src/Gargantext/Core/Viz/Phylo.hs

   1 {-
   2 Module      : Gargantext.Core.Viz.AdaptativePhylo
   3 Description : Phylomemy definitions and types.
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 Specifications of Phylomemy export format.
  11
  12 Phylomemy can be described as a Temporal Graph with different scale of
  13 granularity of group of ngrams (terms and multi-terms).
  14
  15 The main type is Phylo which is synonym of Phylomemy (only difference is
  16 the number of chars).
  17
  18 References:
  19 Chavalarias, D., Cointet, J.-P., 2013. Phylomemetic patterns
  20 in science evolution — the rise and fall of scientific fields. PloS
  21 one 8, e54847.
  22 -}
  23
  24 {-# LANGUAGE DeriveAnyClass   #-}
  25 {-# LANGUAGE TemplateHaskell   #-}
  26
  27 module Gargantext.Core.Viz.Phylo where
  28
  29 import Control.DeepSeq (NFData)
  30 import Control.Lens (makeLenses)
  31 import Data.Aeson
  32 import Data.Aeson.TH (deriveJSON)
  33 import Data.Map (Map)
  34 import Data.Swagger
  35 import Data.Text   (Text, pack)
  36 import Data.Vector (Vector)
  37 import GHC.Generics
  38 import GHC.IO (FilePath)
  39 import Gargantext.Core.Text.Context (TermList)
  40 import Gargantext.Core.Utils.Prefix (unPrefix)
  41 import Gargantext.Core.Utils.Prefix (unPrefixSwagger)
  42 import Gargantext.Prelude
  43 import qualified Data.Text.Lazy as TextLazy
  44
  45 ----------------
  46 -- | PhyloConfig | --
  47 ----------------
  48
  49 data CorpusParser =
  50       Wos  {_wos_limit  :: Int}
  51     | Csv  {_csv_limit  :: Int}
  52     | Csv' {_csv'_limit :: Int}
  53     deriving (Show,Generic,Eq)
  54
  55 instance ToSchema CorpusParser where
  56   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
  57
  58
  59 data ListParser = V3 | V4 deriving (Show,Generic,Eq)
  60 instance ToSchema ListParser
  61
  62
  63 data SeaElevation =
  64       Constante
  65       { _cons_start :: Double
  66       , _cons_step  :: Double }
  67     | Adaptative
  68       { _adap_granularity :: Double }
  69     deriving (Show,Generic,Eq)
  70
  71 instance ToSchema SeaElevation
  72
  73 data Proximity =
  74       WeightedLogJaccard
  75       { _wlj_sensibility   :: Double
  76 {-
  77       -- , _wlj_thresholdInit :: Double
  78       -- , _wlj_thresholdStep :: Double
  79       -- | max height for sea level in temporal matching
  80       -- , _wlj_elevation     :: Double
  81 -}
  82       }
  83     | WeightedLogSim
  84       { _wlj_sensibility   :: Double
  85 {-
  86       -- , _wlj_thresholdInit :: Double
  87       -- , _wlj_thresholdStep :: Double
  88       -- | max height for sea level in temporal matching
  89       -- , _wlj_elevation     :: Double
  90 -}
  91       }
  92     | Hamming { _wlj_sensibility :: Double }
  93
  94     deriving (Show,Generic,Eq)
  95
  96 instance ToSchema Proximity where
  97   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
  98
  99
 100 data SynchronyScope = SingleBranch | SiblingBranches | AllBranches
 101   deriving (Show,Generic,Eq, ToSchema)
 102
 103 data SynchronyStrategy = MergeRegularGroups | MergeAllGroups
 104   deriving (Show,Generic,Eq)
 105
 106 instance ToSchema SynchronyStrategy where
 107   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 108
 109
 110 data Synchrony =
 111       ByProximityThreshold
 112       { _bpt_threshold :: Double
 113       , _bpt_sensibility :: Double
 114       , _bpt_scope :: SynchronyScope
 115       , _bpt_strategy :: SynchronyStrategy }
 116     | ByProximityDistribution
 117       { _bpd_sensibility :: Double
 118       , _bpd_strategy :: SynchronyStrategy }
 119     deriving (Show,Generic,Eq)
