Man pages for JamesStimson/transcluster
Transmission clustering using SNPs and sample dates

clusterTimedTreefind clusters in timed tree
compareClusterscompare similarity of clusters
createModelcreate model to be used for cluster analysis
cutoffLevelcreate levels at which number of transmissions passes the...
makeSNPClustersmake SNP-based clusters for each threshold set in the model
makeTransClustersmake transmission-based clusters for each threshold set in...
makeTransClustersResistmake transmission-based clusters for each threshold set in...
nTransCutoffcreate levels at which number of transmissions passes the...
plotClustersplot of clusters with weighted edges
plotSNPClustersplot of SNP clusters with weighted edges
plotTransClustersplot of transmission clusters with weighted edges
plotTransClustersSpatialplot of transmission clusters with spatial weightings
regionColourreturn colour label
regionWeightreturn region weights
setCutoffsset levels at which number of transmissions passes the...
setCutoffsResistset levels at which number of transmissions passes the...
setCutoffsSpatialset levels at which number of transmissions passes the...
setDatesFromFileset sample dates from a file
setParamsset parameters for existing cluster analysis model
setRegionColoursset region colours
setRegionLabelsset region labels
setRegionsFromFileset regions from a file
setRegionWeightsset region weightings
setSNPFromFileset SNP distance matrix from a file
setSNPResistFromFileset SNP resistant distance matrix from a file
setSNPThresholdsset SNP thresholds for existing cluster analysis model
setTransMatrixFromFileset transmission distance matrix from a file
setTransThresholdsset transmission thresholds for existing cluster analysis...
withinClustertest whether two cases are within the same transmission...
JamesStimson/transcluster documentation built on May 20, 2019, 9:13 p.m.