aldex.cor	aldex.cor
aldex.glm	aldex.glm
aldex2propr	aldex2propr
all	all
alphaThetaW_old	alphaThetaW_old
alphaTheta_old	alphaTheta_old
bokeh	visualize
bowtie	visualize
bucket	visualize
calculateFDR	calculateFDR
calculateFDR_old	calculateFDR_old
calculateTheta	calculateTheta
calculateThetaW_old	calculateThetaW_old
calculateTheta_old	calculateTheta_old
caneToad.counts	caneToad.counts
caneToad.groups	caneToad.groups
corr	propr
cytescape	visualize
decomposed	visualize
dendroCheck	dendroCheck
dendrogram	visualize
gemini	visualize
getAdj	getAdj
getAdjacency	getAdjacency
getColors	getColours
getColours	getColours
getMatrix	getMatrix
getNetwork	getNetwork
getNormTheta	getNormTheta
getRatios	getRatios
getReference	getReference
getResults	getResults
geyser	visualize
ggdend	ggdend
ivar2index	ivar2index
lr2cor	lr2cor
lr2glm	lr2glm
mail	mail
marg.abs	marg.abs
migraph	migraph
migraph.add	migraph
migraph.clean	migraph
migraph.color	migraph
multiplot	multiplot
packageCheck	packageCheck
pals	pals
parallel	visualize
pca	visualize
pd.d	pd.d
pd.e	pd.e
perb	propr
permuteTheta	permuteTheta
permuteTheta_false	permuteTheta_false
permuteTheta_naive	permuteTheta_naive
permuteTheta_old	permuteTheta_old
permuteTheta_prime	permuteTheta_prime
phis	propr
phit	propr
plot,propd,missing-method	visualize
plot,propr,missing-method	visualize
plotCheck	plotCheck
posthoc	posthoc
pra	pra
prism	visualize
progress	progress
promptCheck	promptCheck
propd	propd
propd-class	propd
propd2propr	visualize
propr	propr
propr-class	propr
proprALR	proprALR
proprCLR	proprCLR
proprPairs	proprPairs
proprPerb	proprPerb
proprPhit	proprPhit
proprSym	proprSym
proprTri	proprTri
proprVLR	proprVLR
qtheta	qtheta
ratios	ratios
setActive	propd
setDisjointed	propd
setEmergent	propd
shale	shale
show,propd-method	propd
show,propr-method	propr
simplify	propr
slate	slate
smear	visualize
snapshot	visualize
subset,propr-method	propr
top.counts	top.counts
top.lr	top.lr
updateCutoffs	updateCutoffs
updateCutoffs.propd	propd
updateCutoffs.propr	propr
updateF	propd
visualize	visualize
wide2long	wide2long
[,propr-method	propr
