secsse_single_branch_loglik: Likelihood for SecSSE model Loglikelihood calculation for the SecSSE model given a set of parameters and data, calculated for a single branch

Description

Likelihood for SecSSE model Loglikelihood calculation for the SecSSE model given a set of parameters and data, calculated for a single branch

Usage

secsse_single_branch_loglik(
  parameter,
  phy,
  traits,
  num_concealed_states,
  cond = "proper_cond",
  root_state_weight = "proper_weights",
  sampling_fraction,
  setting_calculation = NULL,
  see_ancestral_states = FALSE,
  loglik_penalty = 0,
  is_complete_tree = FALSE,
  take_into_account_root_edge = FALSE,
  num_threads = 1,
  atol = 1e-08,
  rtol = 1e-07,
  method = "odeint::bulirsch_stoer",
  display_warning = TRUE,
  use_normalization = TRUE
)

Value

The loglikelihood of the data given the parameter.

Arguments

parameter: list where first vector represents lambdas, the second mus and the third transition rates.
phy: phylogenetic tree of class phylo, rooted and with branch lengths. Alternatively, multiple phylogenetic trees can be provided as the multiPhylo class.
traits: vector with trait states for each tip in the phylogeny. The order of the states must be the same as the tree tips. For help, see vignette("starting_secsse", package = "secsse"). When providing a multiPhylo set of multiple phylognies, traits should be a list where each entry in the list corresponds to the matching phylogeny on that position.
num_concealed_states: number of concealed states, generally equivalent to the number of examined states in the dataset.
cond: condition on the existence of a node root: "maddison_cond", "proper_cond" (default). For details, see vignette.
root_state_weight: the method to weigh the states: "maddison_weights", "proper_weights" (default) or "equal_weights". It can also be specified for the root state: the vector c(1, 0, 0) indicates state 1 was the root state. When using a multiPhylo object, root_state_weight should be list where each entry in the list corresponds to the root_state_weight for each tree.
sampling_fraction: vector that states the sampling proportion per trait state. It must have as many elements as there are trait states. When using a multiPhylo object, sampling fraction should be list where each entry in the list corresponds to the sampling proportion for each tree.
setting_calculation: argument used internally to speed up calculation. It should be left blank (default : setting_calculation = NULL).
see_ancestral_states: Boolean for whether the ancestral states should be shown? Defaults to FALSE.
loglik_penalty: the size of the penalty for all parameters; default is 0 (no penalty).
is_complete_tree: logical specifying whether or not a tree with all its extinct species is provided. If set to TRUE, it also assumes that all all extinct lineages are present on the tree. Defaults to FALSE.
take_into_account_root_edge: if TRUE, the LL integration is continued along the root edge. This also affects conditioning (as now, conditioning no longer needs to assume a speciation event at the start of the tree)
num_threads: number of threads to be used. Default is one thread.
atol: A numeric specifying the absolute tolerance of integration.
rtol: A numeric specifying the relative tolerance of integration.
method: integration method used, available are: "odeint::runge_kutta_cash_karp54", "odeint::runge_kutta_fehlberg78", "odeint::runge_kutta_dopri5", "odeint::bulirsch_stoer" and "odeint::runge_kutta4". Default method is: "odeint::bulirsch_stoer".
display_warning: display a warning if necessary
use_normalization: normalize the density vector during integration, more accurate but slower (default = TRUE)