compare_beta_diversity: Calculate beta diversity statistics over time.

In twbattaglia/btools: A suite of R function for all types of microbial diversity analyses

Description

Compute p-values and multiple comparisons adjusted q-values for two-group comparisons using PERMANOVA on beta diversity metrics across multiple timepoints.

Usage

compare_beta_diversity(phylo, x = as.character(),
  group = as.character(), test = c("adonis", "anosim"),
  bdiv = c("weighted", "unweighted"), write = F,
  filename = "results", fdr = T, fdr_test = "fdr", seed = 918, ...)

Arguments

phylo	A phyloseq object
x	The variable that describes Time
group	The variable that describes 2 or more groups
test	The PERMANOVA test to use.
bdiv	Beta diversity metric to calculate significance.
write	Should results be written to a file in the current working directory.
filename	The name of the output file if write is TRUE.
fdr	Should FDR correction be applied.
fdr_test	The test to use to correct for multiple comparisons. Default is FDR.
seed	The seed number to use when calculating beta diversity metrics. Default is 918.
...	Any additional arguments for external functions.

Value

A dataframe for an PERMANOVA test over each timepoint from each two group comparison.

twbattaglia/btools documentation built on May 3, 2019, 1:51 p.m.