gam.score {UCS}R Documentation

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


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


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


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)


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.


a vector of real numbers representing generalised association scores

See Also

add.gams, gam.iso, builtin.gams


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

gam.score("t.score", o=1:10, e=(1:10)/2)

[Package UCS version 0.5 Index]