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Setting up configuration file

Source: vignettes/setting-up-the-configuration-file.qmd
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Introduction

Since lifelihood allows for a large number of combinations on which parameters to estimate for a given dataset, it makes it easier to have a separate configuration file to specify what you want to fit. Under the hood, the program will use this file to only estimate what you have specified and returns the estimations.

The needed configuration file must be in the YAML format, a convenient kind of file that is both easy to read (for humans) and to parse (for the program). It relies on indentation to represent structure. Learn more about YAML.

Parameters

There are 3 main sections in the required YAML configuration file:

  • mortality: parameters related to mortality
  • maturity: parameters related to maturity
  • reproduction: parameters related to reproduction

Estimations

Possible values

Assuming you have 2 covariables in your dataset (named covar1 and covar2), for each of the estimation parameters, the following values are possible:

  • not_fitted: do not estimate this parameter.
  • 1: only fit the intercept.
  • covar1: fit the intercept and the parameter of covar1.
  • covar1 + covar2: fit the intercept, the parameter of covar1 and the parameter of covar1.
  • covar1 + covar2 + covar1*covar2: fit the intercept, the parameter of covar1, the parameter of covar1 and the interaction between covar1 and covar2.

Note: covar1 and covar2 are arbitrary names. The only rule is that they should be the name of one of your columns in your dataset.

Mortality
  • expt_death: Expected time to death
  • survival_shape: Survival shape parameter
  • ratio_expt_death: Ratio between expected time to death for male vs expected time to death for female
  • prob_death: Probability of death before critical time
  • sex_ratio: Sex ratio
Maturity
  • expt_maturity: Expected time to maturity
  • maturity_shape: Maturity shape parameter
  • ratio_expt_maturity: Ratio between expected time to maturity for male and expected time to maturity for female
Reproduction
  • expt_reproduction: Expected time until next reproduction
  • reproduction_shape: Reproduction shape parameter
  • n_offspring: Number of offspring per reproduction event or fitness
  • increase_death_hazard: Increase in death hazard following a reproduction event
  • tof_reduction_date: Trade-off of reduction rate
  • increase_tof_n_offspring: Increase in trade-off proportional to the number of offspring
  • lin_decrease_hazard: Linear decrease in hazard rate with time since maturity
  • quad_decrease_hazard: Quadratic decrease in hazard rate with time since maturity
  • lin_change_n_offspring: Linear change in number of offspring with time since maturity
  • quad_change_n_offspring: Quadratic change in number of offsprings with time since maturity
  • tof_n_offspring: Trade-off between previous reproductive interval and current number of offspring

Example 

---
mortality:
  expt_death: geno
  survival_shape: geno + type + geno*type
  ratio_expt_death: geno
  prob_death: geno
  sex_ratio: not_fitted
maturity:
  expt_maturity: geno + type
  maturity_shape: geno
  ratio_expt_maturity: geno + type
reproduction:
  expt_reproduction: geno
  reproduction_shape: not_fitted
  n_offspring: geno
  increase_death_hazard: geno + type + geno*type
  tof_reduction_date: geno
  increase_tof_n_offspring: geno
  lin_decrease_hazard: geno + type + geno*type
  quad_decrease_hazard: geno
  lin_change_n_offspring: geno
  quad_change_n_offspring: geno
  tof_n_offspring: not_fitted

Next step

The next step is to actually use the package.