rexpokit v0.26.6.4

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R Wrappers for EXPOKIT; Other Matrix Functions

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.

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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: Build Status

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: DOI

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

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

Functions in rexpokit

Name Description
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
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Details

Type Package
Date 2019-07-02
LinkingTo Rcpp (>= 0.11.0)
Copyright See /inst/LAPACK_LICENSE.txt for code in /src.
URL http://phylo.wikidot.com/rexpokit
License GPL (>= 2)
LazyLoad yes
ByteCompile yes
Packaged 2019-07-02 03:31:26 UTC; nmat471
NeedsCompilation yes
Repository CRAN
Date/Publication 2019-07-02 05:40:03 UTC

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