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 data PhyloSubConfig =
 198   PhyloSubConfig { _sc_phyloProximity :: Double
 199                  , _sc_phyloSynchrony :: Double
 200                  , _sc_phyloQuality   :: Double
 201                  , _sc_timeUnit       :: TimeUnit
 202                  , _sc_clique         :: Cluster
 203                  , _sc_exportFilter   :: Double
 204                  , _sc_defaultMode    :: Bool
 205                  }
 206   deriving (Show,Generic,Eq)
 207
 208
 209 subConfig2config :: PhyloSubConfig -> PhyloConfig
 210 subConfig2config subConfig = defaultConfig { similarity     = WeightedLogJaccard (_sc_phyloProximity subConfig) 1
 211                                            , phyloSynchrony = ByProximityThreshold (_sc_phyloSynchrony subConfig) 0 AllBranches MergeAllGroups
 212                                            , phyloQuality   = Quality (_sc_phyloQuality   subConfig) 1
 213                                            , timeUnit       = _sc_timeUnit       subConfig
 214                                            , clique         = _sc_clique         subConfig
 215                                            , defaultMode    = _sc_defaultMode    subConfig
 216                                            , exportFilter   = [ByBranchSize $ _sc_exportFilter   subConfig]
 217                                            }
 218
 219 ------------------------------------------------------------------------
 220 defaultConfig :: PhyloConfig
 221 defaultConfig =
 222      PhyloConfig { corpusPath = "corpus.csv" -- useful for commandline only
 223             , listPath       = "list.csv"   -- useful for commandline only
 224             , outputPath     = "data/"
 225             , corpusParser   = Csv 100000
 226             , listParser     = V4
 227             , phyloName      = pack "Phylo Name"
 228             , phyloScale     = 2
 229             , similarity     = WeightedLogJaccard 0.5 1
 230             , seaElevation   = Constante 0.1 0.1
 231             , defaultMode    = False
 232             , findAncestors  = False
 233             , phyloSynchrony = ByProximityThreshold 0.5 0 AllBranches MergeAllGroups
 234             , phyloQuality   = Quality 0.3 1
 235             , timeUnit       = Year 3 1 5
 236             , clique         = Fis 3 1 -- MaxClique 5 0.0001 ByThreshold
 237             , exportLabel    = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2]
 238             , exportSort     = ByHierarchy Desc
 239             , exportFilter   = [ByBranchSize 3]
 240             }
 241
 242 -- Main Instances
 243 instance ToSchema PhyloConfig
 244 instance ToSchema PhyloSubConfig
 245
 246 instance FromJSON PhyloConfig
 247 instance ToJSON PhyloConfig
 248
 249 instance FromJSON PhyloSubConfig
 250 instance ToJSON PhyloSubConfig
 251
 252 instance FromJSON CorpusParser
 253 instance ToJSON CorpusParser
 254
 255 instance FromJSON ListParser
 256 instance ToJSON ListParser
 257
 258 instance FromJSON PhyloSimilarity
 259 instance ToJSON PhyloSimilarity
 260
 261 instance FromJSON SeaElevation
 262 instance ToJSON SeaElevation
 263
 264 instance FromJSON TimeUnit
 265 instance ToJSON TimeUnit
 266
 267 instance FromJSON MaxCliqueFilter
 268 instance ToJSON MaxCliqueFilter
 269
 270 instance FromJSON Cluster
 271 instance ToJSON Cluster
 272
 273 instance FromJSON PhyloLabel
 274 instance ToJSON PhyloLabel
 275
 276 instance FromJSON Tagger
 277 instance ToJSON Tagger
 278
 279 instance FromJSON Sort
 280 instance ToJSON Sort
 281
 282 instance FromJSON Order
 283 instance ToJSON Order
 284
 285 instance FromJSON Filter
 286 instance ToJSON Filter
 287
 288 instance FromJSON SynchronyScope
 289 instance ToJSON SynchronyScope
 290
 291 instance FromJSON SynchronyStrategy
 292 instance ToJSON SynchronyStrategy
 293
 294 instance FromJSON Synchrony
 295 instance ToJSON Synchrony
 296
 297 instance FromJSON Quality
 298 instance ToJSON Quality
 299
 300
 301 -- | Software parameters
 302 data Software =
 303      Software { _software_name    :: Text
 304               , _software_version :: Text
