# A Method for 'Connecting The Dots' in Weighted Graphs

## Documentation for package ‘CTD’ version 1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

cohorts_coded | Disease cohorts with coded identifiers
data.combineData | Combine datasets
data.imputeData | Impute missing values
data.surrogateProfiles | Generate surrogate profiles
data.zscoreData | Z-transform available data
graph.connectToExt | Connect a node to its unvisited "extended" neighbors
graph.diffuseP1 | Diffuse Probability P1 from a starting node
graph.diffusionSnapShot | Capture the current state of probability diffusion
graph.naivePruning | Network pruning for disease-specific network determination
graph.netWalkSnapShot | Capture the current location of a network walker
Miller2015 | Miller et al. (2015)
mle.getEncodingLength | Minimum encoding length
mle.getMinPtDistance | Get minimum patient distances
mle.getPtBSbyK | Generate patient-specific bitstrings
mle.getPtDist | CTDncd: A network-based distance metric.
multiNode.getNodeRanks | Generate multi-node node rankings ("adaptive" walk)
singleNode.getNodeRanksN | Generate single-node node rankings ("fixed" walk)
stat.entropyFunction | Entropy of a bit-string
stat.fishersMethod | Fisher's Combined P-value
stat.getDirSim | DirSim: The Jaccard distance with directionality incorporated.
Thistlethwaite2020 | Thistlethwaite et al. (2020)
Wangler2017 | Wangler et al. (2017)