Man pages for smvargas/PERMANOVA
Power estimation for microbiome studies using pairwise distances and PERMANOVA.
| bootDM | Take a bootstrap sample from a square distance matrix. |
| bootPower | Perform bootstrap power analysis on a list of square distance... |
| calcOmega2 | Calculate omega-squared. |
| calcPERMANOVAp | Calculate the PERMANOVA p-value. |
| calcR2 | Calculate the coefficient of determination (R-squared). |
| calcUJsample | Calculate unweighted Jaccard distance between two OTU vectors |
| calcUJstudy | Calculate pairwise unweighted Jaccard distances from an OTU... |
| calcWJsample | Calculate weighted Jaccard distance between two OTU vectors |
| calcWJstudy | Calculate pairwise weighted Jaccard distances from an OTU... |
| groupNames | Convert distance matrix subject names to group-level names. |
| hashMean | Simulate a list of OTU tables to create a hash table relating... |
| hashSD | Simulate a list of OTU tables to create a hash table relating... |
| lowerTriDM | Extract the pairwise distances from the lower triangle of a... |
| PERMANOVA | Perform PERMANOVA testing. |
| rareSamp | Rarefy a simulated OTU vector |
| readDM | Read QIIME-formatted distance matrices |
| readDMdir | Read all QIIME-formatted distance matrices in working... |
| readDMmetric | Read all QIIME-formatted distance matrices in working... |
| simNull | Simulate OTU table with null group-level effect for... |
| simPower | Simulate a list of OTU tables encoding a range of effect... |
| simSamp | Simulate a sample OTU vector |
| simStudy | Simulate OTU table for presence-absence or abundance-weighted... |
| simTreeList | Simulate a phylogenetic tree with specified OTU names |
| simTreeTable | Simulate a phylogenetic tree with specified OTU names |
| writeOTUlist | Export a list of simulated OTU tables to permit analysis of... |
| writeOTUtable | Export a simulated OTU table to permit analysis of... |
