lmm_benchmark.ml 813 Bytes
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open Codepi

let benchmark d =
  let open Simulation_dataset in
  Utils.recall_precision_curve
    ~oracle:(oracle d)
    ~labels:[|"topological";"multinomial";"gemma_score";"tdg09"|]
    ~results:[
      topological d ;
      multinomial_asymptotic_lrt d ;
      gemma ~lmm_test:`Score ~relatedness_mode:`Standardized d ;
      tdg09 d ;
    ]

let () =
  let sim =
    let open Simulation_dataset in
    convdet_simulation
      ~tree:(NHX "example/trees4analyses_db/cyp_coding.Chrysithr_root.nhx")
      ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
      ~n_h0:100 ~n_ha:100 ~ne_s:(2., 2.) ()
  in
  let w = benchmark sim in
  let loggers = [ Bistro_utils.Console_logger.create () ] in
  Bistro_engine.Scheduler.simple_eval_exn ~loggers ~np:4 ~mem:(`GB 4) (Bistro.Workflow.path w)
  |> print_endline