Substitution matrices, log odds matrices, and operations on them.
|
_build_obs_freq_mat(acc_rep_mat)
build_obs_freq_mat(acc_rep_mat): Build the observed frequency matrix,
from an accepted replacements matrix The accRep matrix should be
generated by the user. |
source code
|
|
|
_exp_freq_table_from_obs_freq(obs_freq_mat) |
source code
|
|
|
_build_exp_freq_mat(exp_freq_table)
Build an expected frequency matrix exp_freq_table: should be a
FreqTable instance |
source code
|
|
|
_build_subs_mat(obs_freq_mat,
exp_freq_mat)
Build the substitution matrix |
source code
|
|
|
_build_log_odds_mat(subs_mat,
logbase=2,
factor=10.0,
round_digit=0,
keep_nd=0)
_build_log_odds_mat(subs_mat,logbase=10,factor=10.0,round_digit=1):
Build a log-odds matrix logbase=2: base of logarithm used to build
(default 2) factor=10.: a factor by which each matrix entry is
multiplied round_digit: roundoff place after decimal point keep_nd:
if true, keeps the -999 value for non-determined values (for which
there are no substitutions in the frequency substitutions matrix). |
source code
|
|
|
make_log_odds_matrix(acc_rep_mat,
exp_freq_table=None,
logbase=2,
factor=1.0,
round_digit=9,
keep_nd=0) |
source code
|
|
|
observed_frequency_to_substitution_matrix(obs_freq_mat) |
source code
|
|
|
|
|
two_mat_relative_entropy(mat_1,
mat_2,
logbase=2,
diag=3) |
source code
|
|
|
two_mat_DJS(mat_1,
mat_2,
pi_1=0.5,
pi_2=0.5) |
source code
|
|