Function reference • aphylo

All functions
`LogLike()`	Likelihood of an observed annotated phylogenetic tree
`accuracy_sifter()`	Accuracy calculation as defined in Engelhardt et al. (2011)
`ape-methods`	Available methods from the APE package
`new_aphylo()`	Annotated Phylogenetic Tree
`[`(<aphylo>) `[<-`(<aphylo>)	Indexing aphylo objects
`Nann()` `Nannotated()` `Ntrees()`	Information about `aphylo` and `multiAphylo` objects
`plot(<aphylo>)`	Plot and print methods for `aphylo` objects
`eta()` `psi()` `Pi()` `mu_d()` `mu_s()` `aphylo_formula()`	Formulas in `aphylo`
`aphylo-package`	Statistical Inference in Annotated Phylogenetic Trees
`aphylo_cv()`	Leave-one-out Cross Validation
`print(<aphylo_estimates>)` `coef(<aphylo_estimates>)` `vcov(<aphylo_estimates>)` `plot(<aphylo_estimates>)`	Objects of class `aphylo_estimates`
`aphylo_from_data_frame()`	Create an `aphylo` object with partial annotations
`APHYLO_DEFAULT_MCMC_CONTROL` `aphylo_mcmc()` `APHYLO_PARAM_DEFAULT`	Model estimation using Markov Chain Monte Carlo
`aphylo_mle()`	Model estimation using Maximum Likelihood Estimation
`as.phylo(<matrix>)` `as.phylo(<aphylo>)`	Extensions to the `as.phylo` function
`auc()` `print(<aphylo_auc>)` `plot(<aphylo_auc>)`	Area Under the Curve and Receiving Operating Curve
`balance_ann()`	Functional balance of a tree
`bprior()` `uprior()`	Default priors for aphylo_mcmc
`fakeexperiment`	Fake Experimental Data
`faketree`	Fake Phylogenetic Tree
`imputate_duplications()`	Impute duplication events based on a vector of species
`list_offspring()` `list_parents()`	List each nodes' offspring or parent
`mislabel()`	Switch labels acoording to mislabeling probabilities
`c(<aphylo>)` `print(<multiAphylo>)`	Building Lists of Annotated Trees
`dist2root()` `get_postorder()` `new_aphylo_pruner()`	Pointer to `pruner`
`read_panther()` `read.panther()`	Reads PANTHER db trees
`plot(<aphylo_prediction_score>)`	Visualize predictions
`plot_logLik()`	Plot Log-Likelihood function of the model
`plot_multivariate()`	Multiavariate plot (surface)
`predict(<aphylo_estimates>)` `predict_pre_order()` `predict_brute_force()`	Posterior probabilities based on parameter estimates
`prediction_score()` `print(<aphylo_prediction_score>)`	Calculate prediction score (quality of prediction)
`raphylo()` `rmultiAphylo()`	Simulation of Annotated Phylogenetic Trees
`rdrop_annotations()`	Randomly drop leaf annotations
`read_nhx()`	Read New Hampshire eXtended format for trees
`read_pli()`	Read PLI files from SIFTER
`sim_fun_on_tree()`	Simulate functions on a ginven tree
`sim_tree()`	Random tree generation
`states()`	Matrix of states
`write_pli()`	Write pli files used by SIFTER

Reference

All functions