Description Usage Arguments Value Functions See Also Examples
For a more detailed explanation, see vignette("submodels")
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47  sub_JC69(lambda, mu = 1, gamma_shape = NULL, gamma_k = 5, invariant = 0)
sub_K80(alpha, beta, mu = 1, gamma_shape = NULL, gamma_k = 5, invariant = 0)
sub_F81(pi_tcag, mu = 1, gamma_shape = NULL, gamma_k = 5, invariant = 0)
sub_HKY85(
pi_tcag,
alpha,
beta,
mu = 1,
gamma_shape = NULL,
gamma_k = 5,
invariant = 0
)
sub_F84(
pi_tcag,
beta,
kappa,
mu = 1,
gamma_shape = NULL,
gamma_k = 5,
invariant = 0
)
sub_TN93(
pi_tcag,
alpha_1,
alpha_2,
beta,
mu = 1,
gamma_shape = NULL,
gamma_k = 5,
invariant = 0
)
sub_GTR(
pi_tcag,
abcdef,
mu = 1,
gamma_shape = NULL,
gamma_k = 5,
invariant = 0
)
sub_UNREST(Q, mu = 1, gamma_shape = NULL, gamma_k = 5, invariant = 0)

lambda 
Substitution rate for all possible substitutions. 
mu 
Total rate of substitutions. Defaults to 
gamma_shape 
Numeric shape parameter for discrete Gamma distribution used for
amongsite variability. Values must be greater than zero.
If this parameter is 
gamma_k 
The number of categories to split the discrete Gamma distribution
into. Values must be an integer in the range 
invariant 
Proportion of sites that are invariant.
Values must be in the range 
alpha 
Substitution rate for transitions. 
beta 
Substitution rate for transversions. 
pi_tcag 
Vector of length 4 indicating the equilibrium distributions of T, C, A, and G respectively. Values must be >= 0, and they are forced to sum to 1. 
kappa 
The transition/transversion rate ratio. 
alpha_1 
Substitution rate for T <> C transition. 
alpha_2 
Substitution rate for A <> G transition. 
abcdef 
A vector of length 6 that contains the offdiagonal elements
for the substitution rate matrix.
See 
Q 
Matrix of substitution rates for "T", "C", "A", and "G", respectively.
Item 
A sub_info
object, which is an R6 class that wraps the info needed for
the create_haplotypes
function.
It does not allow the user to directly manipulate the info inside, as that
should be done using the sub_models
functions.
You can use the following methods from the class to view information:
Q()
View a list of substitution rate matrices, one for each Gamma category.
pi_tcag()
View the equilibrium nucleotide frequencies.
gammas()
View the discrete Gammaclass values.
invariant()
View the proportion of invariant sites.
model()
View the substitution model.
U()
View list of the U
matrices (one matrix per Gamma category)
used for calculating transitionprobability matrices.
This is empty for UNREST models.
Ui()
View list of the U^1
matrices (one matrix per Gamma category)
used for calculating transitionprobability matrices.
This is empty for UNREST models.
L()
View list of the lambda vectors (one vector per Gamma category) used for calculating transitionprobability matrices. This is empty for UNREST models.
sub_JC69
: JC69 model.
sub_K80
: K80 model.
sub_F81
: F81 model.
sub_HKY85
: HKY85 model.
sub_F84
: F84 model.
sub_TN93
: TN93 model.
sub_GTR
: GTR model.
sub_UNREST
: UNREST model.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17  # Same substitution rate for all types:
obj_JC69 < sub_JC69(lambda = 0.1)
# Transitions 2x more likely than transversions:
obj_K80 < sub_K80(alpha = 0.2, beta = 0.1)
# Incorporating equilibrium frequencies:
obj_HKY85 < sub_HKY85(pi_tcag = c(0.1, 0.2, 0.3, 0.4),
alpha = 0.2, beta = 0.1)
# 10category Gamma distribution for amongsite variability:
obj_K80 < sub_K80(alpha = 0.2, beta = 0.1,
gamma_shape = 1, gamma_k = 10)
# Invariant sites:
obj_K80 < sub_K80(alpha = 0.2, beta = 0.1,
invariant = 0.25)

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