 120
 121 instance ToSchema Synchrony where
 122   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 123
 124
 125
 126 data TimeUnit =
 127       Epoch
 128       { _epoch_period :: Int
 129       , _epoch_step   :: Int
 130       , _epoch_matchingFrame :: Int }
 131     | Year
 132       { _year_period :: Int
 133       , _year_step   :: Int
 134       , _year_matchingFrame :: Int }
 135     | Month
 136       { _month_period :: Int
 137       , _month_step   :: Int
 138       , _month_matchingFrame :: Int }
 139     | Week
 140       { _week_period :: Int
 141       , _week_step   :: Int
 142       , _week_matchingFrame :: Int }
 143     | Day
 144       { _day_period :: Int
 145       , _day_step   :: Int
 146       , _day_matchingFrame :: Int }
 147       deriving (Show,Generic,Eq)
 148
 149 instance ToSchema TimeUnit where
 150   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 151
 152
 153 data CliqueFilter = ByThreshold | ByNeighbours deriving (Show,Generic,Eq)
 154
 155 instance ToSchema CliqueFilter where
 156   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 157
 158
 159
 160 data Clique =
 161       Fis
 162       { _fis_support :: Int
 163       , _fis_size    :: Int }
 164     | MaxClique
 165       { _mcl_size      :: Int
 166       , _mcl_threshold :: Double
 167       , _mcl_filter    :: CliqueFilter }
 168       deriving (Show,Generic,Eq)
 169
 170 instance ToSchema Clique where
 171   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 172
 173
 174 data Quality =
 175      Quality { _qua_granularity :: Double
 176              , _qua_minBranch   :: Int }
 177       deriving (Show,Generic,Eq)
 178
 179 instance ToSchema Quality where
 180   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_qua_")
 181
 182
 183 data PhyloConfig =
 184      PhyloConfig { corpusPath     :: FilePath
 185             , listPath       :: FilePath
 186             , outputPath     :: FilePath
 187             , corpusParser   :: CorpusParser
 188             , listParser     :: ListParser
 189             , phyloName      :: Text
 190             , phyloLevel     :: Int
 191             , phyloProximity :: Proximity
 192             , seaElevation   :: SeaElevation
 193             , findAncestors  :: Bool
 194             , phyloSynchrony :: Synchrony
 195             , phyloQuality   :: Quality
 196             , timeUnit       :: TimeUnit
 197             , clique         :: Clique
 198             , exportLabel    :: [PhyloLabel]
 199             , exportSort     :: Sort
 200             , exportFilter   :: [Filter]
 201             } deriving (Show,Generic,Eq)
 202
 203
 204 ------------------------------------------------------------------------
 205 data PhyloSubConfig =
 206   PhyloSubConfig { _sc_phyloProximity :: Double
 207                  , _sc_phyloSynchrony :: Double
 208                  , _sc_phyloQuality   :: Double
 209                  , _sc_timeUnit       :: TimeUnit
 210                  , _sc_clique         :: Clique
 211                  , _sc_exportFilter   :: Double
 212                  }
 213   deriving (Show,Generic,Eq)
 214
 215
 216 subConfig2config :: PhyloSubConfig -> PhyloConfig
 217 subConfig2config subConfig = defaultConfig { phyloProximity = WeightedLogJaccard $ _sc_phyloProximity subConfig
 218                                            , phyloSynchrony = ByProximityThreshold (_sc_phyloSynchrony subConfig) 0 AllBranches MergeAllGroups
 219                                            , phyloQuality   = Quality (_sc_phyloQuality   subConfig) 1
 220                                            , timeUnit       = _sc_timeUnit       subConfig
