tabula (version 1.3.0)

test: Tests on Abundance Data

Description

Tests on Abundance Data

Usage

test_diversity(object, ...)
test_fit(object, ...)
# S4 method for CountMatrix
test_fit(object, simplify = FALSE, ...)
# S4 method for CountMatrix
test_diversity(object, adjust = "holm", ...)

Arguments

object

A \(m \times p\) matrix of count data.

...

Further arguments to be passed to internal methods.

simplify

A logical scalar: should the result be simplified to a matrix?

adjust

A character string specifying the method for adjusting \(p\) values (see p.adjust).

Value

If simplify is FALSE, returns a list (default), else returns a matrix.

Details

The following methods are available:

test_diversity

Compare Shannon diversity between samples. This test produces two sided pairwise comparisons: it returns a matrix of adjusted \(p\) values.

test_fit

The Frequency Increment Test (Feder et al. 2014). This test rejects neutrality if the distribution of normalized variant frequency increments exhibits a mean that deviates significantly from zero.

References

Feder, A. F., Kryazhimskiy, S. & Plotkin, J. B. (2014). Identifying Signatures of Selection in Genetic Time Series. Genetics, 196(2), 509-522. DOI: 10.1534/genetics.113.158220.

Magurran, A. E. (1988). Ecological Diversity and its Measurement. Princeton, NJ: Princeton University Press. DOI: 10.1007/978-94-015-7358-0.

Examples

# NOT RUN {
## Shannon diversity test
merzbach_count <- as_count(merzbach)
div <- test_diversity(merzbach_count)

## Frequency Increment Test
## Coerce the merzbach dataset to a count matrix
## Keep only decoration types that have a maximum frequency of at least 50
keep <- apply(X = merzbach, MARGIN = 2, FUN = function(x) max(x) >= 50)
merzbach_count <- as_count(merzbach[, keep])

## The data are grouped by phase
## We use the row names as time coordinates (roman numerals)
set_dates(merzbach_count) <- rownames(merzbach)

fit <- test_fit(merzbach_count, simplify = TRUE)
# }