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.Utils.Prefix (unPrefix)
  40 import Gargantext.Core.Utils.Prefix (unPrefixSwagger)
  41 import Gargantext.Prelude
  42 import qualified Data.Text.Lazy as TextLazy
  43
  44 ---------------------
  45 -- | PhyloConfig | --
  46 ---------------------
  47
  48 data CorpusParser =
  49       Wos  {_wos_limit  :: Int}
  50     | Csv  {_csv_limit  :: Int}
  51     | Csv' {_csv'_limit :: Int}
  52     deriving (Show,Generic,Eq)
  53
  54 instance ToSchema CorpusParser where
  55   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
  56
  57
  58 data ListParser = V3 | V4 deriving (Show,Generic,Eq)
  59 instance ToSchema ListParser
  60
  61
  62 data SeaElevation =
  63       Constante
  64       { _cons_start :: Double
  65       , _cons_gap   :: Double }
  66     | Adaptative
  67       { _adap_steps :: Double }
  68     | Evolving
  69       { _evol_neighborhood :: Bool }
  70     deriving (Show,Generic,Eq)
  71
  72 instance ToSchema SeaElevation
  73
  74 data PhyloSimilarity =
  75       WeightedLogJaccard
  76       { _wlj_sensibility     :: Double
  77       , _wlj_minSharedNgrams :: Int }
  78     | WeightedLogSim
  79       { _wls_sensibility     :: Double
  80       , _wls_minSharedNgrams :: Int }
  81     | Hamming
  82       { _hmg_sensibility     :: Double
  83       , _hmg_minSharedNgrams :: Int}
  84
  85     deriving (Show,Generic,Eq)
  86
  87 instance ToSchema PhyloSimilarity where
  88   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
  89
  90
  91 data SynchronyScope = SingleBranch | SiblingBranches | AllBranches
  92   deriving (Show,Generic,Eq, ToSchema)
  93
  94 data SynchronyStrategy = MergeRegularGroups | MergeAllGroups
  95   deriving (Show,Generic,Eq)
  96
  97 instance ToSchema SynchronyStrategy where
  98   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
  99
 100
 101 data Synchrony =
 102       ByProximityThreshold
 103       { _bpt_threshold :: Double
 104       , _bpt_sensibility :: Double
 105       , _bpt_scope :: SynchronyScope
 106       , _bpt_strategy :: SynchronyStrategy }
 107     | ByProximityDistribution
 108       { _bpd_sensibility :: Double
 109       , _bpd_strategy :: SynchronyStrategy }
 110     deriving (Show,Generic,Eq)
 111
 112 instance ToSchema Synchrony where
 113   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 114
 115
 116
 117 data TimeUnit =
 118       Epoch
 119       { _epoch_period :: Int
 120       , _epoch_step   :: Int
 121       , _epoch_matchingFrame :: Int }
 122     | Year
 123       { _year_period :: Int
 124       , _year_step   :: Int
 125       , _year_matchingFrame :: Int }
 126     | Month
 127       { _month_period :: Int
 128       , _month_step   :: Int
 129       , _month_matchingFrame :: Int }
 130     | Week
 131       { _week_period :: Int
 132       , _week_step   :: Int
 133       , _week_matchingFrame :: Int }
 134     | Day
 135       { _day_period :: Int
 136       , _day_step   :: Int
 137       , _day_matchingFrame :: Int }
 138       deriving (Show,Generic,Eq,NFData)
 139
 140 instance ToSchema TimeUnit where
 141   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 142
 143
 144 data MaxCliqueFilter = ByThreshold | ByNeighbours deriving (Show,Generic,Eq)
 145
 146 instance ToSchema MaxCliqueFilter where
 147   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 148
 149
 150
 151 data Cluster =
 152       Fis
 153       { _fis_support :: Int
 154       , _fis_size    :: Int }
 155     | MaxClique
 156       { _mcl_size      :: Int
 157       , _mcl_threshold :: Double
 158       , _mcl_filter    :: MaxCliqueFilter }
 159       deriving (Show,Generic,Eq)
 160
 161 instance ToSchema Cluster where
 162   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 163
 164
 165 data Quality =
 166      Quality { _qua_granularity :: Double
 167              , _qua_minBranch   :: Int }
 168       deriving (Show,Generic,Eq)
 169
 170 instance ToSchema Quality where
 171   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_qua_")
 172
 173
 174 data PhyloConfig =
 175      PhyloConfig { corpusPath     :: FilePath
 176             , listPath       :: FilePath
 177             , outputPath     :: FilePath
 178             , corpusParser   :: CorpusParser
