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rexpokit

Wraps some of the matrix exponentiation utilities from EXPOKIT, a Fortran 77 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.

Build status on Travis-CI:

NOTE: As of 2018-10-03, a new version of rexpokit, 0.26.6, has been accepted on CRAN. This version fixes warnings due to upgrades in CRAN's FORTRAN compilers, and more importantly, removes some dependencies previously needed by cladoRcpp/BioGeoBEARS. CRAN version is here, binaries should be available in a few days: https://cran.r-project.org/package=rexpokit

Release v0.26.6 registered on Zenodo:

Zenodo link for release: https://zenodo.org/badge/latestdoi/17001945

Zenodo DOI for release: http://dx.doi.org/10.5281/zenodo.1442889

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Version

Install

install.packages('rexpokit')

Monthly Downloads

424

Version

0.26.6.4

License

GPL (>= 2)

Maintainer

Nicholas J. Matzke

Last Published

July 2nd, 2019

Functions in rexpokit (0.26.6.4)

expokit_itscale5_wrapper

wrapper function for FORTRAN itscale5, for FD's maxent
SparseM_coo_to_REXPOKIT_coo

Convert a SparseM COO matrix to a plain matrix
expokit_dgexpv_Qmat

EXPOKIT dgexpv matrix exponentiation on Q matrix
expokit_wrapalldmexpv_tvals

Run EXPOKIT's dmexpv on one or more t-values
expokit_dmexpv_Qmat

EXPOKIT dmexpv matrix exponentiation on Q matrix
expokit_wrapalldgexpv_tvals

Run EXPOKIT's dgexpv on one or more t-values
expokit_dgpadm_Qmat

EXPOKIT dgpadm matrix exponentiation on Q matrix
maxent

Estimating Probabilities via Maximum Entropy: Improved Iterative Scaling
rexpokit-package

Matrix exponentiation with EXPOKIT in R
coo2mat

Convert a COO-formated matrix to standard square format
mat2coo

Convert matrix to COO format using SparseM function
mat2coo_forloop

Convert matrix to COO format using nested for-loops
expm

Simple Interface