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_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-index | Indexing aphylo objects |
aphylo-info | Information about 'aphylo' and 'multiAphylo' objects |
aphylo_mcmc | Model estimation using Markov Chain Monte Carlo |
aphylo-methods | Plot and print methods for 'aphylo' objects |
aphylo_mle | Model estimation using Maximum Likelihood Estimation |
aphylo-model | Formulas in 'aphylo' |
aphylo-package | Statistical Inference in Annotated Phylogenetic Trees |
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 |
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 |
LogLike | Likelihood of an observed annotated phylogenetic tree |
mislabel | Switch labels acoording to mislabeling probabilities |
multiAphylo | Building Lists of Annotated Trees |
new_aphylo_pruner | Pointer to 'pruner' |
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 |
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