Copyright	(c) CNRS 2017-Present
License	AGPL + CECILL v3
Maintainer	team@gargantext.org
Stability	experimental
Portability	POSIX
Safe Haskell	Safe-Inferred
Language	Haskell2010

Gargantext.Core.Viz.Phylo.PhyloTools

Description

Synopsis

printIOMsg :: String -> IO ()
printIOComment :: String -> IO ()
truncate' :: Double -> Int -> Double
getInMap :: Int -> Map Int Double -> Double
roundToStr :: (PrintfArg a, Floating a) => Int -> a -> String
countSup :: Double -> [Double] -> Int
dropByIdx :: Int -> [a] -> [a]
elemIndex' :: Eq a => a -> [a] -> Int
commonPrefix :: Eq a => [a] -> [a] -> [a] -> [a]
isRoots :: Ngrams -> Vector Ngrams -> Bool
ngramsToIdx :: [Ngrams] -> Vector Ngrams -> [Int]
sourcesToIdx :: [Text] -> Vector Text -> [Int]
ngramsToLabel :: Vector Ngrams -> [Int] -> Text
idxToLabel :: [Int] -> String
idxToLabel' :: [Double] -> String
ngramsToText :: Vector Ngrams -> [Int] -> [Text]
periodsToYears :: [(Date, Date)] -> Set Date
findBounds :: [Date] -> (Date, Date)
toPeriods :: [Date] -> Int -> Int -> [(Date, Date)]
toFstDate :: [Text] -> Text
toLstDate :: [Text] -> Text
getTimeScale :: Phylo -> [Char]
toTimeScale :: [Date] -> Int -> [Date]
getTimeStep :: TimeUnit -> Int
getTimePeriod :: TimeUnit -> Int
getTimeFrame :: TimeUnit -> Int
isNested :: Eq a => [a] -> [a] -> Bool
keepFilled :: (Int -> [a] -> [a]) -> Int -> [a] -> [a]
tracePhylo :: (Print s, IsString s) => s -> a -> a
traceClique :: Map (Date, Date) [Clustering] -> String
traceSupport :: Map (Date, Date) [Clustering] -> String
traceFis :: [Char] -> Map (Date, Date) [Clustering] -> Map (Date, Date) [Clustering]
getCliqueSupport :: Cluster -> Int
getCliqueSize :: Cluster -> Int
listToCombi' :: [a] -> [(a, a)]
listToEqual' :: Eq a => [a] -> [(a, a)]
listToKeys :: Eq a => [a] -> [(a, a)]
listToMatrix :: [Int] -> Map (Int, Int) Double
listToMatrix' :: [Ngrams] -> Map (Ngrams, Ngrams) Int
listToSeq :: Eq a => [a] -> [(a, a)]
sumCooc :: Cooc -> Cooc -> Cooc
getTrace :: Cooc -> Double
coocToDiago :: Cooc -> Cooc
coocToAdjacency :: Cooc -> Cooc
ngramsToCooc :: [Int] -> [Cooc] -> Cooc
ngramsToDensity :: [Int] -> [Cooc] -> Map Int Double -> Double
findMaxima :: [(Double, Double)] -> [Bool]
toChunk :: Int -> [a] -> [[a]]
toAverageDegree :: Cooc -> Vector Ngrams -> Double
regimeToDefaultLevel :: Cooc -> Vector Ngrams -> Double
coocToConfidence :: Phylo -> Cooc
sumtest :: [Int] -> [Int] -> Int
findDefaultLevel :: Phylo -> Phylo
getGroupId :: PhyloGroup -> PhyloGroupId
getGroupNgrams :: PhyloGroup -> [Int]
idToPrd :: PhyloGroupId -> Period
groupByField :: Ord a => (PhyloGroup -> a) -> [PhyloGroup] -> Map a [PhyloGroup]
getPeriodPointers :: Filiation -> PhyloGroup -> [Pointer]
filterSimilarity :: PhyloSimilarity -> Double -> Double -> Bool
