default_params_doc: This function does nothing. It is intended to inherit is...
In Giappo/mbd: Multiple Birth Death Diversification

Description Usage Arguments Note Author(s)

This function does nothing. It is intended to inherit is parameters' documentation.

default_params_doc(
  a_abstol,
  a_reltol,
  absorb,
  atol,
  abstol,
  account_name,
  after,
  age,
  alpha,
  alpha0,
  b,
  brts,
  brts_precision,
  changeloglikifnoconv,
  checked_functions,
  colormap,
  cond,
  data_folder,
  debug_mode,
  empty_mat,
  empty_pp,
  empty_qq,
  eq,
  expr,
  fortran,
  func,
  function_name,
  function_names,
  functions_names,
  idparsfix,
  idparsopt,
  initparsopt,
  init_n_lineages,
  initprobs,
  init_probs,
  input_trees_path,
  input_xml,
  interval_max,
  interval_min,
  iterations,
  k,
  lambda,
  lambdas,
  lambda_limit,
  likelihood,
  l_matrix,
  loglik_function,
  loglik_functions,
  logs,
  log_nu_mat,
  log_q_mat,
  lx,
  lx0,
  lx_top,
  lx_condprob_fun,
  m1,
  m2,
  m1_mat,
  m2_mat,
  mm,
  matrices,
  matrix,
  matrix_a,
  matrix_builder,
  max_iter,
  max_k,
  max_number_of_species,
  max_repetitions,
  max_sims,
  maxit,
  maxiter,
  mbd_lambda,
  message,
  methode,
  minimum_multiple_births,
  missnumspec,
  ml_steps,
  models,
  mu,
  mus,
  mu_limit,
  mutation_rate,
  n_0,
  n_0s,
  n_species,
  n_sims,
  n_steps,
  n_subs,
  nee_pars,
  nu,
  nus,
  nu_limit,
  nu_matrix,
  optimmethod,
  optim_ids,
  pp,
  pp2,
  parms,
  parmsvec,
  params,
  pars,
  pars_transform,
  pars_transformed,
  parsfix,
  parsvec,
  pc,
  pool,
  precision,
  print_errors,
  printit,
  project_folder,
  pvec,
  q,
  qs,
  qq,
  qq2,
  q_t,
  q_vector,
  q_threshold,
  quantiles_choice,
  qvec,
  recursive,
  rtol,
  reltol,
  res,
  results,
  results_folder,
  rhs_function,
  runmod,
  s,
  safety_checks,
  saveit,
  seed,
  sample_interval,
  sequence_length,
  ml_sequence,
  sim,
  sim_pars,
  sim_phylo,
  start_pars,
  starting_seed,
  subsamp,
  sum_probs_1,
  sum_probs_2,
  t,
  tcrit,
  times,
  tvec,
  t1,
  t2,
  t_0,
  t_0s,
  tips_interval,
  time_interval,
  tol,
  tr,
  transition_matrix,
  trparsfix,
  trparsopt,
  true_pars,
  values,
  vector,
  verbose,
  x,
  x_name,
  x_splits,
  y,
  y_name,
  y_splits,
  z,
  z_name
)

