Skip to contents

Individual life history modelling

Source: R/lifelihood.R
lifelihood.Rd

Computes the joined likelihood of all the events in an individual life-history (time of maturity, reproductive events, death) and estimates the parameters of the model using maximum likelihood.

Usage

lifelihood(
  lifelihoodData,
  path_config,
  path_to_Lifelihood = NULL,
  n_fit = 1,
  param_bounds_df = NULL,
  group_by_group = FALSE,
  MCMC = 0,
  interval = 25,
  se.fit = FALSE,
  saveprobevent = 0,
  r = 0,
  seeds = NULL,
  ntr = 2,
  nst = 2,
  To = 50,
  Tf = 1,
  climbrate = 1,
  precision = 0.001,
  ratiomax = 10,
  tc = 20,
  tinf = 1000,
  sub_interval = 0.3,
  raise_estimation_warning = TRUE,
  delete_temp_files = TRUE
)

Arguments

lifelihoodData

lifelihoodData object created with as_lifelihoodData().

path_config

A character string specifying the file path to the YAML configuration file.

path_to_Lifelihood

A character string specifying the file path to the compile Lifelihood program (default is NULL)

n_fit

Number of replicates for model fit to check convergence through consistency in log-likelihood values. The seeds argument should be NULL when n_fit > 1.

param_bounds_df

Dataframe with the parameter ranges/boundaries/boundaries

group_by_group

Boolean option to fit the full factorial model with all the interactions between each of the factors

MCMC

Perform MCMC sampling of the parameter after convergence to estimate their 95% confidence interval

interval

TBD - Check the actual meaning

se.fit

If TRUE, Lifelihood computes the standard error of each parameter using the variance-covariance matrix (approximated by the inverse of the negative of the Hessian matrix).

saveprobevent

TBD - Check the actual meaning

r

Reparametrize the model with one parameter as the intrinsic rate of increase

seeds

Vector of length for with seed numbers used to reproduce results (same seeds = same results). This argument should be NULL (default) when n_fit > 1.

ntr

Number of thread for the paralelisation ?

nst

TBD - Check the actual meaning

To

Initial temperature for the simulated annealing

Tf

Initial temperature for the simulated annealing

climbrate

Rate for the simulated annealing ?

precision

TBD - Check the actual meaning

ratiomax

Maximum multiplicative factor for clutch size in models with reproductive senescence (cf CalculRatioEspPoissonTronque function in Lifelihood)

tc

critical age (after the juvenile mortality peak) at which the survival model starts to be fitted

tinf

maximum censoring time (should be greater than the age of the oldest individual observed dead in the dataset)

sub_interval

sub-interval used to integrate the left and right censoring dates of each event

raise_estimation_warning

Whether or not to raise a warning when the estimate of a parameter is too close to its minimum or maximum bound. Default is TRUE.

delete_temp_files

Indicates whether temporary files should be deleted. TRUE by default and recommended.

Value

A lifelihoodResults object