Function reference
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Azores - Birds of Azores archipelago
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Azores_alt_m - Birds of Azores archipelago with alternative mainland species pool size
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bootstrap() - Runs a bootstrapping on a DAISIE model to determine parameter precision
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bootstrap_lr() - Runs a parameteric bootstrapping likelihood ratio test on two DAISIE models
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calc_bic() - Compute Bayesian Information Criterion of a model
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calc_loglik_ratio() - Calculates the loglikelihood ratio between two models
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calc_p_value() - Calculates p-value for rejecting a model from a distribution of likelihood ratios
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calc_power() - Calculates power to detect the true model
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calc_sim_metrics() - Calculates summary metrics from a simulation
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check_rep_seeds() - Checks if jobs were run with the same seed
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check_rep_seeds_depr() - Checks if jobs were run with the same seed on older logs
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choose_best_model() - From multiple seeds, choose the best model fit
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create_output_folder() - Create output folder
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create_results_dir_path() - Create results directory path
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is_on_cluster() - Check if code is running on Hábrók HPCC
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plot_bootstrap_results() - Computes summary results of bootstrap simulations useful for plotting
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plot_sim_metrics() - Plots metrics from simulations
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print_metadata() - Print session and run info to console/log file
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read_model_results() - Reads
run_daisie_ml()results
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run_daisie_2type_ml() - Run 2 type DAISIE analysis
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run_daisie_ml() - Run DAISIE analysis
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run_sim() - Runs a DAISIE simulation
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sensitivity() - Read the results of
run_daisie_ml()and compares model selection
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setup_2type_model() - Set up DAISIE_ML arguments
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setup_model() - Set up DAISIE_ML arguments
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setup_std_pars2() - Fills pars2 vector for most common DAISIE ML CS runs
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summarize_bootstrap_results() - Computes summary results of bootstrap simulations useful for plotting