 179             , listParser     :: ListParser
 180             , phyloName      :: Text
 181             , phyloScale     :: Int
 182             , similarity     :: PhyloSimilarity
 183             , seaElevation   :: SeaElevation
 184             , defaultMode    :: Bool
 185             , findAncestors  :: Bool
 186             , phyloSynchrony :: Synchrony
 187             , phyloQuality   :: Quality
 188             , timeUnit       :: TimeUnit
 189             , clique         :: Cluster
 190             , exportLabel    :: [PhyloLabel]
 191             , exportSort     :: Sort
 192             , exportFilter   :: [Filter]
 193             } deriving (Show,Generic,Eq)
 194
 195
 196 --------------------------------
 197 -- | SubConfig API & 1Click | --
 198 --------------------------------
 199
 200 data PhyloSubConfigAPI =
 201   PhyloSubConfigAPI { _sc_phyloProximity :: Double
 202                     , _sc_phyloSynchrony :: Double
 203                     , _sc_phyloQuality   :: Double
 204                     , _sc_timeUnit       :: TimeUnit
 205                     , _sc_clique         :: Cluster
 206                     , _sc_exportFilter   :: Double
 207                     } deriving (Show,Generic,Eq)
 208
 209
 210 subConfigAPI2config :: PhyloSubConfigAPI -> PhyloConfig
 211 subConfigAPI2config subConfig = defaultConfig
 212                                            { similarity     = WeightedLogJaccard (_sc_phyloProximity subConfig) 2
 213                                            , phyloSynchrony = ByProximityThreshold (_sc_phyloSynchrony subConfig) 0 AllBranches MergeAllGroups
 214                                            , phyloQuality   = Quality (_sc_phyloQuality   subConfig) 3
 215                                            , timeUnit       = _sc_timeUnit       subConfig
 216                                            , clique         = _sc_clique         subConfig
 217                                            , exportFilter   = [ByBranchSize $ _sc_exportFilter   subConfig]
 218                                            }
 219
 220 --------------------------
 221 -- | SubConfig 1Click | --
 222 --------------------------
 223
 224 defaultConfig :: PhyloConfig
 225 defaultConfig =
 226      PhyloConfig { corpusPath = "corpus.csv" -- useful for commandline only
 227             , listPath       = "list.csv"   -- useful for commandline only
 228             , outputPath     = "data/"
 229             , corpusParser   = Csv 150000
 230             , listParser     = V4
 231             , phyloName      = pack "Phylo Name"
 232             , phyloScale     = 2
 233             , similarity     = WeightedLogJaccard 0.5 2
 234             , seaElevation   = Constante 0.1 0.1
 235             , defaultMode    = False
 236             , findAncestors  = True
 237             , phyloSynchrony = ByProximityThreshold 0.6 0 AllBranches MergeAllGroups
 238             , phyloQuality   = Quality 0.5 3
 239             , timeUnit       = Year 3 1 5
 240             , clique         = Fis 2 3
 241             , exportLabel    = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2]
 242             , exportSort     = ByHierarchy Desc
 243             , exportFilter   = [ByBranchSize 3]
 244             }
 245
 246 -- Main Instances
 247 instance ToSchema PhyloConfig
 248 instance ToSchema PhyloSubConfigAPI
 249
 250 instance FromJSON PhyloConfig
 251 instance ToJSON PhyloConfig
 252
 253 instance FromJSON PhyloSubConfigAPI
 254 instance ToJSON PhyloSubConfigAPI
 255
 256 instance FromJSON CorpusParser
 257 instance ToJSON CorpusParser
 258
 259 instance FromJSON ListParser
 260 instance ToJSON ListParser
 261
 262 instance FromJSON PhyloSimilarity
 263 instance ToJSON PhyloSimilarity
 264
 265 instance FromJSON SeaElevation
 266 instance ToJSON SeaElevation
 267
 268 instance FromJSON TimeUnit
 269 instance ToJSON TimeUnit
 270
 271 instance FromJSON MaxCliqueFilter
 272 instance ToJSON MaxCliqueFilter
 273
 274 instance FromJSON Cluster
 275 instance ToJSON Cluster
 276
 277 instance FromJSON PhyloLabel
 278 instance ToJSON PhyloLabel
 279
 280 instance FromJSON Tagger
 281 instance ToJSON Tagger
 282
 283 instance FromJSON Sort
 284 instance ToJSON Sort
 285
 286 instance FromJSON Order
 287 instance ToJSON Order
