Man pages for JamesStimson/transcluster
Transmission clustering using SNPs and sample dates
| clusterTimedTree | find clusters in timed tree |
| compareClusters | compare similarity of clusters |
| createModel | create model to be used for cluster analysis |
| cutoffLevel | create levels at which number of transmissions passes the... |
| makeSNPClusters | make SNP-based clusters for each threshold set in the model |
| makeTransClusters | make transmission-based clusters for each threshold set in... |
| makeTransClustersResist | make transmission-based clusters for each threshold set in... |
| nTransCutoff | create levels at which number of transmissions passes the... |
| plotClusters | plot of clusters with weighted edges |
| plotSNPClusters | plot of SNP clusters with weighted edges |
| plotTransClusters | plot of transmission clusters with weighted edges |
| plotTransClustersSpatial | plot of transmission clusters with spatial weightings |
| regionColour | return colour label |
| regionWeight | return region weights |
| setCutoffs | set levels at which number of transmissions passes the... |
| setCutoffsResist | set levels at which number of transmissions passes the... |
| setCutoffsSpatial | set levels at which number of transmissions passes the... |
| setDatesFromFile | set sample dates from a file |
| setParams | set parameters for existing cluster analysis model |
| setRegionColours | set region colours |
| setRegionLabels | set region labels |
| setRegionsFromFile | set regions from a file |
| setRegionWeights | set region weightings |
| setSNPFromFile | set SNP distance matrix from a file |
| setSNPResistFromFile | set SNP resistant distance matrix from a file |
| setSNPThresholds | set SNP thresholds for existing cluster analysis model |
| setTransMatrixFromFile | set transmission distance matrix from a file |
| setTransThresholds | set transmission thresholds for existing cluster analysis... |
| withinCluster | test whether two cases are within the same transmission... |
