Frequency Increment Test

## Arguments

- object
A \(m \times p\)

`numeric`

`matrix`

or`data.frame`

of count data (absolute frequencies giving the number of individuals for each category, i.e. a contingency table). A`data.frame`

will be coerced to a`numeric`

`matrix`

via`data.matrix()`

.- dates
A length-\(m\)

`numeric`

vector of dates.- ...
Currently not used.

- calendar
A

`TimeScale`

object specifying the calendar of`dates`

(see`calendar()`

). Defaults to Gregorian Common Era.- level
A length-one

`numeric`

vector giving the confidence level.- roll
A

`logical`

scalar: should each time series be subsetted to look for episodes of selection?- window
An odd

`integer`

giving the size of the rolling window. Only used if`roll`

is`TRUE`

.

## 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.

If `roll`

is `TRUE`

, each time series is subsetted according to `window`

to
see if episodes of selection can be identified among variables that might
not show overall selection.

## 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
.

## 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, calendar = NULL)
## Plot time vs abundance
plot(freq, calendar = NULL, ncol = 3, xlab = "Phases")
## Plot time vs abundance and highlight selection
freq <- fit(counts, dates, calendar = NULL, roll = TRUE, window = 5)
plot(freq, calendar = NULL, ncol = 3, xlab = "Phases")
```