Statistical Inference and Prediction of Annotations in Phylogenetic Trees


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Documentation for package ‘aphylo’ version 0.2-1

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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