refactoring

bin/gargantext-phylo/Main.hs

@@ -152,7 +152,7 @@ seaToLabel config = case (seaElevation config) of
 
 
 sensToLabel :: PhyloConfig -> [Char]
-sensToLabel config = case (phyloProximity config) of
+sensToLabel config = case (similarity config) of
       Hamming _ _ -> undefined
       WeightedLogJaccard s _ -> ("WeightedLogJaccard_"  <> show s)
       WeightedLogSim s _ -> ( "WeightedLogSim-sens_"  <> show s)

src/Gargantext/Core/Viz/Phylo.hs

@@ -71,7 +71,7 @@ data SeaElevation =
 
 instance ToSchema SeaElevation
 
-data Proximity =
+data Similarity =
       WeightedLogJaccard
       { _wlj_sensibility     :: Double
       , _wlj_minSharedNgrams :: Int }
@@ -84,7 +84,7 @@ data Proximity =
 
     deriving (Show,Generic,Eq)
 
-instance ToSchema Proximity where
+instance ToSchema Similarity where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 
 
@@ -179,7 +179,7 @@ data PhyloConfig =
             , listParser     :: ListParser
             , phyloName      :: Text
             , phyloScale     :: Int
-            , phyloProximity :: Proximity
+            , similarity     :: Similarity
             , seaElevation   :: SeaElevation
             , findAncestors  :: Bool
             , phyloSynchrony :: Synchrony
@@ -205,7 +205,7 @@ data PhyloSubConfig =
 
 
 subConfig2config :: PhyloSubConfig -> PhyloConfig
-subConfig2config subConfig = defaultConfig { phyloProximity = WeightedLogJaccard (_sc_phyloProximity subConfig) 1 
+subConfig2config subConfig = defaultConfig { similarity     = WeightedLogJaccard (_sc_phyloProximity subConfig) 1 
                                            , phyloSynchrony = ByProximityThreshold (_sc_phyloSynchrony subConfig) 0 AllBranches MergeAllGroups
                                            , phyloQuality   = Quality (_sc_phyloQuality   subConfig) 1
                                            , timeUnit       = _sc_timeUnit       subConfig
@@ -223,7 +223,7 @@ defaultConfig =
             , listParser     = V4
             , phyloName      = pack "Phylo Name"
             , phyloScale     = 2
-            , phyloProximity = WeightedLogJaccard 0.5 1
+            , similarity     = WeightedLogJaccard 0.5 1
             , seaElevation   = Constante 0.1 0.1
             , findAncestors  = False
             , phyloSynchrony = ByProximityThreshold 0.5 0 AllBranches MergeAllGroups
@@ -251,8 +251,8 @@ instance ToJSON CorpusParser
 instance FromJSON ListParser
 instance ToJSON ListParser
 
-instance FromJSON Proximity
-instance ToJSON Proximity
+instance FromJSON Similarity
+instance ToJSON Similarity
 
 instance FromJSON SeaElevation
 instance ToJSON SeaElevation
@@ -592,7 +592,7 @@ instance ToSchema PhyloExport where
 
 makeLenses ''PhyloConfig
 makeLenses ''PhyloSubConfig
-makeLenses ''Proximity
+makeLenses ''Similarity
 makeLenses ''SeaElevation
 makeLenses ''Quality
 makeLenses ''Cluster

