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.

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 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 No Results!