secsse (version 3.5.0)

secsse_loglik_eval: Likelihood for SecSSE model Logikelihood calculation for the SecSSE model given a set of parameters and data, returning also the likelihoods along the branches

Description

Likelihood for SecSSE model Logikelihood calculation for the SecSSE model given a set of parameters and data, returning also the likelihoods along the branches

Usage

secsse_loglik_eval(
  parameter,
  phy,
  traits,
  num_concealed_states,
  cond = "proper_cond",
  root_state_weight = "proper_weights",
  sampling_fraction,
  setting_calculation = NULL,
  loglik_penalty = 0,
  is_complete_tree = FALSE,
  num_threads = 1,
  atol = 1e-08,
  rtol = 1e-07,
  method = "odeint::bulirsch_stoer",
  num_steps = 100
)

Value

A list containing: "output", observed states along evaluated time points along all branches, used for plotting. "states" all ancestral states on the nodes and "duration", indicating the time taken for the total evaluation

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).

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.

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".

num_steps

number of substeps to show intermediate likelihoods along a branch.

Examples

set.seed(5)
phy <- ape::rphylo(n = 4, birth = 1, death = 0)
traits <- c(0, 1, 1, 0)
params <- secsse::id_paramPos(c(0, 1), 2)
params[[1]][] <- c(0.2, 0.2, 0.1, 0.1)
params[[2]][] <- 0.0
params[[3]][, ] <- 0.1
diag(params[[3]]) <- NA

secsse_loglik_eval(parameter = params,
                   phy = phy,
                   traits = traits,
                   num_concealed_states = 2,
                   sampling_fraction = c(1, 1),
                   num_steps = 10)