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,
  num_threads = 1,
  atol = 1e-08,
  rtol = 1e-07,
  method = "odeint::bulirsch_stoer"
)

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.
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").
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.
sampling_fraction: vector that states the sampling proportion per trait state. It must have as many elements as there are trait states.
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.
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".

Value

The loglikelihood of the data given the parameter.

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)
#> Deduced names and order of used states to be: 0, 1, 2
#> if this is incorrect, consider passing states as matching numeric 
#> ordering, e.g. 1 for the first state, 2 for the second etc.
#> [1] -113.0919

#[1] -113.1018