APHYLO_DEFAULT_MCMC_CONTROL
                        Model estimation using Markov Chain Monte Carlo
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
aphylo-class            Annotated Phylogenetic Tree
aphylo-index            Indexing aphylo objects
aphylo-info             Information about 'aphylo' and 'multiAphylo'
                        objects
aphylo-methods          Plot and print methods for 'aphylo' objects
aphylo-model            Formulas in 'aphylo'
aphylo-package          Statistical Inference in Annotated Phylogenetic
                        Trees
aphylo_cv               Leave-one-out Cross Validation
aphylo_estimates        Objects of class 'aphylo_estimates'
aphylo_from_data_frame
                        Create an 'aphylo' object with partial
                        annotations
aphylo_mle              Model estimation using Maximum Likelihood
                        Estimation
as.phylo                Extensions to the 'as.phylo' function
auc                     Area Under the Curve and Receiving Operating
                        Curve
balance_ann             Functional balance of a tree
bprior                  Default priors for aphylo_mcmc
dist2root               Pointer to 'pruner'
fakeexperiment          Fake Experimental Data
faketree                Fake Phylogenetic Tree
imputate_duplications   Impute duplication events based on a vector of
                        species
list_offspring          List each nodes' offspring or parent
mislabel                Switch labels acoording to mislabeling
                        probabilities
multiAphylo             Building Lists of Annotated Trees
panther-tree            Reads PANTHER db trees
plot.aphylo_prediction_score
                        Visualize predictions
plot_logLik             Plot Log-Likelihood function of the model
plot_multivariate       Multiavariate plot (surface)
posterior-probabilities
                        Posterior probabilities based on parameter
                        estimates
prediction_score        Calculate prediction score (quality of
                        prediction)
raphylo                 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
