Package index • ScrambledTreeBuilder

All functions

ConvenientTblTree: Convenient tbl_trees
FocalCladeList(): List of focal clades
Haloarchaea Halo_DF Halo_PercentDiff Halo_FocalClades Halo_Tree: Example Haloarchaea data objects
MRCA_2D_plot(): 2D MRCA plot
MRCAs(): Most recent common ancestors
averageResults(): Average results
checkDivergenceTimeEstimates(): Performs checks on the estimated divergence times.
childSpecies(): Children species of an ancestor
cladeENRtable(): Aggregate ENR scores by clade
computeCumulativeBranchLengths(): Cumulative branch lengths
computeENR(): Compute ENR points (Excess Normalized Residuals over a LOESS trend)
ellipsePlot(): Ellipse plots
eog(): Run eog on a plot for a clade
extractValues(): Extract values from a matrix.
focalClade(): Focal clades (焦点系統群)
formatStats(): Consolidate YAML reports in one data frame
getDivergenceTime(): Divergence time - TimeTree
getLeaves(): Leaves grouped by direct descendants of a given node
getMRCA(): Gets the most recent common ancestor (MRCA) of two nodes.
getTimeTreePairs(): Gets all pairs of nodes with TimeTree info for all nodes.
getTimeTreePairs_onenode(): Gets all pairs of nodes with TimeTree info for a single node.
getTimeline(): Timeline - TimeTree
inferDivTimesFromExtrapolation(): Divergence time based on extrapolation
inferDivTimesFromTimeTree(): Divergence time based on TimeTree
inferDivergenceTimes(): Estimate divergence time for ancestral nodes
makeItConvenient(): Add needed columns to be convenient
makeMatrix(): Pairwise comparison matrix
makeTidyTree(): Make a tidy tree
makeValueTibble(): Project a matrix onto a tree
model_exp(): Exponential model.
model_gam(): Generalized Additive Model (GAM).
model_gamdec(): Generalized Additive Model (GAM) with a decreasing monotonicity constraint.
model_iso(): Isotonic regression.
model_lin(): Linear interpolation.
model_power(): Power-law model.
model_scam(): Shape Constrained Additive Model (SCAM)
oikData: Oikopleura data
orderWithTree(): Order a comparison matrix
plotDivergenceTimesFromTimeTree(): Plot relation between divergence time and cumulative branch length for a clade.
plotDivergenceTimesPerPath(): Plot stats about each path from tip to root.
plotEstimatedDivergenceTimes(): Plot the divergence times estimated with different models by extrapolation.
plotUnknownDistFromTips(): Plot the relation between distance from tips and lack of information from TimeTree.
recordAncestor(): Record ancestor node ID of a pair
recordClades(): Record clade metadata in results table
removeAssemblies(): Remove assemblies
remove_outliers(): Remove outliers based on thresholds or quartiles
residualBootstrapTree(): Residual-resampling bootstrap tree(s) from a distance matrix (UPGMA)
resultFiles(): List YAML result files
subMatrix(): Subset a matrix with a subtree
subTree(): Extract a subtree
thinByMin(): Thin a matrix by a minimum pairwise distance
treeHeatMap(): Clustered heatmap
visualizeTree(): Plot a phylogenetic tree and its node data