expokit_wrapalldmexpv_tvals {rexpokit}

Run EXPOKIT's dmexpv on one or more t-values

Description

The function runs EXPOKIT's dmexpv function on a Q matrix and one or more time values. If Qmat is NULL (default), a default matrix is input.

Usage

  expokit_wrapalldmexpv_tvals(Qmat = NULL, tvals = c(2.1),
    inputprobs_for_fast = NULL, transpose_needed = TRUE,
    transform_to_coo_TF = TRUE, coo_n = NULL,
    force_list_if_1_tval = FALSE, check_for_0_rows = TRUE)

Arguments

Qmat

an input Q transition matrix

tvals

one or more time values to exponentiate by (doesn't have to literally be a time value, obviously)

inputprobs_for_fast

If NULL (default), the full probability matrix (Pmat) is returned. However, the full speed of EXPOKIT on sparse matrices will be exploited if inputprobs_for_fast=c(starting probabilities). In this case these starting probabilities are input to myDMEXPV directly, as v, and w, the output probabilities, are returned.

transpose_needed

If TRUE (default), matrix will be transposed (apparently EXPOKIT needs the input matrix to be transposed compared to normal)

transform_to_coo_TF

Should the matrix be tranposed to COO? COO format is required for EXPOKIT's sparse-matrix functions (like dmexpv and unlike the padm-related functions. Default TRUE; if FALSE, user must put a COO-formated matrix in Qmat. Supplying the coo matrix is probably faster for repeated calculations on large matrices.

coo_n

If a COO matrix is input, coo_n specified the order (# rows, equals # columns) of the matrix.

force_list_if_1_tval

Default FALSE, but set to TRUE if you want a single matrix to be returned inside a list

check_for_0_rows

If TRUE or a numeric value, the input Qmat is checked for all-zero rows, since these will crash the FORTRAN wrapalldmexpv function. A small nonzero value set to check_for_0_rows or the default (0.0000000000001) is input to off-diagonal cells in the row (and the diagonal value is normalized), which should fix the problem.

Value

tmpoutmat the output matrix, if 1 t-value is input; list_of_matrices_output, if more than 1 t-value is input; to get a single output matrix in a list, set force_list_if_1_tval=TRUE

Author(s)

Nicholas J. Matzke [e-mail] and Drew Schmidt [e-mail]

See Also

expokit_dmexpv_Qmat

Examples

# Make a square instantaneous rate matrix (Q matrix)
# This matrix is taken from Peter Foster's (2001) "The Idiot's Guide
# to the Zen of Likelihood in a Nutshell in Seven Days for Dummies,
# Unleashed" at:
# \url{http://www.bioinf.org/molsys/data/idiots.pdf}
#
# The Q matrix includes the stationary base freqencies, which Pmat
# converges to as t becomes large.
Qmat = matrix(c(-1.218, 0.504, 0.336, 0.378, 0.126, -0.882, 0.252, 0.504, 0.168,
0.504, -1.05, 0.378, 0.126, 0.672, 0.252, -1.05), nrow=4, byrow=TRUE)

# Make a series of t values
tvals = c(0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 1, 2, 5, 14)

# DMEXPV and DGEXPV are designed for large, sparse Q matrices (sparse = lots of zeros).
# DMEXPV is specifically designed for Markov chains and so may be slower, but more accurate.

# DGEXPV, single t-value
expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=tvals[1], transpose_needed=TRUE)
expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=2)

# This function runs the for-loop itself (sadly, we could not get mapply() to work
# on a function that calls dmexpv/dgexpv), returning a list of probability matrices.

# DGEXPV functions
list_of_P_matrices_dgexpv = expokit_wrapalldgexpv_tvals(Qmat=Qmat,
tvals=tvals, transpose_needed=TRUE)
list_of_P_matrices_dgexpv