# Statistical Inference and Prediction of Annotations in Phylogenetic Trees

## Documentation for package ‘aphylo’ version 0.3-3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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