src/Gargantext/Core/Viz/Phylo/PhyloExport.hs

@@ -25,7 +25,7 @@ import Data.Vector (Vector)
 import Debug.Trace (trace)
 import Gargantext.Core.Viz.Phylo
 import Gargantext.Core.Viz.Phylo.PhyloTools
-import Gargantext.Core.Viz.Phylo.TemporalMatching (filterDocs, filterDiago, reduceDiagos, toProximity, getNextPeriods)
+import Gargantext.Core.Viz.Phylo.TemporalMatching (filterDocs, filterDiago, reduceDiagos, toSimilarity, getNextPeriods)
 import Gargantext.Prelude hiding (scale)
 import Prelude (writeFile)
 import System.FilePath
@@ -288,9 +288,9 @@ exportToDot phylo export =
         {-  8) create the edges between the branches
         -- _ <- mapM (\(bId,bId') ->
         --         toDotEdge (branchIdToDotId bId) (branchIdToDotId bId')
-        --         (Text.pack $ show(branchIdsToProximity bId bId'
-        --                             (getThresholdInit $ phyloProximity $ getConfig phylo)
-        --                             (getThresholdStep $ phyloProximity $ getConfig phylo))) BranchToBranch
+        --         (Text.pack $ show(branchIdsToSimilarity bId bId'
+        --                             (getThresholdInit $ phyloSimilarity $ getConfig phylo)
+        --                             (getThresholdStep $ phyloSimilarity $ getConfig phylo))) BranchToBranch
         --     ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ map _branch_id $ export ^. export_branches
         -}
 
@@ -595,23 +595,23 @@ getGroupThr step g =
         breaks = (g ^. phylo_groupMeta) ! "breaks"
      in (last' "export" (take (round $ (last' "export" breaks) + 1) seaLvl)) - step
 
-toAncestor :: Double -> Map Int Double -> Proximity -> Double -> [PhyloGroup] -> PhyloGroup -> PhyloGroup
-toAncestor nbDocs diago proximity step candidates ego =
+toAncestor :: Double -> Map Int Double -> Similarity -> Double -> [PhyloGroup] -> PhyloGroup -> PhyloGroup
+toAncestor nbDocs diago similarity step candidates ego =
   let curr = ego ^. phylo_groupAncestors
    in ego & phylo_groupAncestors .~ (curr ++ (map (\(g,w) -> (getGroupId g,w))
          $ filter (\(g,w) -> (w > 0) && (w >= (min (getGroupThr step ego) (getGroupThr step g))))
-         $ map (\g -> (g, toProximity nbDocs diago proximity (ego ^. phylo_groupNgrams) (g ^. phylo_groupNgrams) (g ^. phylo_groupNgrams)))
+         $ map (\g -> (g, toSimilarity nbDocs diago similarity (ego ^. phylo_groupNgrams) (g ^. phylo_groupNgrams) (g ^. phylo_groupNgrams)))
          $ filter (\g -> g ^. phylo_groupBranchId /= ego ^. phylo_groupBranchId ) candidates))
 
 
-headsToAncestors :: Double -> Map Int Double -> Proximity -> Double -> [PhyloGroup] -> [PhyloGroup] -> [PhyloGroup]
-headsToAncestors nbDocs diago proximity step heads acc =
+headsToAncestors :: Double -> Map Int Double -> Similarity -> Double -> [PhyloGroup] -> [PhyloGroup] -> [PhyloGroup]
+headsToAncestors nbDocs diago similarity step heads acc =
   if (null heads)
     then acc
     else
       let ego    = head' "headsToAncestors" heads
           heads' = tail' "headsToAncestors" heads
-       in headsToAncestors nbDocs diago proximity step heads' (acc ++ [toAncestor nbDocs diago proximity step heads' ego])
+       in headsToAncestors nbDocs diago similarity step heads' (acc ++ [toAncestor nbDocs diago similarity step heads' ego])
 
 
 toHorizon :: Phylo -> Phylo
@@ -645,13 +645,13 @@ toHorizon phylo =
           noHeads = groups \\ heads
           nbDocs  = sum $ elems  $ filterDocs  (phylo ^. phylo_timeDocs) [prd]
           diago   = reduceDiagos $ filterDiago (phylo ^. phylo_timeCooc) [prd]
-          proximity = (phyloProximity $ getConfig phylo)
+          sim     = (similarity $ getConfig phylo)
           step = case getSeaElevation phylo of
             Constante  _ s -> s
             Adaptative _ -> 0
-       -- in headsToAncestors nbDocs diago proximity heads groups []
-       in map (\ego -> toAncestor nbDocs diago proximity step noHeads ego)
-        $ headsToAncestors nbDocs diago proximity step heads []
+       -- in headsToAncestors nbDocs diago Similarity heads groups []
+       in map (\ego -> toAncestor nbDocs diago sim step noHeads ego)
+        $ headsToAncestors nbDocs diago sim step heads []
       ) periods
     -- | 3) process this task concurrently
     newGroups :: [[PhyloGroup]]

