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,
param_bounds_df = NULL,
group_by_group = FALSE,
MCMC = 0,
interval = 25,
SEcal = FALSE,
saveprobevent = 0,
fitness = 0,
r = 0,
seeds = NULL,
ntr = 2,
nst = 2,
To = 50,
Tf = 1,
climbrate = 1,
precision = 0.001,
raise_estimation_warning = TRUE,
delete_temp_files = TRUE
)Arguments
- lifelihoodData
lifelihoodDataobject created withlifelihoodData().- 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)
- param_bounds_df
Dataframe with the parameter ranges/boundaries/boundaries
- group_by_group
Boolean option to fit the full factorail 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
- SEcal
If TRUE, Lifelihood computes the standard error of each parameter using the Hessian matrix (output with value of -1 if standard error cannot be computed due to singularity of the Hessian matrix)
- saveprobevent
TBD - Check the actual meaning
- fitness
Reparametrize the model with one parameter as the lifetime reproductive success
- r
Reparametrize the model with one parameter as the intrinsic rate of increase
- seeds
Numbers used to reproduce results (same seeds = same results). This must be a vector of length 4.
- 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
- 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.
Examples
library(lifelihood)
library(tidyverse)
df <- fakesample |>
mutate(
geno = as.factor(geno),
type = as.factor(type)
)
head(df)
#> type geno sex_start sex_end sex mat_start mat_end clutch_start1 clutch_end1
#> 1 1 0 0 1000 0 0 1000 NA NA
#> 2 2 0 0 1000 0 2 3 4 3
#> 3 0 1 0 1000 0 3 4 2 4
#> 4 0 1 0 1000 0 3 4 2 4
#> 5 0 1 0 1000 0 3 4 2 4
#> 6 1 0 0 1000 0 0 1000 NA NA
#> clutch_size1 clutch_start2 clutch_end2 clutch_size2 death_start death_end
#> 1 NA NA NA NA 0.1 1
#> 2 4 2 4 5 9.0 10
#> 3 5 NA NA NA 5.0 6
#> 4 5 NA NA NA 5.0 6
#> 5 5 NA NA NA 5.0 6
#> 6 NA NA NA NA 0.1 1
clutchs <- c(
"clutch_start1", "clutch_end1", "clutch_size1",
"clutch_start2", "clutch_end2", "clutch_size2"
)
dataLFH <- lifelihoodData(
df = df,
sex = "sex",
sex_start = "sex_start",
sex_end = "sex_end",
maturity_start = "mat_start",
maturity_end = "mat_end",
clutchs = clutchs,
death_start = "death_start",
death_end = "death_end",
covariates = c("geno", "type"),
model_specs = c("gam", "lgn", "wei")
)
results <- lifelihood(
lifelihoodData = dataLFH,
path_config = get_config_path("config"),
seeds = c(1, 2, 3, 4),
raise_estimation_warning = FALSE
)
summary(results)
#> LIFELIHOOD RESULTS
#>
#> Likelihood:
#> [1] -829.0578
#>
#> Effects:
#> name estimation stderror
#> 1 int_expt_death -14.95337701 0
#> 2 eff_expt_death_geno_1 2.27064527 0
#> 3 eff_expt_death_type_1 -9.55371757 0
#> 4 eff_expt_death_type_2 0.53315647 0
#> 5 int_survival_shape 10.28792377 0
#> 6 eff_survival_shape_geno_1 -1.93963186 0
#> 7 eff_survival_shape_type_1 7.57026237 0
#> 8 eff_survival_shape_type_2 4.74998927 0
#> 9 eff_survival_shape_type_1:geno_1 -0.24718760 0
#> 10 eff_survival_shape_type_2:geno_1 3.52427897 0
#> 11 int_ratio_expt_death -1.45299283 0
#> 12 eff_ratio_expt_death_geno_1 3.02680049 0
#> 13 int_prob_death -17.15815657 0
#> 14 eff_prob_death_geno_1 0.02066385 0
#> 15 int_expt_maturity -0.07781130 0
#> 16 eff_expt_maturity_geno_1 -0.34729932 0
#> 17 eff_expt_maturity_type_1 -0.76380036 0
#> 18 eff_expt_maturity_type_2 -0.75476253 0
#> 19 int_maturity_shape -10.02261060 0
#> 20 eff_maturity_shape_geno_1 -3.30865726 0
#> 21 int_ratio_expt_maturity 1.74264178 0
#> 22 eff_ratio_expt_maturity_geno_1 3.36233997 0
#> 23 eff_ratio_expt_maturity_type_1 -2.79189482 0
#> 24 eff_ratio_expt_maturity_type_2 -4.87384990 0
#> 25 int_expt_reproduction -1.79104715 0
