Man pages for ramellose/NetworkUtils
Network analysis utitilities for "From hairballs to hypotheses: biological insights from microbial networks"
| analyseDeg | Analyse degree or centrality |
| analyseHubs | Return hubs or central species |
| analyseKlemm | Analyse Klemm matrices |
| analyseOutput | Compute network statistics |
| callTools | Call tools to infer networks |
| computeAdjacency | Compute adjacency |
| computeAUC | Compute AUC |
| computeCentral | Compute centrality |
| computeHub | Compute hubs |
| computePrecision | Compute precision |
| computeSensitivity | Compute sensitivity |
| computeSpecificity | Compute specificity |
| computeStat | Compute assortativity, transitivity or degree |
| envGrowthChanges | Generate growth changes induced by environment |
| generateKlemms | Generate Klemm adjacency matrices |
| generateSets | Generate multiple datasets |
| plotHubs | Generate SuperExactTest-compatible dataset |
| plotPrecisionvsRecall | Plot precision vs recall |
| plotSeries | Plot statistics |
| plotStats | Generate SuperExactTest p-value vector corrected for sampling... |
| plotSuperSet | Generate ggplots using some SuperExactTest code |
| plotUpset | Generate UpSetplot-compatible dataset |
| readCoNet | Read CoNet outputs |
| readSpar | Read SparCC outputs |
| testgCoda | Calls gCoda function |
| testSpear | Calls Spearman correlation |
| testSpiec | Calls SpiecEasi |
| writeFeatures | Write features |
| writeSets | Write datasets |
