rexpokit: R wrappers for EXPOKIT; other matrix functions

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This package 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.

Author
Nicholas J. Matzke [aut, cre, cph], Roger B. Sidje [aut, cph]
Date of publication
2013-07-15 07:25:20
Maintainer
Nicholas J. Matzke <matzke@berkeley.edu>
License
GPL (>= 2)
Version
0.24.1
URLs

View on CRAN

Man pages

coo2mat
Convert a COO-formated matrix to standard square format
expokit_dgexpv_Qmat
EXPOKIT dgexpv matrix exponentiation on Q matrix
expokit_dgexpv_wrapper
EXPOKIT dgexpv wrapper function
expokit_dgpadm_Qmat
EXPOKIT dgpadm matrix exponentiation on Q matrix
expokit_dmexpv_Qmat
EXPOKIT dmexpv matrix exponentiation on Q matrix
expokit_dmexpv_wrapper
EXPOKIT dmexpv wrapper function
expokit_mydgexpv_wrapper
EXPOKIT dgexpv wrapper function, return just output probs
expokit_mydmexpv_wrapper
EXPOKIT dmexpv wrapper function, return just output probs
expokit_wrapalldgexpv_tvals
Run EXPOKIT's dgexpv on one or more t-values
expokit_wrapalldmexpv_tvals
Run EXPOKIT's dmexpv on one or more t-values
fermat.test
Test an integer for primality with Fermat's little theorem.
findrows_w_all_zeros
Check if a Q matrix has rows with all zeros
mat2coo
Convert matrix to COO format using SparseM function
mat2coo_forloop
Convert matrix to COO format using nested for-loops
rexpokit-package
Matrix exponentiation with EXPOKIT in R
row_allzero_TF
Check if a row is all zeros
SparseM_coo_to_REXPOKIT_coo
Convert a SparseM COO matrix to a plain matrix

Files in this package

rexpokit
rexpokit/MD5
rexpokit/src
rexpokit/src/rcpp_module.cpp
rexpokit/src/my_matexp.f
rexpokit/src/my_expokit.f
rexpokit/src/mataid.f
rexpokit/src/lapack.f
rexpokit/src/expokit_wrappers.cpp
rexpokit/src/clock.f
rexpokit/src/blas_mod.f
rexpokit/src/Makevars.win
rexpokit/src/Makevars
rexpokit/man
rexpokit/man/row_allzero_TF.Rd
rexpokit/man/rexpokit-package.Rd
rexpokit/man/mat2coo_forloop.Rd
rexpokit/man/mat2coo.Rd
rexpokit/man/findrows_w_all_zeros.Rd
rexpokit/man/fermat.test.Rd
rexpokit/man/expokit_wrapalldmexpv_tvals.Rd
rexpokit/man/expokit_wrapalldgexpv_tvals.Rd
rexpokit/man/expokit_mydmexpv_wrapper.Rd
rexpokit/man/expokit_mydgexpv_wrapper.Rd
rexpokit/man/expokit_dmexpv_wrapper.Rd
rexpokit/man/expokit_dmexpv_Qmat.Rd
rexpokit/man/expokit_dgpadm_Qmat.Rd
rexpokit/man/expokit_dgexpv_wrapper.Rd
rexpokit/man/expokit_dgexpv_Qmat.Rd
rexpokit/man/coo2mat.Rd
rexpokit/man/SparseM_coo_to_REXPOKIT_coo.Rd
rexpokit/inst
rexpokit/inst/notes
rexpokit/inst/notes/expokit_copyright.txt
rexpokit/inst/notes/EXPOKIT_For_Dummies_notes_v1.txt
rexpokit/inst/REFERENCES.bib
rexpokit/inst/CITATION
rexpokit/R
rexpokit/R/rexpokit_v1.R
rexpokit/R/rexpokit-package.R
rexpokit/R/fermat.R
rexpokit/NEWS
rexpokit/NAMESPACE
rexpokit/DESCRIPTION