#> 26 eff_expt_reproduction_geno_1 -0.89759305 0
#> 27 int_pontn -2.96400432 0
#> 28 eff_pontn_geno_1 -1.03064224 0
#> 29 int_increase_death_hazard 3.32326622 0
#> 30 eff_increase_death_hazard_geno_1 2.18470307 0
#> 31 eff_increase_death_hazard_type_1 -0.38970742 0
#> 32 eff_increase_death_hazard_type_2 -3.84713473 0
#> 33 eff_increase_death_hazard_type_1:geno_1 -1.13985166 0
#> 34 eff_increase_death_hazard_type_2:geno_1 -3.69784224 0
#> 35 int_tof_reduction_date -1.27913674 0
#> 36 eff_tof_reduction_date_geno_1 -3.51198283 0
#> 37 int_increase_tof_n_offspring 0.24026695 0
#> 38 eff_increase_tof_n_offspring_geno_1 -0.32428130 0
#> 39 int_lin_decrease_hazard 0.81074061 0
#> 40 eff_lin_decrease_hazard_geno_1 0.19505972 0
#> 41 eff_lin_decrease_hazard_type_1 5.50927699 0
#> 42 eff_lin_decrease_hazard_type_2 -0.85842716 0
#> 43 eff_lin_decrease_hazard_type_1:geno_1 3.98397092 0
#> 44 eff_lin_decrease_hazard_type_2:geno_1 0.69812447 0
#> 45 int_quad_senescence -0.49711337 0
#> 46 eff_quad_senescence_geno_1 0.47173154 0
#> 47 int_quad_decrease_hazard -0.07370047 0
#> 48 eff_quad_decrease_hazard_geno_1 -0.14027753 0
#> 49 int_quad_change_n_offspring 0.07862816 0
#> 50 eff_quad_change_n_offspring_geno_1 0.00640363 0
#> 51 int_tof_n_offspring -0.21320110 0
#> parameter kind event
#> 1 expt_death intercept mortality
#> 2 expt_death coefficient mortality
#> 3 expt_death coefficient mortality
#> 4 expt_death coefficient mortality
#> 5 survival_shape intercept mortality
#> 6 survival_shape coefficient mortality
#> 7 survival_shape coefficient mortality
#> 8 survival_shape coefficient mortality
#> 9 survival_shape coefficient mortality
#> 10 survival_shape coefficient mortality
#> 11 ratio_expt_death intercept mortality
#> 12 ratio_expt_death coefficient mortality
#> 13 prob_death intercept mortality
#> 14 prob_death coefficient mortality
#> 15 expt_maturity intercept maturity
#> 16 expt_maturity coefficient maturity
#> 17 expt_maturity coefficient maturity
#> 18 expt_maturity coefficient maturity
#> 19 maturity_shape intercept maturity
#> 20 maturity_shape coefficient maturity
#> 21 ratio_expt_maturity intercept maturity
#> 22 ratio_expt_maturity coefficient maturity
#> 23 ratio_expt_maturity coefficient maturity
#> 24 ratio_expt_maturity coefficient maturity
#> 25 expt_reproduction intercept reproduction
#> 26 expt_reproduction coefficient reproduction
#> 27 pontn intercept reproduction
#> 28 pontn coefficient reproduction
#> 29 increase_death_hazard intercept reproduction
#> 30 increase_death_hazard coefficient reproduction
#> 31 increase_death_hazard coefficient reproduction
#> 32 increase_death_hazard coefficient reproduction
#> 33 increase_death_hazard coefficient reproduction
#> 34 increase_death_hazard coefficient reproduction
#> 35 tof_reduction_date intercept reproduction
#> 36 tof_reduction_date coefficient reproduction
#> 37 increase_tof_n_offspring intercept reproduction
#> 38 increase_tof_n_offspring coefficient reproduction
#> 39 lin_decrease_hazard intercept reproduction
#> 40 lin_decrease_hazard coefficient reproduction
#> 41 lin_decrease_hazard coefficient reproduction
#> 42 lin_decrease_hazard coefficient reproduction
#> 43 lin_decrease_hazard coefficient reproduction
#> 44 lin_decrease_hazard coefficient reproduction
#> 45 quad_senescence intercept reproduction
#> 46 quad_senescence coefficient reproduction
#> 47 quad_decrease_hazard intercept reproduction
#> 48 quad_decrease_hazard coefficient reproduction
#> 49 quad_change_n_offspring intercept reproduction
#> 50 quad_change_n_offspring coefficient reproduction
#> 51 tof_n_offspring intercept reproduction
#>