s_matrixacf2: Conservative removal of potential false positives

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

Initial data screening suggested that most data did not need to be differenced seasonally first. Simulations show that structure in residuals for one NTU only does not affect type I error. However, structure in two NTU’s can greatly affect type I error. Check autocorrelation functions for undifferenced modified data (as before). Look at row and column sums for each NTU. Most NTUs have only a few acf’s with structure. Most of the acf’s with structure are found in the top 5 upper 5 more likely to be OK. This is a two part script with commands in between to run manually. Determine an appropriate cutoff (I used 5 script is marked by comments below.

Usage

s_matrixacf2(matrix, boolean, fn)

Arguments

inputParameter1	matrix of NTU abundances in rows and sample dates in columns inputParameter1
inputParameter2	boolean is a matrix of 1's and 0's from the previous linear model code indicating which NTUs are connected (1's) inputParameter2
inputParameter3	fn is a file name for the output of the first function inputParameter3
inputParameter4	fn2 is a file name for the output of the second function inputParameter4
inputParameter5	X is the number of connections at the cutoff inputParameter5

Value

output A boolean matrix of connections that fail (1’s). Results are in the upper triangle. Need to subtract this matrix from the matrix of connections.

Examples

Run diagnostic with this command:  s_matrixacf2(matrix=, boolean=,fn=)

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