format_optim_results_row: Assemble a row of results for run_optim output

In TheoPannetier/DDvTDtools: Compare diversity-dependent (DD) and time-dependent (TD) diversification models

Description

Internal function called by run_optim(). Formats optimisation results and metadata in a data frame row.

Usage

format_optim_results_row(
  mc,
  sim,
  optim,
  brts,
  true_pars,
  init_pars,
  ML_output,
  num_cycles = 1,
  methode,
  optimmethod,
  jobID,
  cond
)

Arguments

mc	numeric between 1 and 1000, the index of a tree within a dataset.
sim	character, name of the simulation model, either "DD" or "TD".
optim	character, name of the optimisation model, either "DD" or "TD".
brts	numeric vector, a set of branching times as given by ape::branching_times().
true_pars	numeric vector. The true parameter values used to simulate the tree.
init_pars	numeric vector. The initial parameter values used for likelihood optimisation.
ML_output	numeric vector. Raw output of DDD::dd_ML() / DDD::bd_ML().
num_cycles	numeric. Maximum number of optimisation cycles.
methode	character. Integration methode for computing the likelihood. See DDD::dd_loglik() / DDD::bd_loglik() for details.
optimmethod	character. Optimisation methode used to compute the maximum likelihood. See DDD::dd_ML() / DDD::bd_ML() for details.
jobID	the ID number of the cluster job that returned the results. Saved in metadata to retrieve logs, for example. A value of NULL means that the result was obtained locally.
cond	numeric, conditionning parameter passed to DDD::dd_ML() / DDD::bd_ML().

Author(s)

Théo Pannetier

TheoPannetier/DDvTDtools documentation built on Oct. 22, 2020, 2:31 p.m.