CamlPaml.PhyloEM: a bit of cleanup

lib/CamlPaml/PhyloEM.ml

@@ -134,21 +134,8 @@ let d_ell_dQ_dxi inst ss i =
 						tot := !tot +. ssbrab *. dPt_dxi_a.(b) /. pa.{b}
 	!tot
 
-let d_ell_dQ_dx inst ss = Array.init (Array.length (PM.P14n.p14n inst).PM.P14n.q_domains) (d_ell_dQ_dxi inst ss)
-
-(* numerical estimate - for debugging *)
-let nd_ell_dQ_dx inst ss =
-	let q_settings = PM.P14n.q_settings inst
-	let np = Array.length (PM.P14n.p14n inst).PM.P14n.q_domains
-	Array.init np
-		fun i ->
-			let f x =
-				let settings = Array.copy q_settings
-				settings.(i) <- x
-				let xinst =	PM.P14n.update ~q_settings:q_settings inst
-				ell (PM.P14n.model xinst) ss
-			let { Gsl_fun.res = res } = Gsl_diff.central f q_settings.(i)
-			res
+let d_ell_dQ_dx inst ss =
+	Array.init (Array.length (PM.P14n.p14n inst).PM.P14n.q_domains) (d_ell_dQ_dxi inst ss)
 
 let d_ell_dbranch inst br ss =
 	let m = PM.P14n.model inst

lib/CamlPaml/PhyloEM.mli

@@ -1,23 +1,29 @@
-(** supporting functions for estimating the parameters of phylogenetic models by expectation-maximization (EM) *)
+(** supporting functions for estimating the parameters of phylogenetic models by
+expectation-maximization (EM) *)
 
 (** {1 E-step} *)
 
-(** sufficient statistics for the E-step, composed of estimates of how many times each character-character substitution occurred on each branch of the tree (summed over all sites)
-*)
+(** sufficient statistics for the E-step, composed of estimates of how many times each
+character-character substitution occurred on each branch of the tree (summed over all sites) *)
 type sufficient_statistics = float array array array
 
 val new_sufficient_statistics : PhyloModel.t -> sufficient_statistics
 
-(** compute the E-step statistics for one site, given the leaves (as would be given to {{:PhyloModel}PhyloModel.prepare_lik}). Update the given [sufficient_statistics] and return the probability of the leaves under the model. This should be called for each site to collect the statistics for the whole alignment. *)
+(** compute the E-step statistics for one site, given the leaves (as would be given to
+{{:PhyloModel}PhyloModel.prepare_lik}). Update the given [sufficient_statistics] and return the
+probability of the leaves under the model. This should be called for each site to collect the
+statistics for the whole alignment. *)
 val collect_sufficient_statistics : ?workspace:PhyloLik.workspace -> PhyloModel.t -> PhyloLik.leaf array -> sufficient_statistics -> float
 
-(** any entry in the sufficient statistics less than [tol] is set to zero. useful if e.g. planning to compress the sufficient statistics for transport between compute nodes *)
+(** any entry in the sufficient statistics less than [tol] is set to zero. useful if e.g. planning
+to compress the sufficient statistics for transport between compute nodes *)
 val clean_sufficient_statistics : ?tol:float -> sufficient_statistics -> unit
 
 (** {1 M-step} *)
 
-(** expected log-likelihood of the model, where the expectation is over the soft assignment of the ancestral characters represented by the sufficient statistics of the E-step. (objective function of the M-step, sometimes called the Q function)
-*)
+(** expected log-likelihood of the model, where the expectation is over the soft assignment of the
+ancestral characters represented by the sufficient statistics of the E-step. (objective function of
+the M-step, sometimes called the Q function) *)
 val ell : PhyloModel.t -> sufficient_statistics -> float
 
 (** compute the portion of the ell arising from the prior over the ancestral sequence *)
@@ -29,16 +35,15 @@ val branches_ell : PhyloModel.t -> sufficient_statistics -> float
 (** compute the portion of the ell arising from the substitutions on a specific branch*)
 val branch_ell : PhyloModel.t -> sufficient_statistics -> int -> float
 
-(** compute the gradient of the ell with respect to the variables in the model's rate matrix p14n, based on their symbolic expressions *)
+(** compute the gradient of the ell with respect to the variables in the model's rate matrix p14n,
+based on their symbolic expressions *)
 val d_ell_dQ_dx : PhyloModel.P14n.instance -> sufficient_statistics -> float array
 
-(** numerically estimate the same *)
-val nd_ell_dQ_dx : PhyloModel.P14n.instance -> sufficient_statistics -> float array
-
-(** compute the derivative with respect to one specific rate matrix variable only *)
+(** compute the partial derivative with respect to one specific rate matrix variable only *)
 val d_ell_dQ_dxi : PhyloModel.P14n.instance -> sufficient_statistics -> int -> float
 
-(** compute the gradient with respect to the variables in the model's p14n for branch lengths, based on their symbolic expressions*)
+(** compute the gradient with respect to the variables in the model's p14n for branch lengths, based
+on their symbolic expressions*)
 val d_ell_dtree : PhyloModel.P14n.instance -> sufficient_statistics -> float array
 
 (** compute the derivative with respect to one specific branch length variable only *)