 288
 289 instance FromJSON Filter
 290 instance ToJSON Filter
 291
 292 instance FromJSON SynchronyScope
 293 instance ToJSON SynchronyScope
 294
 295 instance FromJSON SynchronyStrategy
 296 instance ToJSON SynchronyStrategy
 297
 298 instance FromJSON Synchrony
 299 instance ToJSON Synchrony
 300
 301 instance FromJSON Quality
 302 instance ToJSON Quality
 303
 304
 305 -- | Software parameters
 306 data Software =
 307      Software { _software_name    :: Text
 308               , _software_version :: Text
 309      } deriving (Generic, Show, Eq)
 310
 311 instance ToSchema Software where
 312   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_software_")
 313
 314
 315
 316 defaultSoftware :: Software
 317 defaultSoftware =
 318       Software { _software_name    = pack "GarganText"
 319                , _software_version = pack "v5" }
 320
 321
 322 -- | Global parameters of a Phylo
 323 data PhyloParam =
 324      PhyloParam { _phyloParam_version  :: Text
 325                 , _phyloParam_software :: Software
 326                 , _phyloParam_config   :: PhyloConfig
 327      } deriving (Generic, Show, Eq)
 328
 329 instance ToSchema PhyloParam where
 330   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phyloParam_")
 331
 332
 333
 334 defaultPhyloParam :: PhyloParam
 335 defaultPhyloParam =
 336       PhyloParam { _phyloParam_version  = pack "v3"
 337                  , _phyloParam_software = defaultSoftware
 338                  , _phyloParam_config   = defaultConfig }
 339
 340
 341 ------------------
 342 -- | Document | --
 343 ------------------
 344
 345 -- | Date : a simple Integer
 346 type Date = Int
 347
 348 -- | DateStr : the string version of a Date
 349 type DateStr = Text
 350
 351 -- | Ngrams : a contiguous sequence of n terms
 352 type Ngrams = Text
 353
 354 -- Document : a piece of Text linked to a Date
 355 -- date = computational date; date' = original string date yyyy-mm-dd
 356 -- Export Database to Document
 357 data Document = Document
 358       { date    :: Date   -- datatype Date {unDate :: Int}
 359       , date'   :: DateStr   -- show date
 360       , text    :: [Ngrams]
 361       , weight  :: Maybe Double
 362       , sources :: [Text]
 363       , docTime :: TimeUnit
 364       } deriving (Eq,Show,Generic,NFData)
 365
 366
 367 --------------------
 368 -- | Foundation | --
 369 --------------------
 370
 371
 372 -- | The Foundations of a Phylo created from a given TermList
 373 data PhyloFoundations = PhyloFoundations
 374       { _foundations_roots    :: (Vector Ngrams)
 375       , _foundations_rootsInGroups :: Map Int [PhyloGroupId] -- map of roots associated to groups
 376       } deriving (Generic, Show, Eq)
 377
 378 data PhyloCounts = PhyloCounts
 379       { coocByDate    :: !(Map Date Cooc)
 380       , docsByDate    :: !(Map Date Double)
 381       , rootsCountByDate :: !(Map Date (Map Int Double))
 382       , rootsCount    :: !(Map Int  Double)
 383       , rootsFreq     :: !(Map Int  Double)
 384       , lastRootsFreq :: !(Map Int  Double)
 385       } deriving (Generic, Show, Eq)
 386
 387 data PhyloSources = PhyloSources
 388       { _sources :: !(Vector Text) } deriving (Generic, Show, Eq)
 389
 390 instance ToSchema PhyloFoundations where
 391   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_foundations_")
 392 instance ToSchema PhyloCounts where
 393   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 394 instance ToSchema PhyloSources where
 395   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 396
 397 ---------------------------
 398 -- | Coocurency Matrix | --
 399 ---------------------------
 400
 401
 402 -- | Cooc : a coocurency matrix between two ngrams
 403 type Cooc =  Map (Int,Int) Double
 404
 405
 406 -------------------
 407 -- | Phylomemy | --
 408 -------------------
 409
 410 -- | Period : a tuple of Dates
 411 type Period = (Date,Date)
 412
 413 -- | PeriodStr : a tuple of DateStr
 414 type PeriodStr = (DateStr,DateStr)
 415
 416
 417
 418
 419 -- | Phylo datatype of a phylomemy
 420 --  foundations : the foundations of the phylo
 421 --  timeCooc : a Map of coocurency by minimal unit of time (ex: by year)
 422 --  timeDocs : a Map with the numbers of docs by minimal unit of time (ex: by year)
