gam.score {UCS} R Documentation

Compute GAM Scores in Standard or EBO-Coordinates (gam)

Description

Computes scores of a generalised association measure (GAM) in standard or ebo-coordinates.

Usage

```  gam.score(name, f, f1, f2, N)
gam.score(name, o, e, b=1, N=1e6)
```

Arguments

 `name` name of a generalised association measure (GAM) `f, f1, f2, N` numerical vectors specifying the (generalised) frequency signatures of candidates `o, e, b` numerical vectors specifying the ebo-coordinates of candidates (if the balance b is not specified, it defaults to `1`) `N` optional numerical vector specifying the sample size N when computing scores of a GAM that is not size-invariant in ebo-coordinates (defaults to `1e6`)

Details

Note that all function arguments except for `name` must be passed explicitly by name in order to distinguish the two operating modes of `gam.score` (standard vs. ebo-coordinates).

The components of the generalised frequency signature ```(f, f1, f2, N)``` can be arbitrary positive real numbers.

When ebo-coordinates are used, the argument `N` (sample size) can safely be omitted for any size-invariant GAM (in ebo-coordinates). For other GAMs, a default value of `1e6` will be used, corresponding to the typical size of a co-occurrence data set. The argument `b` (balance) can be omitted for any central GAMs. Otherwise, it defaults to a value of `1`, corresponding to the centralized version of the respective GAM.

The `gam.score` function automatically converts between standard and ebo-coordinates, depending on the requirements of the GAM implementation.

Value

a vector of real numbers representing generalised association scores

`add.gams`, `gam.iso`, `builtin.gams`
```gam.score("t.score", f=1:10, f1=(1:10)*5, f2=100, N=1000)