compare_alpha_diversity: Calculate alpha diversity statistics

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 across multiple timepoints.

Usage

compare_alpha_diversity(physeq, x = "Day", group = "Treatment",
  diversity = c("Observed", "Shannon", "Simpson"),
  test_type = c("nonparametric", "parametric"),
  col_var = "PD_whole_tree_alpha", num_perm = 999,
  multiple_corrections = T, write = F, filename = "results", ...)

Arguments

physeq	A phyloseq object
x	Variable that describes Time
group	Variable the describes different groups for comparisons
diversity	Diversity metric to use for alpha diversity calculations
test_type	type of test to use for significance testing
col_var	Column name if diversity measurements are in mapping file
num_perm	Number of permutations for non parametric tests
multiple_corrections	Should multiple comparisons be corrected on pvalues
write	Write table to file
filename	Filename of the output results table
...	Additional arguments

Value

A dataframe with taxa information and sample metadata

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