| BHS | Multiplicity adjustment by Bonferroni-Holm-Shaffer's rule |
| DesM | Design Matrix For Pairwise Differences |
| dummyze | From Factor To Dummy Variables |
| FWEminP | FWE Adjustment Using Permutation |
| initialize-methods | Methods for function 'initialize' in package 'SOUP':... |
| iterNPC | Iterated NonParametric Combination |
| makePermSpaceID | Constructs Row Indices Permutation Space |
| makePValueMat | Construct Univariate _p_-Values Matrix |
| NPC | NonParametric Combination of Test Statistic |
| orthoX | Residualises the response variables _w.r.t._ the matrix of... |
| PermSpace-class | Class 'PermSpace' |
| print-methods | 'signature(x = "PermSpace")' It prints the whole object on... |
| PValueMat-class | Class 'PValueMat' |
| rankingRule | Performs the ranking |
| RankResults-class | Ranking Results |
| RankResults-method | Methods for function 'as.list' in package 'SOUP' |
| show-methods | 'signature(object = "PermSpace")' Shows only the main... |
| SOUP | SOUP Main Function |
| SoupObject-class | Class 'SoupObject' |
| t2p | From Test Statistics To _p_-Values |
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