 305      } deriving (Generic, Show, Eq)
 306
 307 instance ToSchema Software where
 308   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_software_")
 309
 310
 311
 312 defaultSoftware :: Software
 313 defaultSoftware =
 314       Software { _software_name    = pack "GarganText"
 315                , _software_version = pack "v5" }
 316
 317
 318 -- | Global parameters of a Phylo
 319 data PhyloParam =
 320      PhyloParam { _phyloParam_version  :: Text
 321                 , _phyloParam_software :: Software
 322                 , _phyloParam_config   :: PhyloConfig
 323      } deriving (Generic, Show, Eq)
 324
 325 instance ToSchema PhyloParam where
 326   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phyloParam_")
 327
 328
 329
 330 defaultPhyloParam :: PhyloParam
 331 defaultPhyloParam =
 332       PhyloParam { _phyloParam_version  = pack "v3"
 333                  , _phyloParam_software = defaultSoftware
 334                  , _phyloParam_config   = defaultConfig }
 335
 336
 337 ------------------
 338 -- | Document | --
 339 ------------------
 340
 341 -- | Date : a simple Integer
 342 type Date = Int
 343
 344 -- | DateStr : the string version of a Date
 345 type DateStr = Text
 346
 347 -- | Ngrams : a contiguous sequence of n terms
 348 type Ngrams = Text
 349
 350 -- Document : a piece of Text linked to a Date
 351 -- date = computational date; date' = original string date yyyy-mm-dd
 352 -- Export Database to Document
 353 data Document = Document
 354       { date    :: Date   -- datatype Date {unDate :: Int}
 355       , date'   :: DateStr   -- show date
 356       , text    :: [Ngrams]
 357       , weight  :: Maybe Double
 358       , sources :: [Text]
 359       , docTime :: TimeUnit
 360       } deriving (Eq,Show,Generic,NFData)
 361
 362
 363 --------------------
 364 -- | Foundation | --
 365 --------------------
 366
 367
 368 -- | The Foundations of a Phylo created from a given TermList
 369 data PhyloFoundations = PhyloFoundations
 370       { _foundations_roots    :: (Vector Ngrams)
 371       , _foundations_rootsInGroups :: Map Int [PhyloGroupId] -- map of roots associated to groups
 372       } deriving (Generic, Show, Eq)
 373
 374 data PhyloCounts = PhyloCounts
 375       { coocByDate    :: !(Map Date Cooc)
 376       , docsByDate    :: !(Map Date Double)
 377       , rootsCountByDate :: !(Map Date (Map Int Double))
 378       , rootsCount    :: !(Map Int  Double)
 379       , rootsFreq     :: !(Map Int  Double)
 380       , lastRootsFreq :: !(Map Int  Double)
 381       } deriving (Generic, Show, Eq)
 382
 383 data PhyloSources = PhyloSources
 384       { _sources :: !(Vector Text) } deriving (Generic, Show, Eq)
 385
 386 instance ToSchema PhyloFoundations where
 387   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_foundations_")
 388 instance ToSchema PhyloCounts where
 389   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 390 instance ToSchema PhyloSources where
 391   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 392
 393 ---------------------------
 394 -- | Coocurency Matrix | --
 395 ---------------------------
 396
 397
 398 -- | Cooc : a coocurency matrix between two ngrams
 399 type Cooc =  Map (Int,Int) Double
 400
 401
 402 -------------------
 403 -- | Phylomemy | --
 404 -------------------
 405
 406 -- | Period : a tuple of Dates
 407 type Period = (Date,Date)
 408
 409 -- | PeriodStr : a tuple of DateStr
 410 type PeriodStr = (DateStr,DateStr)
 411
 412
 413
 414
 415 -- | Phylo datatype of a phylomemy
 416 --  foundations : the foundations of the phylo
 417 --  timeCooc : a Map of coocurency by minimal unit of time (ex: by year)
 418 --  timeDocs : a Map with the numbers of docs by minimal unit of time (ex: by year)
 419 --  param : the parameters of the phylomemy (with the user's configuration)
 420 --  periods : the temporal steps of a phylomemy
 421 data Phylo =
 422      Phylo { _phylo_foundations  :: PhyloFoundations
 423            , _phylo_sources      :: PhyloSources
 424            , _phylo_counts       :: PhyloCounts
 425            , _phylo_seaLadder    :: [Double]