src/Gargantext/Core/Viz/Phylo/PhyloMaker.hs

@@ -31,10 +31,11 @@ import Gargantext.Core.Viz.Phylo
 import Gargantext.Core.Viz.Phylo.PhyloExport (toHorizon)
 import Gargantext.Core.Viz.Phylo.PhyloTools
 import Gargantext.Core.Viz.Phylo.SynchronicClustering (synchronicClustering)
-import Gargantext.Core.Viz.Phylo.TemporalMatching (temporalMatching, getNextPeriods, filterDocs, filterDiago, reduceDiagos, toProximity)
+import Gargantext.Core.Viz.Phylo.TemporalMatching (temporalMatching, getNextPeriods, filterDocs, filterDiago, reduceDiagos, toSimilarity)
 import Gargantext.Prelude
 
 import qualified Data.Set as Set
+import qualified Data.List as List
 import qualified Data.Vector as Vector
 
 ------------------
@@ -78,6 +79,13 @@ toPhylo phylowithoutLink = trace ("# flatPhylo groups " <> show(length $ getGrou
 -----------------------------
 
 
+{- 
+-- create a square ladder
+-}
+squareLadder :: [Double] -> [Double]
+squareLadder ladder = List.map (\x -> x * x) ladder
+
+
 {- 
 -- create an adaptative diachronic 'sea elevation' ladder
 -}
@@ -107,7 +115,7 @@ constDiachronicLadder curr step ladder =
 -}
 scanSimilarity :: Scale -> Phylo -> Phylo
 scanSimilarity lvl phylo = 
-  let proximity = phyloProximity $ getConfig phylo
+  let proximity = similarity $ getConfig phylo
       scanning  = foldlWithKey (\acc pId pds -> 
                       -- 1) process period by period
                       let egos = map (\g -> (getGroupId g, g ^. phylo_groupNgrams))
@@ -124,7 +132,7 @@ scanSimilarity lvl phylo =
                                         map (\(id',ngrams') -> 
                                             let nbDocs = (sum . elems) $ filterDocs docs    ([idToPrd id, idToPrd id'])
                                                 diago  = reduceDiagos  $ filterDiago diagos ([idToPrd id, idToPrd id'])
-                                             in ((id,id'),toProximity nbDocs diago proximity ngrams ngrams' ngrams')
+                                             in ((id,id'),toSimilarity nbDocs diago proximity ngrams ngrams' ngrams')
                                         ) $ filter (\(_,ngrams') -> (not . null) $ intersect ngrams ngrams') targets 
                                  ) egos
                           pairs' = pairs `using` parList rdeepseq
@@ -173,7 +181,7 @@ clusterToGroup fis pId pId' lvl idx coocs = PhyloGroup pId pId' lvl idx ""
 addTemporalLinksToPhylo :: Phylo -> Phylo
 addTemporalLinksToPhylo phylowithoutLink = case strategy of 
     Constante start gap -> temporalMatching (constDiachronicLadder start gap Set.empty) phylowithoutLink
-    Adaptative steps    -> temporalMatching (adaptDiachronicLadder steps (phylowithoutLink ^. phylo_diaSimScan) Set.empty) phylowithoutLink
+    Adaptative steps    -> temporalMatching (squareLadder $ adaptDiachronicLadder steps (phylowithoutLink ^. phylo_diaSimScan) Set.empty) phylowithoutLink
   where
     strategy :: SeaElevation
     strategy = getSeaElevation phylowithoutLink

src/Gargantext/Core/Viz/Phylo/PhyloTools.hs

@@ -330,16 +330,16 @@ getPeriodPointers fil g =
         ToChildsMemory  -> undefined
         ToParentsMemory -> undefined
 
