dissimilarity: dissimilarity

In OxfordCMS/OCMSutility: Utility functions for OCMS

dissimilarity

Description

Calculate either within-individual or between-individual Bray-Curtis dissimilarity.

Usage

dissimilarity(
  abundance_matrix = NULL,
  metadata = NULL,
  individual_variable = NULL,
  method = "within"
)

Arguments

abundance_matrix	dataframe; samples are columns and features are rows
metadata	dataframe; samples are rows and rownames should match those in abundance_matrix
individual_variable	character; name of the variable in metadata that specifies the individual
method	character; choose 'within' or 'between' depending on whether there are paired samples available

Value

data frame

Examples

abundance_matrix <- data.frame(matrix(rnorm(1000, mean=100, sd=1), ncol=8, nrow=50))
colnames(abundance_matrix) <- LETTERS[1:8]
abundance_matrix <- ocms_relab(abundance_matrix)
metadata <- data.frame(individual = c(rep("1", 2), rep("2", 2),
                                      rep("3", 2), rep("4", 2)))
metadata$other_variable <- rnorm(8)
rownames(metadata) <- LETTERS[1:8]
dissimilarity(abundance_matrix, metadata=metadata,
              individual_variable="individual", method="within")

OxfordCMS/OCMSutility documentation built on Feb. 27, 2025, 8:19 p.m.