 426            , _phylo_param        :: PhyloParam
 427            , _phylo_periods      :: Map Period PhyloPeriod
 428            , _phylo_quality      :: Double
 429            , _phylo_level        :: Double
 430            }
 431            deriving (Generic, Show, Eq)
 432
 433 instance ToSchema Phylo where
 434   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 435
 436 ----------------
 437 -- | Period | --
 438 ----------------
 439
 440 -- | PhyloPeriod : steps of a phylomemy on a temporal axis
 441 --  id: tuple (start date, end date) of the temporal step of the phylomemy
 442 --  scales: scales of synchronic description
 443 data PhyloPeriod =
 444      PhyloPeriod { _phylo_periodPeriod    :: Period
 445                  , _phylo_periodPeriodStr :: PeriodStr
 446                  , _phylo_periodScales    :: Map PhyloScaleId PhyloScale
 447                  } deriving (Generic, Show, Eq)
 448
 449 instance ToSchema PhyloPeriod where
 450   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 451
 452 ---------------
 453 -- | Scale | --
 454 ---------------
 455
 456 -- | Scale : a scale of synchronic description
 457 type Scale = Int
 458
 459 -- | PhyloScaleId : the id of a scale of synchronic description
 460 type PhyloScaleId  = (Period,Scale)
 461
 462 -- | PhyloScale : sub-structure of the phylomemy in scale of synchronic description
 463 data PhyloScale =
 464      PhyloScale { _phylo_scalePeriod    :: Period
 465                 , _phylo_scalePeriodStr :: PeriodStr
 466                 , _phylo_scaleScale     :: Scale
 467                 , _phylo_scaleGroups    :: Map PhyloGroupId PhyloGroup
 468                 }
 469                 deriving (Generic, Show, Eq)
 470
 471 instance ToSchema PhyloScale where
 472   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 473
 474
 475 type PhyloGroupId  = (PhyloScaleId, Int)
 476
 477 -- | BranchId : (a scale, a sequence of branch index)
 478 -- the sequence is a path of heritage from the most to the less specific branch
 479 type PhyloBranchId = (Scale, [Int])
 480
 481 -- | PhyloGroup : group of ngrams at each scale and period
 482 data PhyloGroup =
 483       PhyloGroup { _phylo_groupPeriod   :: Period
 484                  , _phylo_groupPeriod'  :: (Text,Text)
 485                  , _phylo_groupScale    :: Scale
 486                  , _phylo_groupIndex    :: Int
 487                  , _phylo_groupLabel    :: Text
 488                  , _phylo_groupSupport  :: Support
 489                  , _phylo_groupWeight   :: Maybe Double
 490                  , _phylo_groupSources  :: [Int]
 491                  , _phylo_groupNgrams   :: [Int]
 492                  , _phylo_groupCooc     :: !(Cooc)
 493                  , _phylo_groupDensity  :: Double
 494                  , _phylo_groupBranchId :: PhyloBranchId
 495                  , _phylo_groupMeta     :: Map Text [Double]
 496                  , _phylo_groupRootsCount    :: Map Int Double
 497                  , _phylo_groupScaleParents  :: [Pointer]
 498                  , _phylo_groupScaleChilds   :: [Pointer]
 499                  , _phylo_groupPeriodParents :: [Pointer]
 500                  , _phylo_groupPeriodChilds  :: [Pointer]
 501                  , _phylo_groupAncestors     :: [Pointer]
 502                  , _phylo_groupPeriodMemoryParents :: [Pointer']
 503                  , _phylo_groupPeriodMemoryChilds  :: [Pointer']
 504                  }
 505                  deriving (Generic, Show, Eq, NFData)
 506
 507 instance ToSchema PhyloGroup where
 508   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 509
 510
 511 -- | Weight : A generic mesure that can be associated with an Id
 512 type Weight = Double
 513 type Thr = Double
 514
 515 -- | Pointer : A weighted pointer to a given PhyloGroup
 516 type Pointer = (PhyloGroupId, Weight)
 517 -- | Pointer' : A weighted pointer to a given PhyloGroup with a lower bounded threshold
 518 type Pointer' = (PhyloGroupId, (Thr,Weight))
 519
 520 data Filiation = ToParents | ToChilds | ToParentsMemory | ToChildsMemory deriving (Generic, Show)
