The R package `rexpokit`

is a key dependency of the BioGeoBEARS R package
for phylogenetic biogeography.

`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.

**Installation**

As rexpokit contains C++ and FORTRAN code, it is easiest to install the pre-compiled binaries from CRAN. This is done from the R command line, with:

`install.packages("rexpokit")`

If you want to install the GitHub version, you will need gfortran and gcc compilers installed on your machine. Then, install using devtools:

```
library(devtools)
install_github("nmatzke/rexpokit", INSTALL_opts="--byte-compile")
```

To see examples of the matrix exponentiation calculations, see the example code with:

```
library(rexpokit)
?rexpokit
```

**NOTE:** As of 2019-11-04, a new version of
`rexpokit`

, 0.26.6.6, has been accepted on CRAN. This version
fixes some warnings caused by `gfortan`

/`gcc10`

,
currently in beta, but nonetheless checked by CRAN. Binaries should be
available soon. Old binaries have been archived at: https://github.com/nmatzke/Matzke_R_binaries

**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