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.
Readme
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
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 |
| depends | R (>= 3.0.2) |
| imports | Rcpp (>= 0.11.0) , stats |
| Contributors | Drew Schmidt, Roger B. Sidje |
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