secsse (version 3.0.2)

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

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.

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".

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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