coef() retrieve all coefficients from the output of lifelihood()
coeff() retrieve coefficients of one parameter
from the output of lifelihood()
Arguments
- object
output of
lifelihood()- ...
Ignored
- parameter_name
Name of the parameters to extract the estimate from to extract all parameter estimates). All parameters#' can be found here.
Examples
library(lifelihood)
library(tidyverse)
df <- lifelihood::fakesample |>
mutate(
type = as.factor(type),
geno = as.factor(geno)
)
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
)
#> [1] "/private/var/folders/y6/nj790rtn62lfktb1sh__79hc0000gn/T/Rtmp2lbF6M/temp_libpath1e0a2a79ba80/lifelihood/bin/lifelihood/Users/runner/work/Lifelihood/Lifelihood/lifelihood_1_2_3_4/temp_file_data_lifelihood.txt /Users/runner/work/Lifelihood/Lifelihood/lifelihood_1_2_3_4/temp_param_range_path.txt FALSE 0 25 FALSE 0 0 0 1 2 3 4 10 20 1000 0.3 NULL 2 2 50 1 1 0.001"
#> lifelihood Pascal program status code 0
coef(results)
#> int_expt_death eff_expt_death_geno_1
#> -17.78869453 -2.89709225
#> eff_expt_death_type_1 eff_expt_death_type_2
#> -4.48279290 -0.30099192
#> int_survival_shape eff_survival_shape_geno_1
#> 6.14904518 2.96787660
#> eff_survival_shape_type_1 eff_survival_shape_type_2
#> 3.56630436 3.43958754
#> eff_survival_shape_type_1:geno_1 eff_survival_shape_type_2:geno_1
#> -9.78904370 5.39234946
#> int_ratio_expt_death eff_ratio_expt_death_geno_1
#> 7.51220924 4.47236458
#> int_prob_death eff_prob_death_geno_1
#> -19.85150681 -4.66755544
#> int_expt_maturity eff_expt_maturity_geno_1
#> -2.03877432 1.55444499
#> eff_expt_maturity_type_1 eff_expt_maturity_type_2
#> 0.66072953 -0.65520063
#> int_maturity_shape eff_maturity_shape_geno_1
#> -6.13510368 -12.66969959
#> int_ratio_expt_maturity eff_ratio_expt_maturity_geno_1
#> 9.21718291 6.29157951
#> eff_ratio_expt_maturity_type_1 eff_ratio_expt_maturity_type_2
#> 4.82061920 10.81747842
#> int_expt_reproduction eff_expt_reproduction_geno_1
#> -4.45837175 -5.55089666
#> int_pontn eff_pontn_geno_1
#> -7.93134379 -16.20606070
#> int_increase_death_hazard eff_increase_death_hazard_geno_1
#> 7.14071218 2.06010130
#> eff_increase_death_hazard_type_1 eff_increase_death_hazard_type_2
#> 2.45327099 -3.24686063
#> eff_increase_death_hazard_type_1:geno_1 eff_increase_death_hazard_type_2:geno_1
#> 0.05537952 0.48247027
#> int_tof_reduction_date eff_tof_reduction_date_geno_1
#> -5.98084468 4.27436871
#> int_increase_tof_n_offspring eff_increase_tof_n_offspring_geno_1
#> 0.70052182 7.73467571
#> int_lin_decrease_hazard eff_lin_decrease_hazard_geno_1
#> 2.66887494 -2.84465302
#> eff_lin_decrease_hazard_type_1 eff_lin_decrease_hazard_type_2
#> -2.97177934 3.88660973
#> eff_lin_decrease_hazard_type_1:geno_1 eff_lin_decrease_hazard_type_2:geno_1
#> -4.75747643 -0.28970093
#> int_quad_senescence eff_quad_senescence_geno_1
#> 2.49832143 -2.71133455
#> int_quad_decrease_hazard eff_quad_decrease_hazard_geno_1
#> -0.06403036 0.09121032
#> int_quad_change_n_offspring eff_quad_change_n_offspring_geno_1
#> 1.60524468 -0.07882676
#> int_tof_n_offspring
#> -0.26241118
library(lifelihood)
library(tidyverse)
df <- lifelihood::fakesample |>
mutate(
type = as.factor(type),
geno = as.factor(geno)
)
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
)
#> [1] "/private/var/folders/y6/nj790rtn62lfktb1sh__79hc0000gn/T/Rtmp2lbF6M/temp_libpath1e0a2a79ba80/lifelihood/bin/lifelihood/Users/runner/work/Lifelihood/Lifelihood/lifelihood_1_2_3_4/temp_file_data_lifelihood.txt /Users/runner/work/Lifelihood/Lifelihood/lifelihood_1_2_3_4/temp_param_range_path.txt FALSE 0 25 FALSE 0 0 0 1 2 3 4 10 20 1000 0.3 NULL 2 2 50 1 1 0.001"
#> lifelihood Pascal program status code 0
coeff(results, "expt_death")
#> int_expt_death eff_expt_death_geno_1 eff_expt_death_type_1
#> -17.7886945 -2.8970923 -4.4827929
#> eff_expt_death_type_2
#> -0.3009919