secsse_loglik: Likelihood for SecSSE model Loglikelihood calculation for the...

In secsse: Several Examined and Concealed States-Dependent Speciation and Extinction

Likelihood for SecSSE model Loglikelihood calculation for the SecSSE model given a set of parameters and data

Description

Likelihood for SecSSE model Loglikelihood calculation for the SecSSE model given a set of parameters and data

Usage

secsse_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::runge_kutta_cash_karp54",
  display_warning = TRUE,
  use_normalization = TRUE,
  return_root_state = FALSE
)

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), ⁠"equal_weights"'. or ⁠"stationary_weights"⁠It can also be specified for the root state: the vector⁠c(1, 0, 0)⁠ indicates state 1 was the root state. When using a⁠multiPhylo' 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. This should be left blank (default : setting_calculation = NULL).
see_ancestral_states	Boolean for whether the ancestral states for each of the internal nodes should be output. 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	ODE integration method. Choose from: "odeint::runge_kutta_cash_karp54", "odeint::runge_kutta_fehlberg78", "odeint::runge_kutta_dopri5", "odeint::bulirsch_stoer" and "odeint::runge_kutta4". Default method is: "odeint::runge_kutta_cash_karp54".
display_warning	display a warning if necessary
use_normalization	normalize the density vector during integration, more accurate but slower (default = TRUE)
return_root_state	if TRUE, returns the state of the system at the root, this can be useful to use as the starting point of a simulation. When used in ML, after finishing the ML optimization, the found optimum is evaluated one more time to retrieve the root state (to avoid having to store the root state every ML evaluation).

Value

A list with the following elements: $LL the loglikelihood of the data (phylogeny + tip states) given the parameters (speciation, extinction, transition rates). If see_ancestral_states = TRUE, then there will be two additional elements: $ancestral_states: a matrix with the probabilities of each state at the internal nodes $states: a matrix with the probabilities E, D (normalized) and S that are used in the calculations. The ancestral_states matrix is a submatrix of this matrix. This matrix is mostly used for package developers. If return_root_state = TRUE, then there will be one additional element: $root_state: vector with probabilities of each state at the root. This vector is the same as the top row of $ancestral_states We have used the shorthand description of "probabilities of each state", but technically, the probabilities are the normalized probabilities D of the data given each state at the internal nodes.

Examples

rm(list = ls(all = TRUE))
library(secsse)
set.seed(13)
phylotree <- ape::rcoal(31, tip.label = 1:31)
traits <- sample(c(0,1,2),ape::Ntip(phylotree),replace = TRUE)
num_concealed_states <- 2
cond <- "proper_cond"
root_state_weight <- "proper_weights"
sampling_fraction <- c(1,1,1)
drill <- id_paramPos(traits,num_concealed_states)
drill[[1]][] <- c(0.12,0.01,0.2,0.21,0.31,0.23)
drill[[2]][] <- 0
drill[[3]][,] <- 0.1
diag(drill[[3]]) <- NA
secsse_loglik(parameter = drill,
phylotree,
traits,
num_concealed_states,
cond,
root_state_weight,
sampling_fraction,
see_ancestral_states = FALSE)

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secsse documentation built on May 15, 2026, 5:06 p.m.