For a more detailed explanation, see `vignette("sub-models")`

.

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
among-site 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 off-diagonal 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 Gamma-class 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 transition-probability matrices. This is empty for UNREST models.`Ui()`

View list of the

`U^-1`

matrices (one matrix per Gamma category) used for calculating transition-probability matrices. This is empty for UNREST models.`L()`

View list of the lambda vectors (one vector per Gamma category) used for calculating transition-probability 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.

# 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) # 10-category Gamma distribution for among-site 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)