-filterProximity :: Proximity -> Double -> Double -> Bool
-filterProximity proximity thr local =
-    case proximity of
+filterSimilarity :: Similarity -> Double -> Double -> Bool
+filterSimilarity similarity thr local =
+    case similarity of
         WeightedLogJaccard _ _ -> local >= thr
         WeightedLogSim     _ _ -> local >= thr
         Hamming            _ _ -> undefined
 
-getProximityName :: Proximity -> String
-getProximityName proximity =
-    case proximity of
+getSimilarityName :: Similarity -> String
+getSimilarityName similarity =
+    case similarity of
         WeightedLogJaccard _ _ -> "WLJaccard"
         WeightedLogSim     _ _ -> "WeightedLogSim"
         Hamming            _ _ -> "Hamming"
@@ -578,16 +578,16 @@ traceSynchronyStart phylo =
 
 
 -------------------
--- | Proximity | --
+-- | Similarity | --
 -------------------
 
-getSensibility :: Proximity -> Double
+getSensibility :: Similarity -> Double
 getSensibility proxi = case proxi of
     WeightedLogJaccard s _ -> s
     WeightedLogSim     s _ -> s
     Hamming            _ _ -> undefined
 
-getMinSharedNgrams :: Proximity -> Int
+getMinSharedNgrams :: Similarity -> Int
 getMinSharedNgrams proxi = case proxi of
     WeightedLogJaccard _ m -> m
     WeightedLogSim     _ m -> m
@@ -605,8 +605,8 @@ intersectInit acc lst lst' =
          then intersectInit (acc ++ [head' "intersectInit" lst]) (tail lst) (tail lst')
          else acc
 
-branchIdsToProximity :: PhyloBranchId -> PhyloBranchId -> Double -> Double -> Double
-branchIdsToProximity id id' thrInit thrStep = thrInit + thrStep * (fromIntegral $ length $ intersectInit [] (snd id) (snd id'))
+branchIdsToSimilarity :: PhyloBranchId -> PhyloBranchId -> Double -> Double -> Double
+branchIdsToSimilarity id id' thrInit thrStep = thrInit + thrStep * (fromIntegral $ length $ intersectInit [] (snd id) (snd id'))
 
 ngramsInBranches :: [[PhyloGroup]] -> [Int]
 ngramsInBranches branches = nub $ foldl (\acc g -> acc ++ (g ^. phylo_groupNgrams)) [] $ concat branches
@@ -662,4 +662,4 @@ traceTemporalMatching groups =
 
 traceGroupsProxi :: [Double] -> [Double]
 traceGroupsProxi l =
-    trace ( "\n" <> "-- | " <> show(List.length l) <> " computed pairs of groups proximity" <> "\n") l
+    trace ( "\n" <> "-- | " <> show(List.length l) <> " computed pairs of groups Similarity" <> "\n") l

src/Gargantext/Core/Viz/Phylo/SynchronicClustering.hs

@@ -124,7 +124,7 @@ toDiamonds groups = foldl' (\acc groups' ->
                   $ foldl' (\acc g -> acc ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodParents)  ) [] groups
 
 
-groupsToEdges :: Proximity -> Synchrony -> Double -> Map Int Double -> [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)]
+groupsToEdges :: Similarity -> Synchrony -> Double -> Map Int Double -> [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)]
 groupsToEdges prox sync nbDocs diago groups =
     case sync of
         ByProximityThreshold  thr sens _ strat ->
@@ -153,7 +153,7 @@ toParentId :: PhyloGroup -> PhyloGroupId
 toParentId child = ((child ^. phylo_groupPeriod, child ^. phylo_groupScale + 1), child ^. phylo_groupIndex) 
 
