em_cpp: function to perform one step of the E-M algorithm

In franciscorichter/emphasis: Evolutionary Modeling on Phylogenetic Applications with Simulations and Importance Sampling

function to perform one step of the E-M algorithm

Description

function to perform one step of the E-M algorithm

function to perform one step of the E-M algorithm

Usage

em_cpp(
  brts,
  pars,
  sample_size,
  maxN,
  soc,
  max_missing,
  max_lambda,
  lower_bound,
  upper_bound,
  xtol_rel,
  num_threads,
  copy_trees,
  rconditional = NULL
)

em_cpp(
  brts,
  pars,
  sample_size,
  maxN,
  soc,
  max_missing,
  max_lambda,
  lower_bound,
  upper_bound,
  xtol_rel,
  num_threads,
  copy_trees,
  rconditional = NULL
)

Arguments

brts	vector of branching times
sample_size	number of samples
maxN	maximum number of failed trees
soc	number of lineages at the root/crown (1/2)
max_missing	maximum number of species missing
max_lambda	maximum speciation rate
lower_bound	vector of lower bound values for optimization, should be equal in length to the vector of init_pars
upper_bound	vector of upper bound values for optimization, should be equal in length to the vector of init_pars
xtol_rel	relative tolerance for optimization
num_threads	number of threads used.
copy_trees	if set to true, the trees generated are returned as well
rconditional	R function that evaluates the GAM function.
init_pars	vector of initial parameter files

Value

a list with the following components:

• treeslist of trees

• rejectednumber of rejected trees

• rejected_overrunsnumber of trees rejected due to too large size

• rejected_lambdanumber of trees rejected due to lambda errors

• rejected_zero_weightsnumber of trees rejected to zero weight

• estimatesvector of estimates

• nloptnlopt status

• fhatvector of fhat values

• timetime elapsed

• weightsvector of weights

a list with the following components:

• treeslist of trees

• rejectednumber of rejected trees

• rejected_overrunsnumber of trees rejected due to too large size

• rejected_lambdanumber of trees rejected due to lambda errors

• rejected_zero_weightsnumber of trees rejected to zero weight

• estimatesvector of estimates

• nloptnlopt status

• fhatvector of fhat values

• timetime elapsed

• weightsvector of weights

franciscorichter/emphasis documentation built on Feb. 19, 2024, 7:36 p.m.