Verify: Verifying Microbial and Social Network Data

In kyarlagadda/499-project: Network Analysis in R

Description

This function takes data imported into R and checks the format to ensure compatability with following analyses. It also adds the row names to the matrices if provided.

Usage

Verify(x, s.names = NULL)

Arguments

x	A list of either 2 or 3 matrices. For correct statistical testing downstream, the first matrix should be made up of kinship network data. The second and third matrix can be a microbial dissimilarity matrix and/or behavioral statistic matrix in either or order, and only one is required. This maintains kinship as the independent variable in downstream analyses.
s.names	A vector of strings that matches the column headers of the imported matrices. The order is important, as this vector will be used to add row names to the matrices once they are confirmed to be of the correct dimensions. If your matrices already have the correct row names, the default value of NULL can be kept to skip this process.

Details

For further use in the package, the output is stored as a list, which will contain the 2 or 3 correctly formatted matrices. These will be used by the Analysis function to apply the Mantel and Partial Mantel tests.

Value

Verify returns a list with three matrices, to be used in later analyses.

Author(s)

Karthik Yarlagadda

See Also

Analysis

Output.table

Examples

a <- matrix(c(0,0.0106,0.384,0.0106,0,0.002,0.384,0.002,0), nrow=3, ncol=3, byrow = TRUE)
colnames(a) <- c("Sample1","Sample2","Sample3")

b <- matrix(c(0,0.014,0.0352,0.014,0,0.0235,0.0352,0.0235,0), nrow=3, ncol=3, byrow = TRUE)
colnames(b) <- c("Sample1","Sample2","Sample3")

example.list <- list(a,b)

sample.names <- c("Sample1","Sample2","Sample3")

Example.data <- Verify(example.list,sample.names)
Example.data


a <- matrix(c(0,0.0106,0.384,0.0106,0,0.002,0.384,0.002,0), nrow=3, ncol=3, byrow = TRUE)
colnames(a) <- c("Sample1","Sample2","Sample3")

b <- matrix(c(0,0.014,0.0352,0.014,0,0.0235,0.0352,0.0235,0), nrow=3, ncol=3, byrow = TRUE)
colnames(b) <- c("Sample1","Sample2","Sample3")

c <- matrix(c(0,0.04,0.02,0.04,0,0.01,0.02,0.01,0), nrow=3, ncol=3, byrow = TRUE)
colnames(c) <- c("Sample1","Sample2","Sample3")

example.list <- list(a,b,c)

sample.names <- c("Sample1","Sample2","Sample3")

Example.data <- Verify(example.list,sample.names)
Example.data

kyarlagadda/499-project documentation built on May 13, 2019, 6:15 p.m.