cla_secsse_loglik: Likelihood for SecSSE model, using Rcpp Loglikelihood...

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

Likelihood for SecSSE model, using Rcpp Loglikelihood calculation for the cla_SecSSE model given a set of parameters and data using Rcpp

Description

Likelihood for SecSSE model, using Rcpp Loglikelihood calculation for the cla_SecSSE model given a set of parameters and data using Rcpp

Usage

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

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.
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".
atol	A numeric specifying the absolute tolerance of integration.
rtol	A numeric specifying the relative tolerance of integration.

Value

The loglikelihood of the data given the parameters

Examples

rm(list=ls(all=TRUE))
library(secsse)
set.seed(13)
phylotree <- ape::rcoal(12, tip.label = 1:12)
traits <- sample(c(0,1,2),ape::Ntip(phylotree),replace=TRUE)
num_concealed_states <- 3
sampling_fraction <- c(1,1,1)
phy <- phylotree
# the idparlist for a ETD model (dual state inheritance model of evolution)
# would be set like this:
idparlist <- cla_id_paramPos(traits,num_concealed_states)
lambd_and_modeSpe <- idparlist$lambdas
lambd_and_modeSpe[1,] <- c(1,1,1,2,2,2,3,3,3)
idparlist[[1]] <- lambd_and_modeSpe
idparlist[[2]][] <- 0
masterBlock <- matrix(4,ncol=3,nrow=3,byrow=TRUE)
diag(masterBlock) <- NA
idparlist [[3]] <- q_doubletrans(traits,masterBlock,diff.conceal = FALSE)
# Now, internally, clasecsse sorts the lambda matrices, so they look like:
prepare_full_lambdas(traits,num_concealed_states,idparlist[[1]])
# which is a list with 9 matrices, corresponding to the 9 states
# (0A,1A,2A,0B,etc)
# if we want to calculate a single likelihood:
parameter <- idparlist
lambda_and_modeSpe <- parameter$lambdas
lambda_and_modeSpe[1,] <- c(0.2,0.2,0.2,0.4,0.4,0.4,0.01,0.01,0.01)
parameter[[1]] <- prepare_full_lambdas(traits,num_concealed_states,
lambda_and_modeSpe)
parameter[[2]] <- rep(0,9)
masterBlock <- matrix(0.07, ncol=3, nrow=3, byrow=TRUE)
diag(masterBlock) <- NA
parameter [[3]] <- q_doubletrans(traits,masterBlock,diff.conceal = FALSE)
cla_secsse_loglik(parameter, phy, traits, num_concealed_states,
                 cond = 'maddison_cond',
                 root_state_weight = 'maddison_weights', sampling_fraction,
                 setting_calculation = NULL,
                 see_ancestral_states = FALSE,
                 loglik_penalty = 0)
# LL = -42.18407

secsse documentation built on Oct. 22, 2023, 1:13 a.m.