 
-reduceGroups :: Proximity -> Synchrony -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
+reduceGroups :: Similarity -> Synchrony -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
 reduceGroups prox sync docs diagos branch =
     --  1) reduce a branch as a set of periods & groups
     let periods = fromListWith (++)
@@ -197,7 +197,7 @@ levelUpAncestors groups =
 
 synchronicClustering :: Phylo -> Phylo
 synchronicClustering phylo =
-    let prox = phyloProximity $ getConfig phylo
+    let prox = similarity $ getConfig phylo
         sync = phyloSynchrony $ getConfig phylo
         docs = phylo ^. phylo_timeDocs
         diagos = map coocToDiago $ phylo ^. phylo_timeCooc

src/Gargantext/Core/Viz/Phylo/TemporalMatching.hs

@@ -119,9 +119,9 @@ weightedLogSim' sens nbDocs diago ego_ngrams target_ngrams
 {- 
 -- perform a seamilarity measure between a given group and a pair of targeted groups
 -}
-toProximity :: Double -> Map Int Double -> Proximity -> [Int] -> [Int] -> [Int] -> Double
-toProximity nbDocs diago proximity egoNgrams targetNgrams targetNgrams' =
-  case proximity of
+toSimilarity :: Double -> Map Int Double -> Similarity -> [Int] -> [Int] -> [Int] -> Double
+toSimilarity nbDocs diago similarity egoNgrams targetNgrams targetNgrams' =
+  case similarity of
     WeightedLogJaccard sens _ ->
       let pairNgrams = if targetNgrams == targetNgrams'
                           then targetNgrams
@@ -147,7 +147,7 @@ findLastPeriod fil periods = case fil of
     ToChildsMemory  -> undefined
     ToParentsMemory -> undefined
 
-removeOldPointers :: [Pointer] -> Filiation -> Double -> Proximity -> Period
+removeOldPointers :: [Pointer] -> Filiation -> Double -> Similarity -> Period
                   -> [((PhyloGroupId,[Int]),(PhyloGroupId,[Int]))]
                   -> [((PhyloGroupId,[Int]),(PhyloGroupId,[Int]))]
 removeOldPointers oldPointers fil thr prox prd pairs
@@ -166,11 +166,11 @@ removeOldPointers oldPointers fil thr prox prd pairs
                                || (((fst . fst . fst) id') > (fst lastMatchedPrd))) pairs
   | otherwise = []
 
-filterPointers :: Proximity -> Double -> [Pointer] -> [Pointer]
-filterPointers proxi thr pts = filter (\(_,w) -> filterProximity proxi thr w) pts
+filterPointers :: Similarity -> Double -> [Pointer] -> [Pointer]
+filterPointers proxi thr pts = filter (\(_,w) -> filterSimilarity proxi thr w) pts
 
-filterPointers' :: Proximity -> Double -> [(Pointer,[Int])] -> [(Pointer,[Int])]
-filterPointers' proxi thr pts = filter (\((_,w),_) -> filterProximity proxi thr w) pts
+filterPointers' :: Similarity -> Double -> [(Pointer,[Int])] -> [(Pointer,[Int])]
+filterPointers' proxi thr pts = filter (\((_,w),_) -> filterSimilarity proxi thr w) pts
 
