Statistical Inference and Prediction of Annotations in
Phylogenetic Trees
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Documentation for package ‘aphylo’ version 0.3-3
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 |