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
childSpecies(): Children species of an ancestor
cladeENRtable(): Aggregate ENR scores by clade
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
makeItConvenient(): Add needed columns to be convenient
makeMatrix(): Pairwise comparison matrix
makeTidyTree(): Make a tidy tree
makeValueTibble(): Project a matrix onto a tree
oikData: Oikopleura data
orderWithTree(): Order a comparison matrix
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