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