 423 --  param : the parameters of the phylomemy (with the user's configuration)
 424 --  periods : the temporal steps of a phylomemy
 425 data Phylo =
 426      Phylo { _phylo_foundations  :: PhyloFoundations
 427            , _phylo_sources      :: PhyloSources
 428            , _phylo_counts       :: PhyloCounts
 429            , _phylo_seaLadder    :: [Double]
 430            , _phylo_param        :: PhyloParam
 431            , _phylo_periods      :: Map Period PhyloPeriod
 432            , _phylo_quality      :: Double
 433            , _phylo_level        :: Double
 434            }
 435            deriving (Generic, Show, Eq)
 436
 437 instance ToSchema Phylo where
 438   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 439
 440
 441 ----------------
 442 -- | Period | --
 443 ----------------
 444
 445 -- | PhyloPeriod : steps of a phylomemy on a temporal axis
 446 --  id: tuple (start date, end date) of the temporal step of the phylomemy
 447 --  scales: scales of synchronic description
 448 data PhyloPeriod =
 449      PhyloPeriod { _phylo_periodPeriod    :: Period
 450                  , _phylo_periodPeriodStr :: PeriodStr
 451                  , _phylo_periodScales    :: Map PhyloScaleId PhyloScale
 452                  } deriving (Generic, Show, Eq)
 453
 454 instance ToSchema PhyloPeriod where
 455   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 456
 457 ---------------
 458 -- | Scale | --
 459 ---------------
 460
 461 -- | Scale : a scale of synchronic description
 462 type Scale = Int
 463
 464 -- | PhyloScaleId : the id of a scale of synchronic description
 465 type PhyloScaleId  = (Period,Scale)
 466
 467 -- | PhyloScale : sub-structure of the phylomemy in scale of synchronic description
 468 data PhyloScale =
 469      PhyloScale { _phylo_scalePeriod    :: Period
 470                 , _phylo_scalePeriodStr :: PeriodStr
 471                 , _phylo_scaleScale     :: Scale
 472                 , _phylo_scaleGroups    :: Map PhyloGroupId PhyloGroup
 473                 }
 474                 deriving (Generic, Show, Eq)
 475
 476 instance ToSchema PhyloScale where
 477   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 478
 479
 480 type PhyloGroupId  = (PhyloScaleId, Int)
 481
 482 -- | BranchId : (a scale, a sequence of branch index)
 483 -- the sequence is a path of heritage from the most to the less specific branch
 484 type PhyloBranchId = (Scale, [Int])
 485
 486 -- | PhyloGroup : group of ngrams at each scale and period
 487 data PhyloGroup =
 488       PhyloGroup { _phylo_groupPeriod   :: Period
 489                  , _phylo_groupPeriod'  :: (Text,Text)
 490                  , _phylo_groupScale    :: Scale
 491                  , _phylo_groupIndex    :: Int
 492                  , _phylo_groupLabel    :: Text
 493                  , _phylo_groupSupport  :: Support
 494                  , _phylo_groupWeight   :: Maybe Double
 495                  , _phylo_groupSources  :: [Int]
 496                  , _phylo_groupNgrams   :: [Int]
 497                  , _phylo_groupCooc     :: !(Cooc)
 498                  , _phylo_groupDensity  :: Double
 499                  , _phylo_groupBranchId :: PhyloBranchId
 500                  , _phylo_groupMeta     :: Map Text [Double]
 501                  , _phylo_groupRootsCount    :: Map Int Double
 502                  , _phylo_groupScaleParents  :: [Pointer]
 503                  , _phylo_groupScaleChilds   :: [Pointer]
 504                  , _phylo_groupPeriodParents :: [Pointer]
 505                  , _phylo_groupPeriodChilds  :: [Pointer]
 506                  , _phylo_groupAncestors     :: [Pointer]
 507                  , _phylo_groupPeriodMemoryParents :: [Pointer']
 508                  , _phylo_groupPeriodMemoryChilds  :: [Pointer']
 509                  }
 510                  deriving (Generic, Show, Eq, NFData)
 511
 512 instance ToSchema PhyloGroup where
 513   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 514
 515
 516 -- | Weight : A generic mesure that can be associated with an Id
 517 type Weight = Double
 518 type Thr = Double
 519
 520 -- | Pointer : A weighted pointer to a given PhyloGroup
 521 type Pointer = (PhyloGroupId, Weight)
 522 -- | Pointer' : A weighted pointer to a given PhyloGroup with a lower bounded threshold