getSimilarityName :: PhyloSimilarity -> String
addPointers :: Filiation -> PointerType -> [Pointer] -> PhyloGroup -> PhyloGroup
toPointer' :: Double -> Pointer -> Pointer'
addMemoryPointers :: Filiation -> PointerType -> Double -> [Pointer] -> PhyloGroup -> PhyloGroup
getPeriodIds :: Phylo -> [(Date, Date)]
getLastDate :: Phylo -> Date
getLevelParentId :: PhyloGroup -> PhyloGroupId
getLastLevel :: Phylo -> Scale
getScales :: Phylo -> [Scale]
getSeaElevation :: Phylo -> SeaElevation
getSimilarity :: Phylo -> PhyloSimilarity
getPhyloSeaRiseStart :: Phylo -> Double
getPhyloSeaRiseSteps :: Phylo -> Double
getConfig :: Phylo -> PhyloConfig
getLevel :: Phylo -> Double
getLadder :: Phylo -> [Double]
getCoocByDate :: Phylo -> Map Date Cooc
getRootsCountByDate :: Phylo -> Map Date (Map Int Double)
getDocsByDate :: Phylo -> Map Date Double
getRootsCount :: Phylo -> Map Int Double
getRootsFreq :: Phylo -> Map Int Double
getLastRootsFreq :: Phylo -> Map Int Double
setConfig :: PhyloConfig -> Phylo -> Phylo
getRoots :: Phylo -> Vector Ngrams
getRootsInGroups :: Phylo -> Map Int [PhyloGroupId]
getSources :: Phylo -> Vector Text
phyloLastScale :: Phylo -> [[PhyloGroup]]
getGroupsFromScale :: Scale -> Phylo -> [PhyloGroup]
getGroupsFromScalePeriods :: Scale -> [Period] -> Phylo -> [PhyloGroup]
getGroupsFromPeriods :: Scale -> Map Period PhyloPeriod -> [PhyloGroup]
updatePhyloGroups :: Scale -> Map PhyloGroupId PhyloGroup -> Phylo -> Phylo
updatePeriods :: Map (Date, Date) (Text, Text) -> Phylo -> Phylo
updateQuality :: Double -> Phylo -> Phylo
updateLevel :: Double -> Phylo -> Phylo
traceToPhylo :: Scale -> Phylo -> Phylo
mergeBranchIds :: [[Int]] -> [Int]
mergeMeta :: [Int] -> [PhyloGroup] -> Map Text [Double]
groupsToBranches' :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
relatedComponents :: Ord a => [[a]] -> [[a]]
toRelatedComponents :: [PhyloGroup] -> [((PhyloGroup, PhyloGroup), Double)] -> [[PhyloGroup]]
traceSynchronyEnd :: Phylo -> Phylo
traceSynchronyStart :: Phylo -> Phylo
getSensibility :: PhyloSimilarity -> Double
getMinSharedNgrams :: PhyloSimilarity -> Int
intersectInit :: Eq a => [a] -> [a] -> [a] -> [a]
branchIdsToSimilarity :: PhyloBranchId -> PhyloBranchId -> Double -> Double -> Double
ngramsInBranches :: [[PhyloGroup]] -> [Int]
traceMatchSuccess :: Double -> Double -> Double -> [[[PhyloGroup]]] -> [[[PhyloGroup]]]
traceMatchFailure :: Double -> Double -> Double -> [[PhyloGroup]] -> [[PhyloGroup]]
traceMatchNoSplit :: [[PhyloGroup]] -> [[PhyloGroup]]
traceMatchLimit :: [[PhyloGroup]] -> [[PhyloGroup]]
traceMatchEnd :: [PhyloGroup] -> [PhyloGroup]
traceTemporalMatching :: [PhyloGroup] -> [PhyloGroup]
traceGroupsProxi :: [Double] -> [Double]

