distadj: Phylogenetically weighted connectivity

In kevinvergin/BATSLSA: R scripts for the analysis of data presented in the article "Marine bacterioplankton consortia follow deterministic, non-neutral community assembly rules" by Vergin et al.

Description

This analysis measures the similarity of connections for each pair of NTUs. The similarities are weighted by phylogenetic distance. A profile is created for each NTU and compared, such that matching, or near matching, connections score higher. It is necessary to have phylogenetic distances between NTUs. This script does not provide a matrix of those values but future versions of this package may include that script.

Usage

distadj(distmat, namesvec)

Arguments

inputParameter1	distmat is a 3 column matrix. Column 1 has all NTUs repeated appropriately, column 2 has the 5 upstream and 5 downstream (if appropriate) NTUs paired with each corresponding NTU from column 1, and column 3 has the distance between the two NTUs from columns 1 and 2 inputParameter1
inputParameter2	boolean is a matrix of 1's and 0's from the final diagnostic scripts indicating #' which NTUs are connected (1's) inputParameter2
inputParameter3	fname is a file name for the output of the function inputParameter3
inputParameter4	namesvec is a vector of names for the NTUs inputParameter4

Value

output A matrix of similarity scores for the connections between each pair of NTUs weighted by their phylogenetic distance within a +/- 5 NTU window

Examples

Run script with this command:  sim_metric_csv(boolean,distmat,namesvec, fname)

kevinvergin/BATSLSA documentation built on May 20, 2019, 9:20 a.m.