`a_abstol`	absolute error tolerance for the numerical integration using deSolve.
`a_reltol`	relative error tolerance for the numerical integration using deSolve.
`absorb`	set absorbing states when maximum number of allowed species is reached
`atol`	absolute error tolerance for the numerical integration using deSolve.
`abstol`	absolute error tolerance for the numerical integration using deSolve.
`account_name`	something
`after`	something
`age`	the age of the tree.
`alpha`	something
`alpha0`	something
`b`	the number of simultaneous births on a given branching time.
`brts`	A set of branching times of a phylogeny.
`brts_precision`	set the level of approximation on the branching times.
`changeloglikifnoconv`	something
`checked_functions`	something
`colormap`	something
`cond`	sets the conditioning cond = 0: no conditioning; cond = 1: conditioning on stem or crown age and non-extinction of the phylogeny;
`data_folder`	The data folder insider the project folder.
`debug_mode`	If TRUE allows to run even when there are errors and expose them.
`empty_mat`	an empty matrix
`empty_pp`	empty pp matrix. See `pp`.
`empty_qq`	empty qq matrix. See `qq`.
`eq`	the equation approach you want to use. It can be "q_eq" for the Q-equation of "p_eq" for the P-equation.
`expr`	and expression
`fortran`	Set it to TRUE if you want to use FORTRAN routine.
`func`	a function
`function_name`	function name
`function_names`	function names
`functions_names`	function names
`idparsfix`	something
`idparsopt`	the ids of the parameters that must be optimized. The ids are defined as follows: pars[1] is lambda, the sympatric speciation rate; pars[2] is mu, the extinction rate; pars[3] is nu, the multiple allopatric speciation trigger rate; pars[4] is q, the single-lineage speciation probability_
`initparsopt`	something
`init_n_lineages`	the number of lineages at time equals zero.
`initprobs`	initial probabilities
`init_probs`	initial probabilities
`input_trees_path`	Path to `.trees` file.
`input_xml`	something
`interval_max`	something
`interval_min`	something
`iterations`	something
`k`	the number of visible species in the phylogeny at a given time.
`lambda`	the sympatric speciation rate.
`lambdas`	the sympatric speciation rates.
`lambda_limit`	Upper limit to lambda estimations.
`likelihood`	the likelihood
`l_matrix`	the l-table
`loglik_function`	the loglik function
`loglik_functions`	the loglik_functions you want to use
`logs`	something
`log_nu_mat`	logarithmic nu-matrix, used for condprob
`log_q_mat`	logarithmic q-matrix, used for condprob
`lx`	it is the number of ODEs considered for the computation.
`lx0`	something
`lx_top`	maximum lx to produce pre-calculated matrices for condprob
`lx_condprob_fun`	function to determine the right lx for condprob
`m1`	a matrix keeping track of columns
`m2`	a matrix keeping track of rows
`m1_mat`	a matrix keeping track of columns
`m2_mat`	a matrix keeping track of rows
`mm`	indexes of missing species
`matrices`	matrices
`matrix`	a matrix
`matrix_a`	The A matrix from the theory that represents the ODE system.
`matrix_builder`	function used to build the transition matrix. Default option is `hyper_matrix2`
`max_iter`	Sets the maximum number of iterations in the optimization
`max_k`	something
`max_number_of_species`	something
`max_repetitions`	something
`max_sims`	something
`maxit`	maximum number of subplex iterations
`maxiter`	maximum number of subplex iterations
`mbd_lambda`	something
`message`	a message
`methode`	specifies how the integration must be performed: `lsodes`: use `lsodes` and `deSolve::ode` `ode45`: use `ode45` and `deSolve::ode` `lsoda`: use `lsoda` and `deSolve::ode`
`minimum_multiple_births`	minimum amount of multiple births that have to be present in the simulated phylogeny.
`missnumspec`	The number of species that are in the clade, but missing in the phylogeny.
`ml_steps`	number of increasing precision steps to adopt in the ml routine. Each step will increment the absolute and relative tolerances of the optimizer as well as the number of equations used by the likelihood function.
`models`	the models you want to use to define the likelihood
`mu`	the extinction rate.
`mus`	the extinction rates.
`mu_limit`	Upper limit to mu estimations.
`mutation_rate`	something
`n_0`	the number of lineages at time equals zero.
`n_0s`	starting number of lineages for all the clades
`n_species`	number of species.
`n_sims`	number of simulations
`n_steps`	something
`n_subs`	something
`nee_pars`	the equivalent parameters in Nee et al.'s approach
