app/Lmm_benchmark: cleanup

app/lmm_benchmark.ml

@@ -60,8 +60,8 @@ let meth ?(requires_rooted_tree = false) f label =
   { f ; label ; requires_rooted_tree }
 
 let methods = Pipeline.[
-  (* meth tdg09 "tdg09" ;
-  meth pcoc "pcoc" ; *)
+  meth tdg09 "tdg09" ;
+  (* meth pcoc "pcoc" ; *)
   (* meth pcoc_v2 ~col:3 "pcoc v2" ; *)
   meth (gemma ~lmm_test:`Score ~relatedness_mode:`Standardized) "gemma" ;
   meth inhouse_lmm "LMM" ;
@@ -74,7 +74,7 @@ let benchmark_rds ?(seed = 42) { tree = t ; rooted ; ne_s ; branch_scale ; _ } =
   let q =
     Pipeline.query ~seed ~tree:(NHX t) ~branch_scale ~ne_s
       ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
-      ~n_h0:900 ~n_ha:100 ()
+      ~n_h0:9000 ~n_ha:1000 ()
   in
   let methods =
     List.filter_map methods ~f:(fun m ->
@@ -88,8 +88,7 @@ let benchmark_rds ?(seed = 42) { tree = t ; rooted ; ne_s ; branch_scale ; _ } =
 
 let () =
   let open Bistro_utils.Repo in
-  (* let datasets = [ besnard2009 ; rubisco ; oneline_rodent ; orthomam_echolocation ] in *)
-  let datasets = [ besnard2009 ] in
+  let datasets = [ besnard2009 ; rubisco ; oneline_rodent ; orthomam_echolocation ] in
   let repo =
     List.map datasets ~f:(fun d ->
         item [d.label ^ ".rds"] (benchmark_rds d)