Enveomics collection

TRIBS.test.R

Estimates the empirical difference between all the distances in a set of objects and a subset, together with its statistical significance.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• R.
• R package optparse.
• R package enveomics.R.

§ Usage

TRIBS.test.R --dist in_file --selection in_file [opts] out_file [opts]

§ Arguments

Dist*

 --dist in_file  A tab-delimited matrix of distances.

Selection*

 --selection in_file  A list of names with the selection to evaluate.

Replicates

 --replicates integer  Number of replications per point.

Summary fx

 --summary-fx string  Function to summarize the distance distributions in a given replicate. By default, the median distance is estimated.

Dist method

 --dist-method string  Distance method between random points and samples in the transformed space. See the R function 'dist'.

Dimensions

 --dimensions integer  Dimensions to use in the NMDS. By default, 5% of the selection length.

Threads

 --threads integer  Number of threads to use.

Verbosity

 --verbosity integer  Verbosity. Use 0 to run quietly, increase for additional information.

Output file*

 out_file  Output file with the TRIBS test R object.

Bins

 integer  Number of bins to evaluate in the range of distances.

* Mandatory.