default_params_doc: This function does nothing. It is intended to inherit is...

In Giappo/sls: Likelihood model for diversification processes with single lineage rate shifts

Description

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

Usage

default_params_doc(
  age,
  brts,
  brts_m,
  brts_s,
  brts_clade,
  cond,
  convolve_function,
  clade,
  crown_age,
  d_0,
  d_0s,
  data,
  data_folder,
  delta_n,
  delta_t,
  deltas,
  dropextinct,
  e_0,
  event,
  final_time,
  fun,
  fun1,
  fun2,
  function_name,
  function_names,
  functions_names,
  k,
  lambda,
  lambdas,
  max_iterations,
  mu,
  mus,
  ks,
  l_0,
  l_1,
  l_2,
  l_matrix_size,
  l_matrix,
  log_scale,
  lambdaterms,
  loglik_function,
  loglik_functions,
  lx,
  matrix_size,
  message,
  missnumspec,
  models,
  n,
  n_0,
  n_0s,
  n_max,
  optim_ids,
  output,
  pars,
  pars_m,
  pars_s,
  pars_clade,
  pars_transformed,
  project_folder,
  results,
  results_folder,
  shift_time,
  sim,
  sim_pars,
  start_pars,
  t,
  t_c,
  t_d,
  ts,
  t_0,
  t_0s,
  tf,
  t_f,
  td,
  t_p,
  tds,
  t_ds,
  times,
  tbar,
  true_pars,
  vec,
  verbose,
  ddep,
  trparsopt,
  trparsfix,
  idparsopt,
  idparsfix,
  idparsnoshift,
  initparsopt,
  optimmethod,
  tolerance,
  pars2,
  seed
)

Arguments

age	the age of the phylogeny
brts	branching times provided as a list of vectors, one for the main clade, one for the subclade
brts_m	branching times for the Main-clade
brts_s	branching times for the Sub-clade
brts_clade	branching times for a single clade
cond	type of conditioning: cond = 0 no conditiong; cond = 1 conditions on the survival of crown descendents; cond = 2 conditions on the survival of subclade and on the other crown descendents in the main clade; cond = 3 conditions on the survival of the subclade and both crown descendents in the main clade;
convolve_function	function used to calculate the convolution
clade	the id of the clade
crown_age	the age of the phylogeny
d_0	starting value for BiSSE's D function
d_0s	starting values for BiSSE's D functions
data	contains all the information about the simulated process
data_folder	The data folder insider the project folder.
delta_n	in the Doob-Gillespie algorithm, the change in number of species
delta_t	in the Doob-Gillespie algorithm, the waiting time for the next event to occur
deltas	in the Doob-Gillespie algorithm, the collection of delta_n and delta_t, which are, respectively, the change in number of species and the waiting time for the next event to occur
dropextinct	TRUE if you want to remove the dead species from the tree. FALSE otherwise.
e_0	starting value for BiSSE's E function
event	the event occurring in the simulated process at a given time
final_time	the final time that you want to consider for the survival of the species considered in the l table
fun	a function
fun1	a function
fun2	another function
function_name	function name
function_names	function names
functions_names	function names
k	frequencies in the Discrete Fourier Transform (DFT)
lambda	speciation rate
lambdas	speciation rates, for all the clades
max_iterations	maximum number of iterations for the optimizer
mu	extinction rate
mus	extinction rate, for all the clades
ks	carrying capacities, for all the clades
l_0	the l table, for a single clade
l_1	the collection of all the l tables, for all the clades
l_2	the matrix containing the information about how the subclades are nested into the main clade. See sim_get_standard_l_2 for more info.
l_matrix_size	the initial length of the l matrix. It will be increased if necessary
l_matrix	the l table
log_scale	set it to TRUE if you desire the output in log form
lambdaterms	set it to TRUE if you desire the powers of lambda in the likelihood
loglik_function	the loglik function you want to use
loglik_functions	the loglik_functions you want to use
lx	size of the matrix
matrix_size	size of the matrix
message	the message to print
missnumspec	number of missing (unseen) species in the phylogeny
models	the models you want to use to define the likelihood
n	number of lineages
n_0	starting number of lineages
n_0s	starting number of lineages for all the clades
n_max	maximum number of lineages to consider
optim_ids	ids of the parameters you want to optimize.
output	the mle output
pars	parameters of the likelihood functions: pars[1] is lambda_m, i.e. speciation rate of the main clade; pars[2] is mu_m, i.e. extinction rate of the main clade; pars[3] is lambda_s, i.e. speciation rate of the sub clade; pars[4] is mu_s, i.e. extinction rate of the sub clade;
pars_m	parameters for the main clade (lambda, mu)
pars_s	parameters for the sub clade (lambda, mu)
pars_clade	parameters for a single clade
pars_transformed	parameters of the likelihood functions, transformed according to y = x / (1 + x)
project_folder	the folder where you want to save data and results
results	mle results
results_folder	The results folder insider the project folder.
shift_time	the time of the shift
sim	the results of a sim run
sim_pars	parameters of the simulation
start_pars	parameters to start from for the search of the likelihood maximum
t	time
t_c	crown time
t_d	decoupling time
ts	times
t_0	starting time
t_0s	starting time for each clade
tf	ending time
t_f	ending time
td	decoupling time
t_p	present time
tds	decoupling times
t_ds	decoupling times
times	times
tbar	time left from shift time to the present
true_pars	true parameter values when running the ml process.
vec	a vector or a matrix to be transformed
verbose	set it to TRUE if you want to see the outputs on screen
ddep	see DDD package
trparsopt	see DDD package
trparsfix	see DDD package
idparsopt	see DDD package
idparsfix	see DDD package
idparsnoshift	see DDD package
initparsopt	see DDD package
optimmethod	see DDD package
tolerance	see DDD package
pars2	see DDD package
seed	the seed

Giappo/sls documentation built on Feb. 1, 2021, 9:55 a.m.