 
 reduceDiagos :: Map Date Cooc -> Map Int Double
@@ -231,7 +231,7 @@ groupsToBranches groups =
 {- 
 -- find the best pair/singleton of parents/childs for a given group
 -}
-makePairs :: (PhyloGroupId,[Int]) -> [(PhyloGroupId,[Int])] -> [Period] -> [Pointer] -> Filiation -> Double -> Proximity
+makePairs :: (PhyloGroupId,[Int]) -> [(PhyloGroupId,[Int])] -> [Period] -> [Pointer] -> Filiation -> Double -> Similarity
            -> Map Date Double -> Map Date Cooc -> [((PhyloGroupId,[Int]),(PhyloGroupId,[Int]))]
 makePairs (egoId, egoNgrams) candidates periods oldPointers fil thr prox docs diagos =
     if (null periods)
@@ -248,7 +248,7 @@ makePairs (egoId, egoNgrams) candidates periods oldPointers fil thr prox docs di
                     $ filter (\(id,ngrams) ->
                           let nbDocs = (sum . elems) $ filterDocs docs    ([(fst . fst) egoId, (fst . fst) id])
                               diago  = reduceDiagos  $ filterDiago diagos ([(fst . fst) egoId, (fst . fst) id])
-                           in (toProximity nbDocs diago prox egoNgrams egoNgrams ngrams) >= thr
+                           in (toSimilarity nbDocs diago prox egoNgrams egoNgrams ngrams) >= thr
                       ) candidates
       --------------------------------------
       lastPrd :: Period
@@ -258,7 +258,7 @@ makePairs (egoId, egoNgrams) candidates periods oldPointers fil thr prox docs di
 {- 
 -- find the best temporal links between a given group and its parents/childs
 -}
-phyloGroupMatching :: [[(PhyloGroupId,[Int])]] -> Filiation -> Proximity -> Map Date Double -> Map Date Cooc
+phyloGroupMatching :: [[(PhyloGroupId,[Int])]] -> Filiation -> Similarity -> Map Date Double -> Map Date Cooc
                    -> Double -> [Pointer] -> (PhyloGroupId,[Int]) -> [Pointer]
 phyloGroupMatching candidates filiation proxi docs diagos thr oldPointers (id,ngrams) =
         if (null $ filterPointers proxi thr oldPointers)
@@ -266,10 +266,10 @@ phyloGroupMatching candidates filiation proxi docs diagos thr oldPointers (id,ng
           then if null nextPointers
             then []
             else filterPointersByPeriod filiation
-               -- 2) keep only the best set of pointers grouped by proximity
+               -- 2) keep only the best set of pointers grouped by Similarity
                $ head' "phyloGroupMatching"
                $ groupBy (\pt pt' -> (snd . fst) pt == (snd . fst) pt')
-               -- 1) find the first time frame where at leats one pointer satisfies the proximity threshold
+               -- 1) find the first time frame where at leats one pointer satisfies the Similarity threshold
                $ sortBy (comparing (Down . snd . fst)) $ head' "pointers" nextPointers
         else oldPointers
     where
@@ -277,29 +277,29 @@ phyloGroupMatching candidates filiation proxi docs diagos thr oldPointers (id,ng
         nextPointers = take 1
                  -- stop as soon as we find a time frame where at least one singleton / pair satisfies the threshold 
                  $ dropWhile (null)
-                 -- for each time frame, process the proximity on relevant pairs of targeted groups
+                 -- for each time frame, process the Similarity on relevant pairs of targeted groups
                  $ scanl (\acc targets ->
                             let periods = nub $ map (fst . fst . fst) targets
                                 lastPrd = findLastPeriod filiation periods
                                 nbdocs  = sum $ elems $ (filterDocs docs ([(fst . fst) id] ++ periods))
                                 diago   = reduceDiagos
                                         $ filterDiago diagos ([(fst . fst) id] ++ periods)
-                                singletons = processProximity nbdocs diago $ map (\g -> (g,g)) $ filter (\g -> (fst . fst . fst) g == lastPrd) targets
+                                singletons = processSimilarity nbdocs diago $ map (\g -> (g,g)) $ filter (\g -> (fst . fst . fst) g == lastPrd) targets
                                 pairs = makePairs (id,ngrams) targets periods oldPointers filiation thr proxi docs diagos
                             in 
                               if (null singletons) 
-                                then acc ++ ( processProximity nbdocs diago pairs )
+                                then acc ++ ( processSimilarity nbdocs diago pairs )
                                 else acc ++ singletons
                           ) [] $ map concat $ inits candidates -- groups from [[1900],[1900,1901],[1900,1901,1902],...] 
         -----------------------------
-        processProximity :: Double -> Map Int Double -> [((PhyloGroupId,[Int]),(PhyloGroupId,[Int]))] -> [(Pointer,[Int])]
-        processProximity nbdocs diago targets =  filterPointers' proxi thr
+        processSimilarity :: Double -> Map Int Double -> [((PhyloGroupId,[Int]),(PhyloGroupId,[Int]))] -> [(Pointer,[Int])]
+        processSimilarity nbdocs diago targets =  filterPointers' proxi thr
                                         $ concat
                                         $ map (\(c,c') ->
-                                            let proximity = toProximity nbdocs diago proxi ngrams (snd c) (snd c')
+                                            let similarity = toSimilarity nbdocs diago proxi ngrams (snd c) (snd c')
                                             in if ((c == c') || (snd c == snd c'))
-                                               then [((fst c,proximity),snd c)]
-                                               else [((fst c,proximity),snd c),((fst c',proximity),snd c')] ) targets    
+                                               then [((fst c,similarity),snd c)]
+                                               else [((fst c,similarity),snd c),((fst c',similarity),snd c')] ) targets    
 
