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Tests on Abundance Data
test_diversity(object, ...)test_fit(object, ...)
# S4 method for CountMatrix
test_fit(object, simplify = FALSE, ...)
# S4 method for CountMatrix
test_diversity(object, adjust = "holm", ...)
A
Further arguments to be passed to internal methods.
A logical scalar: should the result be
simplified to a matrix?
If simplify is FALSE, returns a list (default), else returns
a matrix.
The following methods are available:
test_diversityCompare Shannon diversity between samples.
This test produces two sided pairwise comparisons: it returns a matrix of
adjusted
test_fitThe 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.
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.
# 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)
# }
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