Copyright	(c) CNRS 2017-Present
License	AGPL + CECILL v3
Maintainer	team@gargantext.org
Stability	experimental
Portability	POSIX
Safe Haskell	None
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]
traceClique :: Map (Date, Date) [PhyloClique] -> String
traceSupport :: Map (Date, Date) [PhyloClique] -> String
traceFis :: [Char] -> Map (Date, Date) [PhyloClique] -> Map (Date, Date) [PhyloClique]
getCliqueSupport :: Clique -> Int
getCliqueSize :: Clique -> 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
ngramsToCooc :: [Int] -> [Cooc] -> Cooc
getGroupId :: PhyloGroup -> PhyloGroupId
idToPrd :: PhyloGroupId -> PhyloPeriodId
groupByField :: Ord a => (PhyloGroup -> a) -> [PhyloGroup] -> Map a [PhyloGroup]
getPeriodPointers :: Filiation -> PhyloGroup -> [Pointer]
filterProximity :: Proximity -> Double -> Double -> Bool
getProximityName :: Proximity -> String
addPointers :: Filiation -> PointerType -> [Pointer] -> PhyloGroup -> PhyloGroup
getPeriodIds :: Phylo -> [(Date, Date)]
getLevelParentId :: PhyloGroup -> PhyloGroupId
getLastLevel :: Phylo -> Level
getLevels :: Phylo -> [Level]
getSeaElevation :: Phylo -> SeaElevation
getConfig :: Phylo -> Config
setConfig :: Config -> Phylo -> Phylo
getRoots :: Phylo -> Vector Ngrams
getSources :: Phylo -> Vector Text
phyloToLastBranches :: Phylo -> [[PhyloGroup]]
getGroupsFromLevel :: Level -> Phylo -> [PhyloGroup]
getGroupsFromLevelPeriods :: Level -> [PhyloPeriodId] -> Phylo -> [PhyloGroup]
getGroupsFromPeriods :: Level -> Map PhyloPeriodId PhyloPeriod -> [PhyloGroup]
updatePhyloGroups :: Level -> Map PhyloGroupId PhyloGroup -> Phylo -> Phylo
updatePeriods :: Map (Date, Date) (Text, Text) -> Phylo -> Phylo
traceToPhylo :: Level -> 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 :: Proximity -> Double
intersectInit :: Eq a => [a] -> [a] -> [a] -> [a]
branchIdsToProximity :: 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 :: Map (PhyloGroupId, PhyloGroupId) Double -> Map (PhyloGroupId, PhyloGroupId) Double

Documentation

printIOMsg :: String -> IO () Source #

Io | --

To print an important message as an IO()

printIOComment :: String -> IO () Source #

To print a comment as an IO()

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

Misc | --

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

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

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

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

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

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

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

Foundations | --

Is this Ngrams a Foundations Root ?

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

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

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

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

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

To transform a list of Ngrams Indexes into a Label

idxToLabel :: [Int] -> String Source #

idxToLabel' :: [Double] -> String Source #

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

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

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

Time | --

To transform a list of periods into a set of Dates

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

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

toFstDate :: [Text] -> Text Source #

toLstDate :: [Text] -> Text Source #

getTimeScale :: Phylo -> [Char] Source #

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

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

getTimeStep :: TimeUnit -> Int Source #

getTimePeriod :: TimeUnit -> Int Source #

getTimeFrame :: TimeUnit -> Int Source #

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

Fis | --

To find if l' is nested in l

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

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

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

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

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

getCliqueSupport :: Clique -> Int Source #

Clique| --

getCliqueSize :: Clique -> Int Source #

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

Cooc | --

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

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

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

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

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

sumCooc :: Cooc -> Cooc -> Cooc Source #

getTrace :: Cooc -> Double Source #

coocToDiago :: Cooc -> Cooc Source #

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

To build the local cooc matrix of each phylogroup

getGroupId :: PhyloGroup -> PhyloGroupId Source #

PhyloGroup | --

idToPrd :: PhyloGroupId -> PhyloPeriodId Source #

groupByField :: Ord a => (PhyloGroup -> a) -> [PhyloGroup] -> Map a [PhyloGroup] Source #

getPeriodPointers :: Filiation -> PhyloGroup -> [Pointer] Source #

filterProximity :: Proximity -> Double -> Double -> Bool Source #

getProximityName :: Proximity -> String Source #

addPointers :: Filiation -> PointerType -> [Pointer] -> PhyloGroup -> PhyloGroup Source #

Phylo | --

getPeriodIds :: Phylo -> [(Date, Date)] Source #

getLevelParentId :: PhyloGroup -> PhyloGroupId Source #

getLastLevel :: Phylo -> Level Source #

getLevels :: Phylo -> [Level] Source #

getSeaElevation :: Phylo -> SeaElevation Source #

getConfig :: Phylo -> Config Source #

setConfig :: Config -> Phylo -> Phylo Source #

getRoots :: Phylo -> Vector Ngrams Source #

getSources :: Phylo -> Vector Text Source #

phyloToLastBranches :: Phylo -> [[PhyloGroup]] Source #

getGroupsFromLevel :: Level -> Phylo -> [PhyloGroup] Source #

getGroupsFromLevelPeriods :: Level -> [PhyloPeriodId] -> Phylo -> [PhyloGroup] Source #

getGroupsFromPeriods :: Level -> Map PhyloPeriodId PhyloPeriod -> [PhyloGroup] Source #

updatePhyloGroups :: Level -> Map PhyloGroupId PhyloGroup -> Phylo -> Phylo Source #

updatePeriods :: Map (Date, Date) (Text, Text) -> Phylo -> Phylo Source #

traceToPhylo :: Level -> Phylo -> Phylo Source #

mergeBranchIds :: [[Int]] -> [Int] Source #

Clustering | --

mergeMeta :: [Int] -> [PhyloGroup] -> Map Text [Double] Source #

groupsToBranches :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]] Source #

relatedComponents :: Ord a => [[a]] -> [[a]] Source #

traceSynchronyEnd :: Phylo -> Phylo Source #

traceSynchronyStart :: Phylo -> Phylo Source #

getSensibility :: Proximity -> Double Source #

Proximity | --

intersectInit :: Eq a => [a] -> [a] -> [a] -> [a] Source #

Branch | --

branchIdsToProximity :: PhyloBranchId -> PhyloBranchId -> Double -> Double -> Double Source #

ngramsInBranches :: [[PhyloGroup]] -> [Int] Source #

traceMatchSuccess :: Double -> Double -> Double -> [[[PhyloGroup]]] -> [[[PhyloGroup]]] Source #

traceMatchFailure :: Double -> Double -> Double -> [[PhyloGroup]] -> [[PhyloGroup]] Source #

traceMatchNoSplit :: [[PhyloGroup]] -> [[PhyloGroup]] Source #

traceMatchLimit :: [[PhyloGroup]] -> [[PhyloGroup]] Source #

traceMatchEnd :: [PhyloGroup] -> [PhyloGroup] Source #

traceTemporalMatching :: [PhyloGroup] -> [PhyloGroup] Source #

traceGroupsProxi :: Map (PhyloGroupId, PhyloGroupId) Double -> Map (PhyloGroupId, PhyloGroupId) Double Source #