 521 data PointerType = TemporalPointer | ScalePointer deriving (Generic, Show)
 522
 523
 524 --------------------------
 525 -- | Phylo Clustering | --
 526 --------------------------
 527
 528 -- | Support : Number of Documents where a Cluster occurs
 529 type Support  = Int
 530
 531 data Clustering = Clustering
 532   { _clustering_roots   :: [Int]
 533   , _clustering_support :: Support
 534   , _clustering_period  :: Period
 535   -- additional materials for visualization
 536   , _clustering_visWeighting :: Maybe Double
 537   , _clustering_visFiltering :: [Int]
 538   } deriving (Generic,NFData,Show,Eq)
 539
 540 ----------------
 541 -- | Export | --
 542 ----------------
 543
 544 type DotId = TextLazy.Text
 545
 546 data EdgeType = GroupToGroup | GroupToGroupMemory | BranchToGroup | BranchToBranch | GroupToAncestor | PeriodToPeriod deriving (Show,Generic,Eq)
 547
 548 data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq)
 549 instance ToSchema Filter where
 550   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 551
 552
 553 data Order = Asc | Desc deriving (Show,Generic,Eq, ToSchema)
 554
 555 data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy {_sort_order :: Order } deriving (Show,Generic,Eq)
 556 instance ToSchema Sort where
 557   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_sort_")
 558
 559
 560 data Tagger = MostInclusive | MostEmergentInclusive | MostEmergentTfIdf deriving (Show,Generic,Eq)
 561 instance ToSchema Tagger where
 562   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 563
 564
 565 data PhyloLabel =
 566       BranchLabel
 567       { _branch_labelTagger :: Tagger
 568       , _branch_labelSize   :: Int }
 569     | GroupLabel
 570       { _group_labelTagger  :: Tagger
 571       , _group_labelSize    :: Int }
 572     deriving (Show,Generic,Eq)
 573
 574 instance ToSchema PhyloLabel where
 575   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 576
 577
 578 data PhyloBranch =
 579       PhyloBranch
 580       { _branch_id :: PhyloBranchId
 581       , _branch_canonId  :: [Int]
 582       , _branch_seaLevel :: [Double]
 583       , _branch_x        :: Double
 584       , _branch_y        :: Double
 585       , _branch_w        :: Double
 586       , _branch_t        :: Double
 587       , _branch_label    :: Text
 588       , _branch_meta     :: Map Text [Double]
 589       } deriving (Generic, Show, Eq)
 590
 591 instance ToSchema PhyloBranch where
 592   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_branch_")
 593
 594 data PhyloExport =
 595       PhyloExport
 596       { _export_groups    :: [PhyloGroup]
 597       , _export_branches  :: [PhyloBranch]
 598       } deriving (Generic, Show)
 599 instance ToSchema PhyloExport where
 600   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_export_")
 601
 602
 603 ----------------
 604 -- | Lenses | --
 605 ----------------
 606
 607 makeLenses ''PhyloConfig
 608 makeLenses ''PhyloSubConfig
 609 makeLenses ''PhyloSimilarity
 610 makeLenses ''SeaElevation
 611 makeLenses ''Quality
 612 makeLenses ''Cluster
 613 makeLenses ''PhyloLabel
 614 makeLenses ''TimeUnit
 615 makeLenses ''PhyloFoundations
 616 makeLenses ''Clustering
 617 makeLenses ''Phylo
 618 makeLenses ''PhyloPeriod
 619 makeLenses ''PhyloScale
 620 makeLenses ''PhyloGroup
 621 makeLenses ''PhyloParam
 622 makeLenses ''PhyloExport
 623 makeLenses ''PhyloBranch
 624
 625 ------------------------
 626 -- | JSON instances | --
 627 ------------------------
 628
 629 instance FromJSON Phylo
 630 instance ToJSON Phylo
 631
 632 instance FromJSON PhyloSources
 633 instance ToJSON PhyloSources
 634
 635 instance FromJSON PhyloParam
 636 instance ToJSON PhyloParam
 637
 638 instance FromJSON PhyloCounts
 639 instance ToJSON PhyloCounts
 640
 641 instance FromJSON PhyloPeriod
 642 instance ToJSON PhyloPeriod
 643
 644 instance FromJSON PhyloScale
 645 instance ToJSON PhyloScale
 646
 647 instance FromJSON Software
 648 instance ToJSON Software
 649
 650 instance FromJSON PhyloGroup
 651 instance ToJSON PhyloGroup
 652
 653 $(deriveJSON (unPrefix "_foundations_"  ) ''PhyloFoundations)