Man pages for propr
Calculating Proportionality Between Vectors of Compositional Data
| aldex2propr | Import 'ALDEx2' Object |
| aldex.cor | Correlate CLR Data with a Continuous Measurement |
| aldex.glm | Build a Generalized Linear Model from CLR Data |
| all | A list of most parameters. |
| alphaTheta_old | Calculate alpha Theta |
| alphaThetaW_old | Calculate Weighted Theta |
| calculateFDR | Calculate FDR Cutoffs |
| calculateFDR_old | Calculate FDR Cutoffs |
| calculateTheta | Calculate Theta |
| calculateTheta_old | Calculate Theta |
| calculateThetaW_old | Calculate Weighted Theta |
| caneToad.counts | Example Cane Toad Count Data |
| caneToad.groups | Example Cane Toad Group Data |
| dendroCheck | Dendrogram Plot Check |
| getAdj | Get Object as Adjacency Matrix |
| getAdjacency | Get Object as Adjacency Matrix |
| 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 |
| 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 |
| 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 |
| posthoc | Perform Post-Hoc Testing |
| 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 |