Documentation

printIOMsg :: String -> IO () #

Io | --

To print an important message as an IO()

printIOComment :: String -> IO () #

To print a comment as an IO()

truncate' :: Double -> Int -> Double #

Misc | --

getInMap :: Int -> Map Int Double -> Double #

roundToStr :: (PrintfArg a, Floating a) => Int -> a -> String #

countSup :: Double -> [Double] -> Int #

dropByIdx :: Int -> [a] -> [a] #

elemIndex' :: Eq a => a -> [a] -> Int #

commonPrefix :: Eq a => [a] -> [a] -> [a] -> [a] #

isRoots :: Ngrams -> Vector Ngrams -> Bool #

Foundations | --

Is this Ngrams a Foundations Root ?

ngramsToIdx :: [Ngrams] -> Vector Ngrams -> [Int] #

To transform a list of nrams into a list of foundation's index

sourcesToIdx :: [Text] -> Vector Text -> [Int] #

To transform a list of sources into a list of sources' index

ngramsToLabel :: Vector Ngrams -> [Int] -> Text #

To transform a list of Ngrams Indexes into a Label

idxToLabel :: [Int] -> String #

idxToLabel' :: [Double] -> String #

ngramsToText :: Vector Ngrams -> [Int] -> [Text] #

To transform a list of Ngrams Indexes into a list of Text

periodsToYears :: [(Date, Date)] -> Set Date #

Time | --

To transform a list of periods into a set of Dates

findBounds :: [Date] -> (Date, Date) #

toPeriods :: [Date] -> Int -> Int -> [(Date, Date)] #

toFstDate :: [Text] -> Text #

toLstDate :: [Text] -> Text #

getTimeScale :: Phylo -> [Char] #

toTimeScale :: [Date] -> Int -> [Date] #

Get a regular & ascendante timeScale from a given list of dates

getTimeStep :: TimeUnit -> Int #

getTimePeriod :: TimeUnit -> Int #

getTimeFrame :: TimeUnit -> Int #

isNested :: Eq a => [a] -> [a] -> Bool #

Fis | --

To find if l' is nested in l

keepFilled :: (Int -> [a] -> [a]) -> Int -> [a] -> [a] #

To filter Fis with small Support but by keeping non empty Periods

tracePhylo :: (Print s, IsString s) => s -> a -> a #

General workhorse to use in lieu of trace. It decides at compile time whether or not debug logs are enabled.

traceClique :: Map (Date, Date) [Clustering] -> String #

traceSupport :: Map (Date, Date) [Clustering] -> String #

traceFis :: [Char] -> Map (Date, Date) [Clustering] -> Map (Date, Date) [Clustering] #

getCliqueSupport :: Cluster -> Int #

Cluster| --

getCliqueSize :: Cluster -> Int #

listToCombi' :: [a] -> [(a, a)] #

Cooc | --

listToEqual' :: Eq a => [a] -> [(a, a)] #

listToKeys :: Eq a => [a] -> [(a, a)] #

listToMatrix :: [Int] -> Map (Int, Int) Double #

listToMatrix' :: [Ngrams] -> Map (Ngrams, Ngrams) Int #

listToSeq :: Eq a => [a] -> [(a, a)] #

sumCooc :: Cooc -> Cooc -> Cooc #

getTrace :: Cooc -> Double #

coocToDiago :: Cooc -> Cooc #

coocToAdjacency :: Cooc -> Cooc #

ngramsToCooc :: [Int] -> [Cooc] -> Cooc #

To build the local cooc matrix of each phylogroup

ngramsToDensity :: [Int] -> [Cooc] -> Map Int Double -> Double #

Density | --

To build the density of a phylogroup density is defined in Callon M, Courtial JP, Laville F (1991) Co-word analysis as a tool for describing the network of interaction between basic and technological research: The case of polymer chemistry. Scientometric 22: 155–205.

findMaxima :: [(Double, Double)] -> [Bool] #

Defaults | --

find the local maxima in a list of values

toChunk :: Int -> [a] -> [[a]] #

split a list into chunks of size n

toAverageDegree :: Cooc -> Vector Ngrams -> Double #

To compute the average degree from a cooc matrix http://networksciencebook.com/chapter/2#degree

regimeToDefaultLevel :: Cooc -> Vector Ngrams -> Double #

Use the giant component regime to estimate the default level http://networksciencebook.com/chapter/3#networks-supercritical

coocToConfidence :: Phylo -> Cooc #

sumtest :: [Int] -> [Int] -> Int #

findDefaultLevel :: Phylo -> Phylo #