 523 type Pointer' = (PhyloGroupId, (Thr,Weight))
 524
 525 data Filiation = ToParents | ToChilds | ToParentsMemory | ToChildsMemory deriving (Generic, Show)
 526 data PointerType = TemporalPointer | ScalePointer deriving (Generic, Show)
 527
 528
 529 --------------------------
 530 -- | Phylo Clustering | --
 531 --------------------------
 532
 533 -- | Support : Number of Documents where a Cluster occurs
 534 type Support  = Int
 535
 536 data Clustering = Clustering
 537   { _clustering_roots   :: [Int]
 538   , _clustering_support :: Support
 539   , _clustering_period  :: Period
 540   -- additional materials for visualization
 541   , _clustering_visWeighting :: Maybe Double
 542   , _clustering_visFiltering :: [Int]
 543   } deriving (Generic,NFData,Show,Eq)
 544
 545 ----------------
 546 -- | Export | --
 547 ----------------
 548
 549 type DotId = TextLazy.Text
 550
 551 data EdgeType = GroupToGroup | GroupToGroupMemory | BranchToGroup | BranchToBranch | GroupToAncestor | PeriodToPeriod deriving (Show,Generic,Eq)
 552
 553 data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq)
 554 instance ToSchema Filter where
 555   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 556
 557
 558 data Order = Asc | Desc deriving (Show,Generic,Eq, ToSchema)
 559
 560 data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy {_sort_order :: Order } deriving (Show,Generic,Eq)
 561 instance ToSchema Sort where
 562   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_sort_")
 563
 564
 565 data Tagger = MostInclusive | MostEmergentInclusive | MostEmergentTfIdf deriving (Show,Generic,Eq)
 566 instance ToSchema Tagger where
 567   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 568
 569
 570 data PhyloLabel =
 571       BranchLabel
 572       { _branch_labelTagger :: Tagger
 573       , _branch_labelSize   :: Int }
 574     | GroupLabel
 575       { _group_labelTagger  :: Tagger
 576       , _group_labelSize    :: Int }
 577     deriving (Show,Generic,Eq)
 578
 579 instance ToSchema PhyloLabel where
 580   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 581
 582
 583 data PhyloBranch =
 584       PhyloBranch
 585       { _branch_id :: PhyloBranchId
 586       , _branch_canonId  :: [Int]
 587       , _branch_seaLevel :: [Double]
 588       , _branch_x        :: Double
 589       , _branch_y        :: Double
 590       , _branch_w        :: Double
 591       , _branch_t        :: Double
 592       , _branch_label    :: Text
 593       , _branch_meta     :: Map Text [Double]
 594       } deriving (Generic, Show, Eq)
 595
 596 instance ToSchema PhyloBranch where
 597   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_branch_")
 598
 599 data PhyloExport =
 600       PhyloExport
 601       { _export_groups    :: [PhyloGroup]
 602       , _export_branches  :: [PhyloBranch]
 603       } deriving (Generic, Show)
 604 instance ToSchema PhyloExport where
 605   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_export_")
 606
 607
 608 ----------------
 609 -- | Lenses | --
 610 ----------------
 611
 612 makeLenses ''PhyloConfig
 613 makeLenses ''PhyloSubConfigAPI
 614 makeLenses ''PhyloSimilarity
 615 makeLenses ''SeaElevation
 616 makeLenses ''Quality
 617 makeLenses ''Cluster
 618 makeLenses ''PhyloLabel
 619 makeLenses ''TimeUnit
 620 makeLenses ''PhyloFoundations
 621 makeLenses ''Clustering
 622 makeLenses ''Phylo
 623 makeLenses ''PhyloPeriod
 624 makeLenses ''PhyloScale
 625 makeLenses ''PhyloGroup
 626 makeLenses ''PhyloParam
 627 makeLenses ''PhyloExport
 628 makeLenses ''PhyloBranch
 629
 630 ------------------------
 631 -- | JSON instances | --
 632 ------------------------
 633
 634 instance FromJSON Phylo
 635 instance ToJSON Phylo
 636
 637 instance FromJSON PhyloSources
 638 instance ToJSON PhyloSources
 639
 640 instance FromJSON PhyloParam
 641 instance ToJSON PhyloParam
 642
 643 instance FromJSON PhyloCounts
 644 instance ToJSON PhyloCounts
 645
 646 instance FromJSON PhyloPeriod
 647 instance ToJSON PhyloPeriod
 648
 649 instance FromJSON PhyloScale
 650 instance ToJSON PhyloScale
 651
 652 instance FromJSON Software
 653 instance ToJSON Software
 654
 655 instance FromJSON PhyloGroup
 656 instance ToJSON PhyloGroup
 657
 658 $(deriveJSON (unPrefix "_foundations_"  ) ''PhyloFoundations)