expokit_itscale5_wrapper: wrapper function for FORTRAN itscale5, for FD's maxent
In rexpokit: R Wrappers for EXPOKIT; Other Matrix Functions

expokit_itscale5_wrapper

R Documentation

wrapper function for FORTRAN itscale5, for FD's maxent

Description

This function wraps the .C call to EXPOKIT for the itscale5 function.

Usage

  expokit_itscale5_wrapper(SXT, ngroups, ntraits, const, prior, 
    prob, entropy, niter, tol, denom)

Arguments

`SXT`	is a Groups (rows) X Traits (columns) matrix
`ngroups`	is an integer (nb: NJM's interpretation)
`ntraits`	is an integer (nb: NJM's interpretation)
`const`	is a vector of the constraint values (means, variances)
`prior`	is the prior distribution
`prob`	is the return vector of the maximum entropy
`entropy`	is the maximum entropy probabilities
`niter`	is the number of iterations required
`tol`	is the convergence tolerance value; tolerance is mean square difference
`denom`	are final moments

Details

The itscale5 function is in the "itscale5.f" FORTRAN file. itscale5 is used by the FD::maxent function.

The maxent function is used by BioGeoBEARS, merely to provide a simple method of putting flat or skewed probability distributions on the ordered categorical variable "size of smaller daughter range").

As the package FD has a number of other dependencies, some of which cause problems on some machines, I am just including maxent and itscale5 here, in order to avoid "dependency hell".

I am putting it in rexpokit rather than BioGeoBEARS, to make rexpokit the only package using FORTRAN code (which has a list of its own issues).