 
 {- 
@@ -329,8 +329,8 @@ getCandidates minNgrams ego targets =
 {- 
 -- set up and start performing the upstream/downstream inter‐temporal matching period by period
 -}
-reconstructTemporalLinks :: Int -> [Period] -> Proximity -> Double -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
-reconstructTemporalLinks frame periods proximity thr docs coocs groups =
+reconstructTemporalLinks :: Int -> [Period] -> Similarity -> Double -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
+reconstructTemporalLinks frame periods similarity thr docs coocs groups =
   let groups' = groupByField _phylo_groupPeriod groups
    in foldl' (\acc prd ->
         let -- 1) find the parents/childs matching periods
@@ -347,9 +347,9 @@ reconstructTemporalLinks frame periods proximity thr docs coocs groups =
             diagoChi = filterDiago (map coocToDiago coocs) ([prd] ++ periodsPar)
             --  5) match in parallel all the groups (egos) to their possible candidates
             egos  = map (\ego ->
-                      let pointersPar = phyloGroupMatching (getCandidates (getMinSharedNgrams proximity) ego candidatesPar) ToParents proximity docsPar diagoPar
+                      let pointersPar = phyloGroupMatching (getCandidates (getMinSharedNgrams similarity) ego candidatesPar) ToParents similarity docsPar diagoPar
                                         thr (getPeriodPointers ToParents ego) (getGroupId ego, ego ^. phylo_groupNgrams)
-                          pointersChi = phyloGroupMatching (getCandidates (getMinSharedNgrams proximity) ego candidatesChi) ToChilds  proximity docsChi diagoChi
+                          pointersChi = phyloGroupMatching (getCandidates (getMinSharedNgrams similarity) ego candidatesChi) ToChilds  similarity docsChi diagoChi
                                         thr (getPeriodPointers ToChilds  ego) (getGroupId ego, ego ^. phylo_groupNgrams)
                        in addPointers ToChilds  TemporalPointer pointersChi
                         $ addPointers ToParents TemporalPointer pointersPar
@@ -364,7 +364,7 @@ reconstructTemporalLinks frame periods proximity thr docs coocs groups =
 {- 
 -- reconstruct a phylomemetic network from a list of groups and from a given threshold
 -}
-toPhylomemeticNetwork :: Int -> [Period] -> Proximity -> Double -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [Branch]
+toPhylomemeticNetwork :: Int -> [Period] -> Similarity -> Double -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [Branch]
 toPhylomemeticNetwork timescale periods similarity thr docs coocs groups = 
   groupsToBranches $ fromList $ map (\g -> (getGroupId g, g))
                    $ reconstructTemporalLinks timescale periods similarity thr docs coocs groups
@@ -523,7 +523,7 @@ thrToMeta thr branches =
 -- done = all the already separated branches
 -- rest = all the branches we still have to separate
 -}
-separateBranches :: Double -> Proximity -> Double -> Map Int Double -> Int -> Double -> Double
+separateBranches :: Double -> Similarity -> Double -> Map Int Double -> Int -> Double -> Double
               -> Int -> Map Date Double -> Map Date Cooc -> [Period] 
               -> [(Branch,ShouldTry)] -> (Branch,ShouldTry) -> [(Branch,ShouldTry)] 
               -> [(Branch,ShouldTry)]
