rexpokit

R Wrappers for EXPOKIT; Other Matrix Functions

Roger B. Sidje, Drew Schmidt, Nicholas J. Matzke

Last update: 22 November 2023

Copyright license: GNU General Public License, version 3.0, GNU General Public License, version 2.0

Software version identifier: 0.26.6.7, 0.23, 0.24.1, 0.24, 0.26.1, 0.26.2, 0.26.3, 0.26.6.2, 0.26.6.4, 0.26.6.5, 0.26.6.6, 0.26.6.7, 0.26.6.9, 0.26.6.12, 0.26.6, 0.26.6.14

Description

Wraps some of the matrix exponentiation utilities from EXPOKIT (<http://www.maths.uq.edu.au/expokit/>), a FORTRAN library that is widely recommended for matrix exponentiation (Sidje RB, 1998. "Expokit: A Software Package for Computing Matrix Exponentials." ACM Trans. Math. Softw. 24(1): 130-156). EXPOKIT includes functions for exponentiating both small, dense matrices, and large, sparse matrices (in sparse matrices, most of the cells have value 0). Rapid matrix exponentiation is useful in phylogenetics when we have a large number of states (as we do when we are inferring the history of transitions between the possible geographic ranges of a species), but is probably useful in other ways as well. NOTE: In case FORTRAN checks temporarily get rexpokit archived on CRAN, see archived binaries at GitHub in: nmatzke/Matzke_R_binaries (binaries install without compilation of source code).

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