hilldiv (version 1.5.1)

div_test: Diversity test

Description

Diversity comparison test between groups of samples. The function automatically assesses whether the data meets the properties for parametric statistics and performs the appropriate test accordingly: Students' T, ANOVA, Wilcoxon or Kruskal-Wallis. If the posthoc argument is set as TRUE, multiple group comparisons are complemented with post hoc pairwise tests, either Tukey test (parametric) or Dunn test with Benjamini-Hochberg correction (non-parametric).

Usage

div_test(countable, qvalue, hierarchy, tree, posthoc)

Arguments

countable

A matrix indicating the relative abundances of multiple samples. Columns should be samples and rows OTUs.

qvalue

A positive integer or decimal number (>=0), usually between 0 and 3.

hierarchy

A two-column matrix indicating the relation between samples (first column) and groups (second column).

tree

A phylogenetic tree of class 'phylo'. The tip labels must match the row names in the OTU table. Use the function match_data() if the OTU names do not match.

posthoc

Whether to run post hoc pairwise analyses or not. If TRUE, an ANOVA will be complemented with a Tukey test and a Kruskal-Wallis test will be complemented with a Dunn test.

Value

A statistical test output.

Details

Diversity test

References

Alberdi, A., Gilbert, M.T.P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources, 19, 804-817. Chao, A., Chiu, C.H., & Jost, L. (2014). Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through hill numbers. Annual Review of Ecology Evolution and Systematics, 45, 297-324.

See Also

hill_div, div_part

Examples

# NOT RUN {
data(bat.diet.otutable)
data(bat.diet.tree)
data(bat.diet.hierarchy)
div_test(bat.diet.otutable,qvalue=0,hierarchy=bat.diet.hierarchy)
div_test(bat.diet.otutable,qvalue=1,hierarchy=bat.diet.hierarchy,tree=bat.diet.tree)
div_test(bat.diet.otutable,2,bat.diet.hierarchy,bat.diet.tree)
div_test(bat.diet.otutable,qvalue=1,hierarchy=bat.diet.hierarchy,posthoc=TRUE)
# }