Package: rexpokit 0.26.6.14
rexpokit: 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. NOTE: In case FORTRAN checks temporarily get rexpokit archived on CRAN, see archived binaries at GitHub in: nmatzke/Matzke_R_binaries (binaries install without compilation of source code).
Authors:
rexpokit_0.26.6.14.tar.gz
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rexpokit.pdf |rexpokit.html✨
rexpokit/json (API)
NEWS
| # Install 'rexpokit' in R: |
| install.packages('rexpokit', repos = c('https://nmatzke.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nmatzke/rexpokit/issues
Last updated 5 months agofrom:c614ed8ce0. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 25 2024 |
| R-4.5-win-x86_64 | OK | Oct 25 2024 |
| R-4.5-linux-x86_64 | OK | Oct 25 2024 |
| R-4.4-win-x86_64 | OK | Oct 25 2024 |
| R-4.4-mac-x86_64 | OK | Oct 25 2024 |
| R-4.4-mac-aarch64 | OK | Oct 25 2024 |
| R-4.3-win-x86_64 | OK | Oct 25 2024 |
| R-4.3-mac-x86_64 | OK | Oct 25 2024 |
| R-4.3-mac-aarch64 | OK | Oct 25 2024 |
Exports:coo2matexpmexpokit_dgexpv_Qmatexpokit_dgpadm_Qmatexpokit_dmexpv_Qmatexpokit_wrapalldgexpv_tvalsexpokit_wrapalldmexpv_tvalsmat2coomat2coo_forloopmaxentSparseM_coo_to_REXPOKIT_coo
Dependencies:Rcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Matrix exponentiation with EXPOKIT in R | rexpokit-package rexpokit |
| Convert a COO-formated matrix to standard square format | coo2mat |
| Simple Interface | expm |
| EXPOKIT dgexpv matrix exponentiation on Q matrix | expokit_dgexpv_Qmat |
| EXPOKIT dgpadm matrix exponentiation on Q matrix | expokit_dgpadm_Qmat |
| EXPOKIT dmexpv matrix exponentiation on Q matrix | expokit_dmexpv_Qmat |
| wrapper function for FORTRAN itscale5, for FD's maxent | expokit_itscale5_wrapper |
| Run EXPOKIT's dgexpv on one or more t-values | expokit_wrapalldgexpv_tvals |
| Run EXPOKIT's dmexpv on one or more t-values | expokit_wrapalldmexpv_tvals |
| Convert matrix to COO format using SparseM function | mat2coo |
| Convert matrix to COO format using nested for-loops | mat2coo_forloop |
| Estimating Probabilities via Maximum Entropy: Improved Iterative Scaling | maxent |
| Convert a SparseM COO matrix to a plain matrix | SparseM_coo_to_REXPOKIT_coo |