 221                                            , clique         = _sc_clique         subConfig
 222                                            , exportFilter   = [ByBranchSize $ _sc_exportFilter   subConfig]
 223                                            }
 224
 225 ------------------------------------------------------------------------
 226 defaultConfig :: PhyloConfig
 227 defaultConfig =
 228      PhyloConfig { corpusPath     = "corpus.csv" -- useful for commandline only
 229             , listPath       = "list.csv"   -- useful for commandline only
 230             , outputPath     = "data/"
 231             , corpusParser   = Csv 100000
 232             , listParser     = V4
 233             , phyloName      = pack "Phylo Name"
 234             , phyloLevel     = 2
 235             , phyloProximity = WeightedLogJaccard 0.5
 236             , seaElevation   = Constante 0.1 0.1
 237             , findAncestors  = False
 238             , phyloSynchrony = ByProximityThreshold 0.5 0 AllBranches MergeAllGroups
 239             , phyloQuality   = Quality 0.5 1
 240             , timeUnit       = Year 3 1 5
 241             , clique         = MaxClique 5 0.0001 ByThreshold
 242             , exportLabel    = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2]
 243             , exportSort     = ByHierarchy Desc
 244             , exportFilter   = [ByBranchSize 3]
 245             }
 246
 247 -- Main Instances
 248 instance ToSchema PhyloConfig
 249 instance ToSchema PhyloSubConfig
 250
 251 instance FromJSON PhyloConfig
 252 instance ToJSON PhyloConfig
 253
 254 instance FromJSON PhyloSubConfig
 255 instance ToJSON PhyloSubConfig
 256
 257 instance FromJSON CorpusParser
 258 instance ToJSON CorpusParser
 259
 260 instance FromJSON ListParser
 261 instance ToJSON ListParser
 262
 263 instance FromJSON Proximity
 264 instance ToJSON Proximity
 265
 266 instance FromJSON SeaElevation
 267 instance ToJSON SeaElevation
 268
 269 instance FromJSON TimeUnit
 270 instance ToJSON TimeUnit
 271
 272 instance FromJSON CliqueFilter
 273 instance ToJSON CliqueFilter
 274
 275 instance FromJSON Clique
 276 instance ToJSON Clique
 277
 278 instance FromJSON PhyloLabel
 279 instance ToJSON PhyloLabel
 280
 281 instance FromJSON Tagger
 282 instance ToJSON Tagger
 283
 284 instance FromJSON Sort
 285 instance ToJSON Sort
 286
 287 instance FromJSON Order
 288 instance ToJSON Order
 289
 290 instance FromJSON Filter
 291 instance ToJSON Filter
 292
 293 instance FromJSON SynchronyScope
 294 instance ToJSON SynchronyScope
 295
 296 instance FromJSON SynchronyStrategy
 297 instance ToJSON SynchronyStrategy
 298
 299 instance FromJSON Synchrony
 300 instance ToJSON Synchrony
 301
 302 instance FromJSON Quality
 303 instance ToJSON Quality
 304
 305
 306 -- | Software parameters
 307 data Software =
 308      Software { _software_name    :: Text
 309               , _software_version :: Text
 310      } deriving (Generic, Show, Eq)
 311
 312 instance ToSchema Software where
 313   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_software_")
 314
 315
 316
 317 defaultSoftware :: Software
 318 defaultSoftware =
 319       Software { _software_name    = pack "Gargantext"
 320                , _software_version = pack "v4" }
 321
 322
 323 -- | Global parameters of a Phylo
 324 data PhyloParam =
 325      PhyloParam { _phyloParam_version  :: Text
 326                 , _phyloParam_software :: Software
 327                 , _phyloParam_config   :: PhyloConfig
 328      } deriving (Generic, Show, Eq)
 329
 330 instance ToSchema PhyloParam where
 331   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phyloParam_")
