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| abstract | Abstract Two propr Objects |
| adjacent | The propr Package |
| aldex.cor | Correlate CLR with a Continuous Measurement |
| aldex2propr | Import 'ALDEx2' Object |
| alphaTheta | Calculate alpha Theta |
| alphaThetaW_old | Calculate Weighted Theta |
| alphaTheta_old | Calculate alpha Theta |
| bokeh | Visualize Proportionality |
| bowtie | The propd Method |
| 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 | Calculate Proportionality |
| cytescape | Visualize Proportionality |
| decomposed | The propd Method |
| dendroCheck | Dendrogram Plot Check |
| dendrogram | Visualize Proportionality |
| differentialCheck | Differential Proportionality Check |
| gemini | The propd Method |
| geyser | The propd Method |
| ggdend | Dendrogram Plot Wrapper |
| initialize-method | Calculate Proportionality |
| ivar2index | Build Index from ivar Argument |
| lr2cor | Correlate CLR with a Continuous Measurement |
| 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 |
| pca | Visualize Proportionality |
| pd.d | Example propd Object |
| pd.e | Example propd Object |
| perb | Calculate Proportionality |
| permuteTheta | Permute Theta |
| permuteTheta_false | Permute Theta |
| permuteTheta_naive | Permute Theta |
| permuteTheta_old | Permute Theta |
| permuteTheta_prime | Permute Theta |
| phis | Calculate Proportionality |
| phit | Calculate Proportionality |
| plot-method | The propd Method |
| plot-method | The propr Package |
| plotCheck | Plot Check |
| prism | Visualize Proportionality |
| progress | Make Progress Bar |
| promptCheck | Feature Check |
| prop2prob | Calculate Probability from Proportionality |
| propd | The propd Method |
| propd-class | The propd Method |
| propd2propr | The propd Method |
| proportionality | Calculate 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. |
| ratios | Recast Matrix as Feature Ratios |
| setActive | The propd Method |
| setDisjointed | The propd Method |
| setEmergent | The propd Method |
| shale | The propd Method |
| show-method | The propd Method |
| show-method | The propr Package |
| simplify | The propr Package |
| slate | Visualize Proportionality |
| slice | The propd Method |
| smear | Visualize Proportionality |
| snapshot | Visualize Proportionality |
| subset-method | The propr Package |
| top.counts | Example propr Object |
| top.lr | Example propr Object |
| updateCutoffs | The propd Method |
| updateF | The propd Method |
| visualize | Visualize Proportionality |
| [-method | The propr Package |