@@ -578,13 +578,13 @@ separateBranches fdt similarity lambda frequency minBranch thr rise timescale do
 {- 
 -- perform the sea-level rise algorithm, browse the similarity ladder and check that we can try out the next step
 -}
-seaLevelRise :: Double -> Proximity -> Double -> Int -> Map Int Double 
+seaLevelRise :: Double -> Similarity -> Double -> Int -> Map Int Double 
              -> [Double] -> Double
              -> Int -> [Period] 
              -> Map Date Double -> Map Date Cooc 
              -> [(Branch,ShouldTry)] 
              -> ([(Branch,ShouldTry)],FinalQuality)
-seaLevelRise fdt proximity lambda minBranch frequency ladder rise frame periods docs coocs branches =
+seaLevelRise fdt similarity lambda minBranch frequency ladder rise frame periods docs coocs branches =
   -- if the ladder is empty or thr > 1 or there is no branch to break then stop
   if (null ladder) || ((List.head ladder) > 1) || (stopRise branches)
     then (branches, toPhyloQuality fdt lambda frequency (map fst branches))
@@ -596,9 +596,9 @@ seaLevelRise fdt proximity lambda minBranch frequency ladder rise frame periods
                                              <> " ξ = " <> printf "%.5f" (globalAccuracy frequency (map fst branches))
                                              <> " ρ = " <> printf "%.5f" (globalRecall frequency (map fst branches))
                                              <> " branches = " <> show(length branches))
-                     $ separateBranches fdt proximity lambda frequency minBranch thr rise frame docs coocs periods
+                     $ separateBranches fdt similarity lambda frequency minBranch thr rise frame docs coocs periods
                                      [] (List.head branches)  (List.tail branches)
-       in seaLevelRise fdt proximity lambda minBranch frequency (List.tail ladder) (rise + 1) frame periods docs coocs branches'
+       in seaLevelRise fdt similarity lambda minBranch frequency (List.tail ladder) (rise + 1) frame periods docs coocs branches'
   where 
     --------
     stopRise :: [(Branch,ShouldTry)] -> Bool
@@ -624,7 +624,7 @@ temporalMatching ladder phylo = updatePhyloGroups 1
     ---  2) process the temporal matching by elevating the similarity ladder
     sea :: ([(Branch,ShouldTry)],FinalQuality)
     sea = seaLevelRise (fromIntegral $ Vector.length $ getRoots phylo)
-                                (phyloProximity $ getConfig phylo)
+                                (similarity $ getConfig phylo)
                                 (_qua_granularity $ phyloQuality $ getConfig phylo)
                                 (_qua_minBranch $ phyloQuality $ getConfig phylo)
                                 (phylo ^. phylo_termFreq)
@@ -641,7 +641,7 @@ temporalMatching ladder phylo = updatePhyloGroups 1
     seabed = map (\b -> (b,(length $ nub $ map _phylo_groupPeriod b) >= (_qua_minBranch $ phyloQuality $ getConfig phylo)))
            $ toPhylomemeticNetwork (getTimeFrame $ timeUnit $ getConfig phylo)
                          (getPeriodIds phylo)
-                         (phyloProximity $ getConfig phylo)
+                         (similarity $ getConfig phylo)
                          (List.head ladder)
                          (phylo ^. phylo_timeDocs)
                          (phylo ^. phylo_timeCooc)