 332
 333
 334
 335 defaultPhyloParam :: PhyloParam
 336 defaultPhyloParam =
 337       PhyloParam { _phyloParam_version  = pack "v2.adaptative"
 338                  , _phyloParam_software = defaultSoftware
 339                  , _phyloParam_config   = defaultConfig }
 340
 341
 342 ------------------
 343 -- | Document | --
 344 ------------------
 345
 346 -- | Date : a simple Integer
 347 type Date = Int
 348
 349 -- | Ngrams : a contiguous sequence of n terms
 350 type Ngrams = Text
 351
 352 -- Document : a piece of Text linked to a Date
 353 -- date = computational date; date' = original string date yyyy-mm-dd
 354 -- Export Database to Document
 355 data Document = Document
 356       { date    :: Date   -- datatype Date {unDate :: Int}
 357       , date'   :: Text   -- show date
 358       , text    :: [Ngrams]
 359       , weight  :: Maybe Double
 360       , sources :: [Text]
 361       } deriving (Eq,Show,Generic,NFData)
 362
 363
 364 --------------------
 365 -- | Foundation | --
 366 --------------------
 367
 368
 369 -- | The Foundations of a Phylo created from a given TermList
 370 data PhyloFoundations = PhyloFoundations
 371       { _foundations_roots   :: !(Vector Ngrams)
 372       , _foundations_mapList :: TermList
 373       } deriving (Generic, Show, Eq)
 374
 375 instance ToSchema PhyloFoundations where
 376   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_foundations_")
 377
 378
 379
 380 data PhyloSources = PhyloSources
 381       { _sources :: !(Vector Text) } deriving (Generic, Show, Eq)
 382
 383 instance ToSchema PhyloSources where
 384   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 385
 386 ---------------------------
 387 -- | Coocurency Matrix | --
 388 ---------------------------
 389
 390
 391 -- | Cooc : a coocurency matrix between two ngrams
 392 type Cooc =  Map (Int,Int) Double
 393
 394
 395 -------------------
 396 -- | Phylomemy | --
 397 -------------------
 398
 399
 400 -- | Phylo datatype of a phylomemy
 401 --  foundations : the foundations of the phylo
 402 --  timeCooc : a Map of coocurency by minimal unit of time (ex: by year)
 403 --  timeDocs : a Map with the numbers of docs by minimal unit of time (ex: by year)
 404 --  param : the parameters of the phylomemy (with the user's configuration)
 405 --  periods : the temporal steps of a phylomemy
 406 data Phylo =
 407      Phylo { _phylo_foundations  :: PhyloFoundations
 408            , _phylo_sources      :: PhyloSources
 409            , _phylo_timeCooc     :: !(Map Date Cooc)
 410            , _phylo_timeDocs     :: !(Map Date Double)
 411            , _phylo_termFreq     :: !(Map Int Double)
 412            , _phylo_lastTermFreq :: !(Map Int Double)
 413            , _phylo_horizon      :: !(Map (PhyloGroupId,PhyloGroupId) Double)
 414            , _phylo_groupsProxi  :: !(Map (PhyloGroupId,PhyloGroupId) Double)
 415            , _phylo_param        :: PhyloParam
 416            , _phylo_periods      :: Map PhyloPeriodId PhyloPeriod
 417            }
 418            deriving (Generic, Show, Eq)
 419
 420 instance ToSchema Phylo where
 421   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 422
 423
 424 -- | PhyloPeriodId : the id of a given period
 425 type PhyloPeriodId = (Date,Date)
 426
 427 -- | PhyloPeriod : steps of a phylomemy on a temporal axis
 428 --  id: tuple (start date, end date) of the temporal step of the phylomemy
 429 --  levels: levels of granularity
 430 data PhyloPeriod =
 431      PhyloPeriod { _phylo_periodPeriod  :: (Date,Date)
 432                  , _phylo_periodPeriod' :: (Text,Text)
