Commit bbdd8e37 authored by Philippe Veber's avatar Philippe Veber
Browse files

Simulation_dataset: separate in-house simulation and bppseqgen's

parent 265897c0
This diff is collapsed.
...@@ -9,52 +9,18 @@ type tree = ...@@ -9,52 +9,18 @@ type tree =
branch_length2 : float; branch_length2 : float;
} }
type 's benchmark = {
method_labels : string list ;
method_outputs : float option array list ;
average_precision : (float * (float * float)) list ;
site_model : 's array ;
ancestral_counts : int Phylogenetics.Amino_acid.table array ;
convergent_counts : int Phylogenetics.Amino_acid.table array ;
}
module type S = sig module type S = sig
type t type query
type site_model
include Detection_pipeline.Query with type t := t include Detection_pipeline.S with type query := query
include Detection_pipeline.S with type query := t
val alignment_plot : t -> svg file val alignment_plot : query -> svg file
val benchmark : t -> text file list -> site_model benchmark workflow
val rds_of_benchmark : site_model benchmark workflow -> rds file
end end
type t module Mutsel : sig
include S
val bppseqgen_mixed :
?ne_s:float -> val query :
?seed:int ->
tree:tree ->
profiles:string ->
n_h0:int ->
n_ha:int ->
unit ->
t
val bppseqgen :
hyp:Convergence_hypothesis.t ->
tree:tree ->
profiles:string ->
nb_sites:int ->
seed:int ->
t
module Mutsel_param : sig
type t
val make :
?branch_scale:float -> ?branch_scale:float ->
?ne_s:float * float -> ?ne_s:float * float ->
?gBGC:float * float -> ?gBGC:float * float ->
...@@ -64,62 +30,86 @@ module Mutsel_param : sig ...@@ -64,62 +30,86 @@ module Mutsel_param : sig
n_h0:int -> n_h0:int ->
n_ha:int -> n_ha:int ->
unit -> unit ->
t query
val simulation : val simulation :
t -> query ->
Codepitk.Simulator.Site_independent_mutsel.simulation workflow Codepitk.Simulator.Site_independent_mutsel.simulation workflow
end
val mutsel :
?branch_scale:float ->
?ne_s:float * float ->
?gBGC:float * float ->
?seed:int ->
tree:tree ->
profiles:string ->
n_h0:int ->
n_ha:int ->
unit ->
t
val of_mutsel_param : Mutsel_param.t -> t type benchmark = {
method_labels : string list ;
method_outputs : float option array list ;
average_precision : (float * (float * float)) list ;
site_model : [`Convergent | `Non_convergent] array ;
ancestral_counts : int Phylogenetics.Amino_acid.table array ;
convergent_counts : int Phylogenetics.Amino_acid.table array ;
}
include Detection_pipeline.Query with type t := t
include Detection_pipeline.S with type query := t val benchmark_statistics :
Codepitk.Simulator.Site_independent_mutsel.simulation workflow ->
labels:string list ->
results:(text file * int) list ->
binary_file file
val oracle : t -> text file (* val benchmark : t -> (t -> text file) list -> benchmark workflow
*
* val rds_of_benchmark : benchmark workflow -> rds file *)
val alignment_plot : t -> svg file (** stuff for gbgc SBME paper *)
type gBGC_t =
| Global of float
| Convergent of float * float
val multinomial_benchmark : t -> pdf file type param_t
val benchmark : ?mode:[ `fast | `full ] -> t -> svg file val explore_params : f:(param_t -> 'a) -> ((float * gBGC_t) * 'a) list
val benchmark2 : t -> pdf file val simu_of_param : ?n_h0:int -> param_t -> query
val benchmark_statistics : val filter_results :
Codepitk.Simulator.Site_independent_mutsel.simulation workflow -> f:('a -> bool) -> (param_t * 'a) list -> (param_t * 'a) list
labels:string list ->
results:(text file * int) list ->
binary_file file
(** stuff for gbgc SBME paper *) type record_t
type gBGC_t =
| Global of float
| Convergent of float * float
type param_t val record_of_simu : query -> record_t workflow
val explore_params : f:(param_t -> 'a) -> ((float * gBGC_t) * 'a) list val realistic_result : record_t -> bool
end
val simu_of_param : ?n_h0:int -> param_t -> t module Bppseqgen : sig
type t
val filter_results : val bppseqgen_mixed :
f:('a -> bool) -> (param_t * 'a) list -> (param_t * 'a) list ?ne_s:float ->
?seed:int ->
tree:tree ->
profiles:string ->
n_h0:int ->
n_ha:int ->
unit ->
t
val bppseqgen :
hyp:Convergence_hypothesis.t ->
tree:tree ->
profiles:string ->
nb_sites:int ->
seed:int ->
t
type record_t include Detection_pipeline.Query with type t := t
include Detection_pipeline.S with type query := t
val oracle : t -> text file
val record_of_simu : t -> record_t workflow val alignment_plot : t -> svg file
val multinomial_benchmark : t -> pdf file
val realistic_result : record_t -> bool val benchmark : ?mode:[ `fast | `full ] -> t -> svg file
val benchmark2 : t -> pdf file
end
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