# Get Network parameters Get basic network parameters : Total root mean square Roughness or Total Rrms or totalRMSRoughness_TotalRrms Mean roughness or Ra or MeanRoughness_Ra ```r getNetworkParameters(AFMImageNetworksAnalysis, AFMImage) ## S4 method for signature 'AFMImageNetworksAnalysis' getNetworkParameters(AFMImageNetworksAnalysis, AFMImage) ``` ## Arguments - `AFMImageNetworksAnalysis`: an `AFMImageNetworksAnalysis` - `AFMImage`: an `AFMImage` ## Returns a data.table of network parameters: * totalNumberOfNodes the total number of nodes with degree different of 2 * totalNumberOfNodesWithDegreeTwoOrMore the total number of nodes with degree 2 or more * totalNumberOfNodesWithDegreeOne the total number of nodes with degree one * numberOfNodesPerArea the total number of nodes with degree diffrent of 2 per area * numberOfNodesPerSurfaceArea the total number of nodes with degree diffrent of 2 per surface area * MeanPhysicalDistanceBetweenNodes the mean physical distance between nodes of degree different of two ## Details `getNetworkParameters` returns a data.table of network parameters ## Examples ```r ## Not run: library(AFM) library(parallel) data(AFMImageCollagenNetwork) AFMImage<-AFMImageCollagenNetwork AFMIA = new("AFMImageNetworksAnalysis") AFMIA@heightNetworksslider=10 AFMIA@filterNetworkssliderMin=150 AFMIA@filterNetworkssliderMax=300 AFMIA@smallBranchesTreatment=TRUE clExist<-TRUE cl <- makeCluster(2,outfile="") AFMIA<-transformAFMImageForNetworkAnalysis(AFMImageNetworksAnalysis=AFMIA,AFMImage= AFMImage) AFMIA<-identifyNodesAndEdges(cl=cl,AFMImageNetworksAnalysis= AFMIA,maxHeight= 300) AFMIA<-identifyEdgesFromCircles(cl=cl,AFMImageNetworksAnalysis= AFMIA, MAX_DISTANCE = 75) AFMIA<-identifyIsolatedNodes(AFMIA) AFMIA<-createGraph(AFMIA) AFMIA<-calculateShortestPaths(cl=cl, AFMImageNetworksAnalysis=AFMIA) AFMIA<-calculateNetworkParameters(AFMImageNetworksAnalysis=AFMIA, AFMImage=AFMImage) AFMIA<-calculateHolesCharacteristics(AFMImageNetworksAnalysis=AFMIA) stopCluster(cl) ## End(Not run) ``` ## Author(s) M.Beauvais

getNetworkParameters-methods function