed matrix is calculated.

Author(s)

Daniel A. Dos Santos

References

Dos Santos, D.A., Fernandez, H.R., Cuezzo, M.G., Dominguez, E. Sympatry Inference and Network Analysis in Biogeography. Systematic Biology (in press).

See Also

The statistic PI is calculated by the function Partition_Index

Examples

data(epiphragmophora)
p <- dotinfer(epiphragmophora)
partition(p[[1]], 100)

[Package SyNet version 1.0 Index]