aldex.cor               Correlate CLR Data with a Continuous
                        Measurement
aldex.glm               Build a Generalized Linear Model from CLR Data
aldex2propr             Import 'ALDEx2' Object
all                     A list of most parameters.
alphaThetaW_old         Calculate Weighted Theta
alphaTheta_old          Calculate alpha Theta
calculateFDR            Calculate FDR Cutoffs
calculateFDR_old        Calculate FDR Cutoffs
calculateTheta          Calculate Theta
calculateThetaW_old     Calculate Weighted Theta
calculateTheta_old      Calculate Theta
caneToad.counts         Example Cane Toad Count Data
caneToad.groups         Example Cane Toad Group Data
dendroCheck             Dendrogram Plot Check
getAdjacency            Get Object as Adjacency Matrix
getMatrix               Get Object as Symmetric Matrix
getNetwork              Get Network from Object
getRatios               Get (Log-)ratios from Object
getReference            Get Reference to Approximate CLR
getResults              Get Results from Object
ggdend                  Dendrogram Plot Wrapper
ivar2index              Build Index from ivar Argument
lr2cor                  Correlate CLR Data with a Continuous
                        Measurement
lr2glm                  Build a Generalized Linear Model from CLR Data
mail                    Mock Mail Count Data
marg.abs                Example Absolute mRNA
migraph                 'igraph' Helper Functions
multiplot               Plot Multiple Graphs
packageCheck            Package Check
pals                    Calculate PALs for Pairs
pd.d                    Example propd Object
pd.e                    Example propd Object
permuteTheta            Permute Theta
permuteTheta_false      Permute Theta
permuteTheta_naive      Permute Theta
permuteTheta_old        Permute Theta
permuteTheta_prime      Permute Theta
plotCheck               Plot Check
pra                     Principal Ratio Analysis
progress                Make Progress Bar
promptCheck             Feature Check
propd                   The propd Method
propr                   The propr Package
proprALR                Calculates the additive log-ratio
                        transformation.
proprCLR                Calculates the centered log-ratio
                        transformation.
proprPairs              Recasts proportionality matrix as a table of
                        feature pairs.
proprPerb               Calculate proportionality metric rho (Erb
                        2016).
proprPhit               Calculate proportionality metric phi (Lovell
                        2015).
proprSym                Symmetrizes a proportionality matrix.
proprTri                Retrieve the lower left triangle of a
                        proportionality matrix.
proprVLR                Calculates the variance of the log of the
                        ratios.
qtheta                  Calculate a theta Cutoff
ratios                  Recast Matrix as Feature (Log-)Ratios
shale                   Build 'propd' Results Table
slate                   Build 'propr' Results Table
top.counts              Example propr Object
top.lr                  Example propr Object
updateCutoffs           Update FDR by Permutation
visualize               Visualize Proportionality
wide2long               Make Long Data from Wide Data
