Frequency Increment Test

Frequency Increment Test

Usage

fit(object, dates, ...)

# S4 method for data.frame,numeric
fit(object, dates)

# S4 method for matrix,numeric
fit(object, dates)

Arguments

object

An \(m \times p\) numeric matrix or a data.frame of count data (absolute frequencies).

dates

A numeric vector of dates expressed in CE years (BCE years must be given as negative numbers).

...

Currently not used.

Value

An IncrementTest object.

Details

The Frequency Increment Test (FIT) 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 .

See also

plot()

Other chronological analysis: aoristic(), apportion(), roc()

Author

N. Frerebeau

Examples

## Data from Crema et al. 2016
data("merzbach", package = "folio")

## 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)
counts <- merzbach[, keep]

## Group by phase
## We use the row names as time coordinates (roman numerals)
dates <- as.numeric(utils::as.roman(rownames(counts)))

## Frequency Increment Test
freq <- fit(counts, dates)

## Plot time vs abundance and highlight selection
plot(freq)

plot(freq, roll = TRUE, window = 5)