RERconverge : using Rconsole module to extract results + syntax error fix

app/wip.ml

@@ -13,7 +13,24 @@ let marines =
 let pipeline ~phenotypes =
   Codepi.Orthomam.rer_converge ~db ~phenotypes ()
 
+module Top = Bistro_utils.Toplevel_eval.Make(struct
+    let np = 10
+    let mem = 8 
+  end)()
+
+let result_table_script targets =
+  let open Codepi.R_console in
+  let assignments = 
+    List.map (fun (clade, target) ->
+      path (Codepi.Rer_converge.string_of_clade clade) Codepi.Orthomam.(target.result_table)
+    ) targets
+  in 
+  rconsole (module Top) "library(tidyverse)" assignments
+
 let () =
+    result_table_script (pipeline ~phenotypes:subterraneans)
+
+let main () =
   try
     let loggers = [ Bistro_utils.Console_logger.create () ] in
     let allowed_containers = [ `Docker ] in

lib/R/rer_converge.R

@@ -31,8 +31,7 @@ build_traits_paths <-
   function(phenotypes,
            gene_trees,
            is_continuous,
-           useSpecies = NULL,
-           clade = c("ancestral", "terminal", "all"))
+           clade)
   {
     if (is_continuous) {
       char2Paths(phenotypes, gene_trees)
@@ -40,7 +39,6 @@ build_traits_paths <-
       foreground2Tree(phenotypes,
                       gene_trees,
                       clade = clade,
-                      # useSpecies = useSpecies,
                       plot=F # FIXME : plot=T raises cryptic error
                       ) %>%
         tree2Paths(gene_trees)
@@ -54,7 +52,8 @@ results = lapply(clades, FUN=function(clade){
   traits_paths <- build_traits_paths(
     phenotypes,
     gene_trees,
-    is_continuous
+    is_continuous,
+    clade
   )
 
   res <- if (is_continuous) {