Man pages for grady/kdetrees
Nonparametric method for identifying discordant phylogenetic trees
| adjustClassifierParameter | Adjust Classification Tuning Parameter for fitted kdetrees... |
| apicomplexa | Apicomplexa gene trees sample data set. |
| as.data.frame.kdetrees | Convert kdetrees object to data.frame |
| as.matrix.multiPhylo | dissimilarity map tree vectorization |
| bhv.consts | Find BHV constant lower bound |
| bhv.orthant.lb | Lower orthant bound for tree t with bw h. |
| bw.nn | nearest-neighbor adaptive bandwidth selection |
| cutoff | Find cutoff value based on IQR |
| dG.expPoly | Pfaffian matrix for Exponential-polynomial distribution |
| dist.diss | Compute pairwise tree distances |
| estimate | estimate densities from kernel matrix |
| Gpartial | Evaluate |
| hgm.expPoly | Normalizing constant for Exponential-Polynomial distribution |
| hist.kdetrees | Create a histogram of tree density estimates |
| internal.blens | Extract vector of internal branch lengths |
| kdetrees | Identify discordant trees in a sample |
| kdetrees.complete | Complete kdetrees analysis convenience function |
| kdetrees-package | kdetrees |
| load.trees | Read Newick trees from a set of files. |
| make.theta | Create a theta vector from a phylo object |
| normkern | Generalized Gaussian kernel |
| Northant | Count semi-labeled rooted trees on n taxa |
| plot.kdetrees | Plot the unnormalized density estimates for each tree. |
| print.kdetrees | Summarize a kdetrees object in human-readable form. |
| sort.kdetrees | Reorder objects in a kdetrees object based on current density... |
| which.outliers | Find outlier indices based on Tukey's IQR method. |
