Man pages for ilajaait/deephylo
Infer Parameters from Phylogenies with Deep-Learning
| createEdgesDf | Create edge dataframe |
| createNodesDf | Create node dataframe |
| createPhyloBiSSE | Create one phylogeny under the BiSSE model |
| createPhyloCRBD | Create one phylogeny under the CRBD model |
| drawParamBiSSE | Draw parameters for the BiSSE model |
| drawParamCRBD | Draw parameters for the CRBD model |
| drawPhyloSize | Draw size of a phylogeny |
| extractLadders | Extract ladders from vector |
| fillEdgesAll | Fill all columns of edge dataframe |
| fillEdgesIndex | Fill the "index" column of edge dataframe |
| fillEdgesIsExt | Fill the "isext" column of the edge dataframe |
| fillEdgesLength | Fill the "length" column of edge dataframe |
| fillEdgesParentChild | Fill the "parent" and "child" columns of edge dataframe |
| fillEdgesPart | Fill the "part" column of edge dataframe |
| fillNodesAll | Fill all columns of node dataframe |
| fillNodesColless | Fill the "colless" column of node dataframe |
| fillNodesDepth | Fill the "depth" column of node dataframe |
| fillNodesDist | Fill the "dist" column of node dataframe |
| fillNodesIndex | Fill the "index" column of node dataframe |
| fillNodesIsTip | Fill the "istip" column of node dataframe |
| fillNodesPart | Fill the "part" column of node dataframe |
| fillNodesStair | Fill the "stair" column of node dataframe |
| getBranchLengthStats | Compute branch lengths statistics |
| getChildLeftRight | Left and right child of a node |
| getHeight | Compute phylogeny height |
| getImbalancedNodesProp | Proportion of imbalanced nodes |
| getInLadderNodesProp | Proportion of internal nodes in ladder |
| getLadders | Get ladders of a phylogeny |
| getLttCoords | Sample 20 LTT coordinates |
| getLttSlopes | Compute 10 LTT slopes |
| getMaxLadder | Size of the largest ladder of the phylogeny normalized by the... |
| getMaxWidthDiff | Maximal consecutive width difference of a phylogeny |
| getNodeColless | Compute the colless score of a node |
| getNodeStair | Compute the stairecaseness of a node |
| getRoot | Find root of a phylogeny |
| getSackin | Sackin score |
| getWidthDepthRatio | Width over depth of a phylogeny |
| initializeEdgesDf | Create edge dataframe |
| initializeNodesDf | Create node dataframe |
| isInLadder | Is the node in a ladder? |
| isTip | Is a phylogeny node a tip? |
| lttCoordsNames | Create names for binned LTT coordinate list |
| numberEdges | Compute number of edges of a phylogeny |
| numberNodesInternal | Compute number of internal nodes of a phylogeny |
| numberNodesTotal | Compute total number of nodes of a phylogeny |
| numberTips | Compute number of tips of a phylogeny |
| phyloBiSSE | Attribute of 10 phylogenies created with the BiSSE model |
| phyloCRBD | Attribute of 10 phylogenies created with the CRBD model |
| simulatePhylo | Backbone function to simulate phylogenies |
| simulatePhyloBiSSE | Simulate phylogenies under the BiSSE model |
| simulatePhyloCRBD | Simulate phylogenies under the CRBD model |
| splitLttCoords | Split the LTT coordinates regarding the number of events |
| sumStats | Summary statistics of a phylogeny |
| sumStatsBranchLength | Compute branch lengths summary statistics |
| sumStatsLtt | LTT summary statistics |
| sumStatsTopo | Topological summary statistics |
| writeLadders | Traverse a phylogeny and write ladders |