 433                  , _phylo_periodLevels  :: Map PhyloLevelId PhyloLevel
 434                  } deriving (Generic, Show, Eq)
 435
 436 instance ToSchema PhyloPeriod where
 437   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 438
 439
 440
 441 -- | Level : a level of clustering
 442 type Level = Int
 443
 444 -- | PhyloLevelId : the id of a level of clustering in a given period
 445 type PhyloLevelId  = (PhyloPeriodId,Level)
 446
 447 -- | PhyloLevel : levels of phylomemy on a synchronic axis
 448 -- Levels description:
 449 -- Level 0: The foundations and the base of the phylo
 450 -- Level 1: First level of clustering (the Fis)
 451 -- Level [2..N]: Nth level of synchronic clustering (cluster of Fis)
 452 data PhyloLevel =
 453      PhyloLevel { _phylo_levelPeriod  :: (Date,Date)
 454                 , _phylo_levelPeriod' :: (Text,Text)
 455                 , _phylo_levelLevel   :: Level
 456                 , _phylo_levelGroups  :: Map PhyloGroupId PhyloGroup
 457                 }
 458                 deriving (Generic, Show, Eq)
 459
 460 instance ToSchema PhyloLevel where
 461   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 462
 463
 464 type PhyloGroupId  = (PhyloLevelId, Int)
 465
 466 -- | BranchId : (a level, a sequence of branch index)
 467 -- the sequence is a path of heritage from the most to the less specific branch
 468 type PhyloBranchId = (Level, [Int])
 469
 470 -- | PhyloGroup : group of ngrams at each level and period
 471 data PhyloGroup =
 472       PhyloGroup { _phylo_groupPeriod   :: (Date,Date)
 473                  , _phylo_groupPeriod'  :: (Text,Text)
 474                  , _phylo_groupLevel    :: Level
 475                  , _phylo_groupIndex    :: Int
 476                  , _phylo_groupLabel    :: Text
 477                  , _phylo_groupSupport  :: Support
 478                  , _phylo_groupWeight   :: Maybe Double
 479                  , _phylo_groupSources  :: [Int]
 480                  , _phylo_groupNgrams   :: [Int]
 481                  , _phylo_groupCooc     :: !(Cooc)
 482                  , _phylo_groupBranchId :: PhyloBranchId
 483                  , _phylo_groupMeta     :: Map Text [Double]
 484                  , _phylo_groupLevelParents  :: [Pointer]
 485                  , _phylo_groupLevelChilds   :: [Pointer]
 486                  , _phylo_groupPeriodParents :: [Pointer]
 487                  , _phylo_groupPeriodChilds  :: [Pointer]
 488                  , _phylo_groupAncestors     :: [Pointer]
 489                  , _phylo_groupPeriodMemoryParents :: [Pointer']
 490                  , _phylo_groupPeriodMemoryChilds  :: [Pointer']
 491                  }
 492                  deriving (Generic, Show, Eq, NFData)
 493
 494 instance ToSchema PhyloGroup where
 495   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 496
 497
 498 -- | Weight : A generic mesure that can be associated with an Id
 499 type Weight = Double
 500 type Thr = Double
 501
 502 -- | Pointer : A weighted pointer to a given PhyloGroup
 503 type Pointer = (PhyloGroupId, Weight)
 504 -- | Pointer' : A weighted pointer to a given PhyloGroup with a lower bounded threshold
 505 type Pointer' = (PhyloGroupId, (Thr,Weight))
 506
 507 data Filiation = ToParents | ToChilds | ToParentsMemory | ToChildsMemory deriving (Generic, Show)
 508 data PointerType = TemporalPointer | LevelPointer deriving (Generic, Show)
 509
 510
 511 ----------------------
 512 -- | Phylo Clique | --
 513 ----------------------
 514
 515 -- | Support : Number of Documents where a Clique occurs
 516 type Support  = Int
 517
 518 data PhyloClique = PhyloClique
 519   { _phyloClique_nodes   :: [Int]
