Frequency Increment Test
fit(object, dates, ...) # S4 method for CountMatrix,missing fit(object) # S4 method for CountMatrix,numeric fit(object, dates)
An IncrementTest object.
The Frequency Increment Test (FIT) 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 .
data("merzbach", package = "folio") ## 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) counts <- as_count(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)