aphylo-package	aphylo-package
accuracy_sifter	accuracy_sifter
accuracy_sifter.aphylo_estimates	accuracy_sifter
accuracy_sifter.default	accuracy_sifter
ape-methods	ape-methods
aphylo	aphylo-class
aphylo-class	aphylo-class
aphylo-formula	aphylo-model
aphylo-index	aphylo-index
aphylo-info	aphylo-info
aphylo-methods	aphylo-methods
aphylo-model	aphylo-model
aphylo_cv	aphylo_cv
aphylo_cv.formula	aphylo_cv
APHYLO_DEFAULT_MCMC_CONTROL	aphylo_mcmc
aphylo_estimates	aphylo_estimates
aphylo_formula	aphylo-model
aphylo_from_data_frame	aphylo_from_data_frame
aphylo_mcmc	aphylo_mcmc
aphylo_mle	aphylo_mle
APHYLO_PARAM_DEFAULT	aphylo_mcmc
aphylo_pruner	new_aphylo_pruner
as.phylo	as.phylo
as.phylo.aphylo	as.phylo
as.phylo.matrix	as.phylo
auc	auc
balance_ann	balance_ann
bprior	bprior
c.aphylo	multiAphylo
coef.aphylo_estimates	aphylo_estimates
dist2root	new_aphylo_pruner
eta	aphylo-model
fakeexperiment	fakeexperiment
faketree	faketree
get_postorder	new_aphylo_pruner
imputate_duplications	imputate_duplications
list_offspring	list_offspring
list_parents	list_offspring
LogLike	LogLike
MCMC	aphylo_mcmc
mislabel	mislabel
MLE	aphylo_mle
multiAphylo	multiAphylo
mu_d	aphylo-model
mu_s	aphylo-model
Nann	aphylo-info
Nannotated	aphylo-info
new_aphylo	aphylo-class
new_aphylo.phylo	aphylo-class
new_aphylo_pruner	new_aphylo_pruner
Ntrees	aphylo-info
PANTHER	panther-tree
panther-tree	panther-tree
PANTHERDB	panther-tree
Pi	aphylo-model
plot-prediction	plot.aphylo_prediction_score
plot.aphylo	aphylo-methods
plot.aphylo_auc	auc
plot.aphylo_estimates	aphylo_estimates
plot.aphylo_prediction_score	plot.aphylo_prediction_score
plot_logLik	plot_logLik
plot_logLik.aphylo	plot_logLik
plot_logLik.aphylo_estimates	plot_logLik
plot_logLik.formula	plot_logLik
plot_multivariate	plot_multivariate
posterior-probabilities	posterior-probabilities
predict.aphylo_estimates	posterior-probabilities
prediction_score	prediction_score
prediction_score.aphylo_estimates	prediction_score
predict_brute_force	posterior-probabilities
predict_pre_order	posterior-probabilities
predict_pre_order.aphylo	posterior-probabilities
predict_pre_order.aphylo_estimates	posterior-probabilities
print.aphylo_auc	auc
print.aphylo_estimates	aphylo_estimates
print.aphylo_prediction_score	prediction_score
print.multiAphylo	multiAphylo
psi	aphylo-model
raphylo	raphylo
rdrop_annotations	rdrop_annotations
read.panther	panther-tree
read_nhx	read_nhx
read_panther	panther-tree
read_pli	read_pli
rmultiAphylo	raphylo
sim_fun_on_tree	sim_fun_on_tree
sim_tree	sim_tree
states	states
uprior	bprior
vcov.aphylo_estimates	aphylo_estimates
write_pli	write_pli
[.aphylo	aphylo-index
[<-.aphylo	aphylo-index