`nu`	the multiple allopatric speciation trigger rate.
`nus`	the multiple allopatric speciation trigger rates.
`nu_limit`	Upper limit to nu estimations.
`nu_matrix`	matrix for the nu component. Component m,n is equal to choose(n, m - n) x q ^ (m - n) x (1 - q) ^ (2 * n - m)
`optimmethod`	optimization routine: choose between subplex and simplex
`optim_ids`	ids of the parameters you want to optimize.
`pp`	the matrix p_n1, n2
`pp2`	the matrix p_n1, n2, with an empty frame
`parms`	some parameters to pass on the ode function
`parmsvec`	parameters to pass to the FORTRAN scripts
`params`	transition matrix for the rhs of the ode system.
`pars`	vector of parameters: pars[1] is lambda, the sympatric speciation rate; pars[2] is mu, the extinction rate; pars[3] is nu, the multiple allopatric speciation trigger rate; pars[4] is q, the single-lineage speciation probability;
`pars_transform`	something
`pars_transformed`	parameters of the likelihood functions, transformed according to y = x / (1 + x)
`parsfix`	the values of the parameters that should not be optimized.
`parsvec`	vector of parameters for the FORTRAN subroutine.
`pc`	conditional probability
`pool`	the pool of living species at a given time
`precision`	something
`print_errors`	something
`printit`	something
`project_folder`	the folder when you want to save data and results
`pvec`	a vector of probabilities P
`q`	the single-lineage speciation probability at a triggered event.
`qs`	the single-lineage speciation probabilities at a triggered event.
`qq`	the matrix q_m1, m2
`qq2`	the matrix q_m1, m2, with an empty frame
`q_t`	the q_vector in time
`q_vector`	the `Q` vector from 'Etienne et al. 2012 - Proc. R. Soc. B'.
`q_threshold`	adds a threshold for the evaluation of q. This is due because you never want `q` to actually be equal to zero or one.
`quantiles_choice`	something
`qvec`	a vector of probabilities Q
`recursive`	something
`rtol`	relative error tolerance for the numerical integration using deSolve.
`reltol`	relative error tolerance for the numerical integration using deSolve.
`res`	something
`results`	mle results
`results_folder`	The results folder insider the project folder.
`rhs_function`	a function for the right hand side of the differential equation
`runmod`	FORTRAN subroutine's option
`s`	the seed
`safety_checks`	TRUE if you want the parameters to be limited to a realistic, but not infinite, parameter space
`saveit`	do you want to save the results?
`seed`	the seed
`sample_interval`	something
`sequence_length`	something
`ml_sequence`	defines the sequence of the (increasing) accuracy steps of the ml algorithm. Set it to c(1) (or just 1) if you just want to use the fast algorithm.
`sim`	the results of a sim run
`sim_pars`	vector of starting parameters: sim_pars[1] is lambda, the sympatric speciation rate; sim_pars[2] is mu, the extinction rate; sim_pars[3] is nu, the multiple allopatric speciation trigger rate; sim_pars[4] is q, the single-lineage speciation probability;
`sim_phylo`	something
`start_pars`	starting parameter values for the ml process.
`starting_seed`	the seed to start from
`subsamp`	something
`sum_probs_1`	vector of probability sums, used during the integration of mbd_loglik
`sum_probs_2`	vector of probability sums, used during the integration of mbd_loglik
`t`	time
`tcrit`	the time you don't want to exceed in the integration
`times`	vector of times
`tvec`	vector of times
`t1`	something
`t2`	something
`t_0`	starting time
`t_0s`	starting time for each clade
`tips_interval`	sets tips boundaries constrain on simulated dataset. It works only if cond == 1, otherwise it must be set to c(0, Inf).
`time_interval`	a time interval
`tol`	something
`tr`	a phylogeny of class `phylo`
`transition_matrix`	something
`trparsfix`	something
`trparsopt`	something
`true_pars`	true parameter values when running the ml process. The parameters that are not meant to be optimized specified as FALSE in `optim_ids` will be fixed by the homologous from this vector.
`values`	something
`vector`	a vector
`verbose`	choose if you want to print the output or not
`x`	something
`x_name`	something
`x_splits`	something
`y`	something
`y_name`	something
`y_splits`	something
`z`	something
`z_name`	something

This is an internal function, so it should be marked with @noRd. This is not done, as this will disallow all functions to find the documentation parameters

Documentation by Giovanni Laudanno, use of this function by Richel J.C. Bilderbeek

Giappo/mbd documentation built on March 3, 2020, 3:36 a.m.