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