Man pages for USCbiostats/phylogenetic
Statistical Inference and Prediction of Annotations in Phylogenetic Trees

accuracy_sifterAccuracy calculation as defined in Engelhardt et al. (2011)
ape-methodsAvailable methods from the APE package
aphylo-classAnnotated Phylogenetic Tree
aphylo_cvLeave-one-out Cross Validation
aphylo_estimatesObjects of class 'aphylo_estimates'
aphylo_from_data_frameCreate an 'aphylo' object with partial annotations
aphylo-indexIndexing aphylo objects
aphylo-infoInformation about 'aphylo' and 'multiAphylo' objects
aphylo_mcmcModel estimation using Markov Chain Monte Carlo
aphylo-methodsPlot and print methods for 'aphylo' objects
aphylo_mleModel estimation using Maximum Likelihood Estimation
aphylo-modelFormulas in 'aphylo'
aphylo-packageStatistical Inference in Annotated Phylogenetic Trees
as.phyloExtensions to the 'as.phylo' function
aucArea Under the Curve and Receiving Operating Curve
balance_annFunctional balance of a tree
bpriorDefault priors for aphylo_mcmc
fakeexperimentFake Experimental Data
faketreeFake Phylogenetic Tree
imputate_duplicationsImpute duplication events based on a vector of species
list_offspringList each nodes' offspring or parent
LogLikeLikelihood of an observed annotated phylogenetic tree
mislabelSwitch labels acoording to mislabeling probabilities
multiAphyloBuilding Lists of Annotated Trees
new_aphylo_prunerPointer to 'pruner'
panther-treeReads PANTHER db trees
plot.aphylo_prediction_scoreVisualize predictions
plot_logLikPlot Log-Likelihood function of the model
plot_multivariateMultiavariate plot (surface)
posterior-probabilitiesPosterior probabilities based on parameter estimates
prediction_scoreCalculate prediction score (quality of prediction)
raphyloSimulation of Annotated Phylogenetic Trees
rdrop_annotationsRandomly drop leaf annotations
read_nhxRead New Hampshire eXtended format for trees
read_pliRead PLI files from SIFTER
sim_fun_on_treeSimulate functions on a ginven tree
sim_treeRandom tree generation
statesMatrix of states
write_pliWrite pli files used by SIFTER
USCbiostats/phylogenetic documentation built on Oct. 28, 2023, 7:23 a.m.