# Calculating Proportionality Between Vectors of Compositional Data

## Documentation for package ‘propr’ version 4.2.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
bokeh | Visualize Proportionality
bowtie | Visualize Proportionality
bucket | Visualize Proportionality
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
corr | The propr Package
cytescape | Visualize Proportionality
decomposed | Visualize Proportionality
dendroCheck | Dendrogram Plot Check
dendrogram | Visualize Proportionality
gemini | Visualize Proportionality
getAdj | Get Object as Adjacency Matrix
getAdjacency | Get Object as Adjacency Matrix
getColors | Label 'propd' Pairs by DE Results
getColours | Label 'propd' Pairs by DE Results
getMatrix | Get Object as Symmetric Matrix
getNetwork | Get Network from Object
getNormTheta | Get Per-Feature Theta
getRatios | Get (Log-)ratios from Object
getReference | Get Reference to Approximate CLR
getResults | Get Results from Object
geyser | Visualize Proportionality
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
migraph.add | 'igraph' Helper Functions
migraph.clean | 'igraph' Helper Functions
migraph.color | 'igraph' Helper Functions
multiplot | Plot Multiple Graphs
packageCheck | Package Check
pals | Calculate PALs for Pairs
parallel | Visualize Proportionality
pca | Visualize Proportionality
pd.d | Example propd Object
pd.e | Example propd Object
perb | The propr Package
permuteTheta | Permute Theta
permuteTheta_false | Permute Theta
permuteTheta_naive | Permute Theta
permuteTheta_old | Permute Theta
permuteTheta_prime | Permute Theta
phis | The propr Package
phit | The propr Package
plot-method | Visualize Proportionality
plotCheck | Plot Check
posthoc | Perform Post-Hoc Testing
pra | Principal Ratio Analysis
prism | Visualize Proportionality
progress | Make Progress Bar
promptCheck | Feature Check
propd | The propd Method
propd-class | The propd Method
propd2propr | Visualize Proportionality
propr | The propr Package
propr-class | 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
setActive | The propd Method
setDisjointed | The propd Method
setEmergent | The propd Method
shale | Build 'propd' Results Table
show-method | The propd Method
show-method | The propr Package
simplify | The propr Package
slate | Build 'propr' Results Table
smear | Visualize Proportionality
snapshot | Visualize Proportionality
subset-method | The propr Package
top.counts | Example propr Object
top.lr | Example propr Object
updateCutoffs | Update FDR by Permutation
updateCutoffs.propd | The propd Method
updateCutoffs.propr | The propr Package
updateF | The propd Method
visualize | Visualize Proportionality
wide2long | Make Long Data from Wide Data
[-method | The propr Package