 520   , _phyloClique_support :: Support
 521   , _phyloClique_period  :: (Date,Date)
 522   , _phyloClique_weight  :: Maybe Double
 523   , _phyloClique_sources :: [Int]
 524   } deriving (Generic,NFData,Show,Eq)
 525
 526 ----------------
 527 -- | Export | --
 528 ----------------
 529
 530 type DotId = TextLazy.Text
 531
 532 data EdgeType = GroupToGroup | GroupToGroupMemory | BranchToGroup | BranchToBranch | GroupToAncestor | PeriodToPeriod deriving (Show,Generic,Eq)
 533
 534 data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq)
 535 instance ToSchema Filter where
 536   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 537
 538
 539 data Order = Asc | Desc deriving (Show,Generic,Eq, ToSchema)
 540
 541 data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy {_sort_order :: Order } deriving (Show,Generic,Eq)
 542 instance ToSchema Sort where
 543   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_sort_")
 544
 545
 546 data Tagger = MostInclusive | MostEmergentInclusive | MostEmergentTfIdf deriving (Show,Generic,Eq)
 547 instance ToSchema Tagger where
 548   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 549
 550
 551 data PhyloLabel =
 552       BranchLabel
 553       { _branch_labelTagger :: Tagger
 554       , _branch_labelSize   :: Int }
 555     | GroupLabel
 556       { _group_labelTagger  :: Tagger
 557       , _group_labelSize    :: Int }
 558     deriving (Show,Generic,Eq)
 559
 560 instance ToSchema PhyloLabel where
 561   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 562
 563
 564 data PhyloBranch =
 565       PhyloBranch
 566       { _branch_id :: PhyloBranchId
 567       , _branch_canonId  :: [Int]
 568       , _branch_seaLevel :: [Double]
 569       , _branch_x        :: Double
 570       , _branch_y        :: Double
 571       , _branch_w        :: Double
 572       , _branch_t        :: Double
 573       , _branch_label    :: Text
 574       , _branch_meta     :: Map Text [Double]
 575       } deriving (Generic, Show, Eq)
 576
 577 instance ToSchema PhyloBranch where
 578   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_branch_")
 579
 580 data PhyloExport =
 581       PhyloExport
 582       { _export_groups    :: [PhyloGroup]
 583       , _export_branches  :: [PhyloBranch]
 584       } deriving (Generic, Show)
 585 instance ToSchema PhyloExport where
 586   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_export_")
 587
 588
 589 ----------------
 590 -- | Lenses | --
 591 ----------------
 592
 593 makeLenses ''PhyloConfig
 594 makeLenses ''PhyloSubConfig
 595 makeLenses ''Proximity
 596 makeLenses ''SeaElevation
 597 makeLenses ''Quality
 598 makeLenses ''Clique
 599 makeLenses ''PhyloLabel
 600 makeLenses ''TimeUnit
 601 makeLenses ''PhyloFoundations
 602 makeLenses ''PhyloClique
 603 makeLenses ''Phylo
 604 makeLenses ''PhyloPeriod
 605 makeLenses ''PhyloLevel
 606 makeLenses ''PhyloGroup
 607 makeLenses ''PhyloParam
 608 makeLenses ''PhyloExport
 609 makeLenses ''PhyloBranch
 610
 611 ------------------------
 612 -- | JSON instances | --
 613 ------------------------
 614
 615 instance FromJSON Phylo
 616 instance ToJSON Phylo
 617
 618 instance FromJSON PhyloSources
 619 instance ToJSON PhyloSources
 620
 621 instance FromJSON PhyloParam
 622 instance ToJSON PhyloParam
 623
 624 instance FromJSON PhyloPeriod
 625 instance ToJSON PhyloPeriod
 626
 627 instance FromJSON PhyloLevel
 628 instance ToJSON PhyloLevel
 629
 630 instance FromJSON Software
 631 instance ToJSON Software
 632
 633 instance FromJSON PhyloGroup
 634 instance ToJSON PhyloGroup
 635
 636 $(deriveJSON (unPrefix "_foundations_"  ) ''PhyloFoundations)