# Generated by roxygen2: do not edit by hand

export(AFMImage)
export(AFMImageAnalyser)
export(AFMImageFractalDimensionMethod)
export(AFMImageFractalDimensionsAnalysis)
export(AFMImageGaussianMixAnalysis)
export(AFMImageNetworksAnalysis)
export(AFMImagePSDAnalysis)
export(AFMImagePSDSlopesAnalysis)
export(AFMImageVariogramAnalysis)
export(AFMImageVariogramModel)
export(AreNodesConnected)
export(analyse)
export(calculateDirectionalVariograms)
export(calculateGaussianMixture)
export(calculateHolesCharacteristics)
export(calculateIgraph)
export(calculateNetworkParameters)
export(calculateNetworkSkeleton)
export(calculateOmnidirectionalVariogram)
export(calculatePhysicalDistanceFromPath)
export(calculateShortestPaths)
export(canBeRemoved)
export(checkIsotropy)
export(checkNormality)
export(createGraph)
export(displayColoredNetworkWithVerticesSize)
export(displayHolesIn3D)
export(displayIn3D)
export(displaygridIgraphPlot)
export(displaygridIgraphPlotFromEdges)
export(dnormalmix)
export(existsEdge)
export(existsSegment)
export(exportToSTL)
export(extractAFMImage)
export(filterAFMImage)
export(fusionCloseNodes)
export(generateAFMImageReport)
export(generateCheckReport)
export(generatePolygonEnvelope)
export(generateReport)
export(generateReportFromNanoscopeImageDirectory)
export(get3DImageFullfilename)
export(getAllPointsToRemove)
export(getAngle)
export(getAutoIntersectionForOmnidirectionalVariogram)
export(getAutoIntersectionForRoughnessAgainstLengthscale)
export(getAutomaticWidthForVariogramCalculation)
export(getBresenham2DSegment)
export(getCircleSpatialPoints)
export(getCoordinatesFromVertexId)
export(getFractalDimensions)
export(getHolesStatistics)
export(getIntersectionForRoughnessAgainstLengthscale)
export(getIntersectionPointWithBorder)
export(getListOfDiameters)
export(getLogLogOmnidirectionalSlopeGraph)
export(getMaxCircleMatrix)
export(getNetworkGridLayout)
export(getPaddedAFMImage)
export(getSpplotFromAFMImage)
export(getSurroundingVertexesList)
export(getTopologyAFMImage)
export(getTriangle)
export(getVertexId)
export(gridIgraphPlot)
export(identifyEdgesFromCircles)
export(identifyIsolatedNodes)
export(identifyNodesAndEdges)
export(identifyNodesWithCircles)
export(importFromNanoscope)
export(invertBinaryAFMImage)
export(isAdjacentToBetterVertex)
export(isAngleBetweenEdgesAlwaysSuperiorToMinAngle)
export(isBinary)
export(loglike.normalmix)
export(makeBinaryAFMImage)
export(multiplyHeightsAFMImage)
export(omniVariogramSlopeAnalysis)
export(performAllPSDCalculation)
export(performGaussianMixCalculation)
export(pnormmix)
export(printVariogramModelEvaluations)
export(putImagesFromAnalysisOnDisk)
export(runAFMApp)
export(sampleAFMImage)
export(saveOnDisk)
export(saveOnDiskIntersectionForRoughnessAgainstLengthscale)
export(saveSpplotFromAFMImage)
export(shiftFFT2D)
export(shiftedPSDuv)
export(simplifyAFMImage)
export(simplifyNetwork)
export(thinImage)
export(totalRMSRoughness)
export(updateProgress)
exportClasses(AFMImage)
exportClasses(AFMImageAnalyser)
exportClasses(AFMImageFractalDimensionsAnalysis)
exportClasses(AFMImageNetworksAnalysis)
exportClasses(AFMImagePSDSlopesAnalysis)
exportClasses(AFMImageVariogramAnalysis)
exportClasses(AFMImageVariogramModel)
exportClasses(omniVariogramSlopeAnalysis)
exportMethods(PSD1DAgainstFrequency)
exportMethods(PSD2DAgainstFrequency)
exportMethods(RoughnessByLengthScale)
exportMethods(calculate3DModel)
exportMethods(calculateNetworks)
exportMethods(evaluateVariogramModels)
exportMethods(getDTModelEvaluation)
exportMethods(getDTModelSillRange)
exportMethods(getNetworkParameters)
exportMethods(getNyquistSpatialFrequency)
exportMethods(getRoughnessParameters)
exportMethods(initialize)
exportMethods(putAnalysisOnDisk)
exportMethods(transformAFMImageForNetworkAnalysis)
import(data.table)
import(ggplot2)
import(gstat)
import(igraph)
import(methods)
import(plyr)
import(png)
import(scales)
importFrom(dbscan,dbscan)
importFrom(fractaldim,fd.estim.filter1)
importFrom(fractaldim,fd.estim.isotropic)
importFrom(fractaldim,fd.estim.squareincr)
importFrom(fractaldim,fd.estim.transect.incr1)
importFrom(fractaldim,fd.estim.transect.var)
importFrom(grDevices,blues9)
importFrom(grDevices,chull)
importFrom(grDevices,dev.off)
importFrom(grDevices,heat.colors)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(graphics,lines)
importFrom(graphics,plot)
importFrom(grid,gpar)
importFrom(grid,grid.layout)
importFrom(grid,grid.newpage)
importFrom(grid,grid.raster)
importFrom(grid,grid.text)
importFrom(grid,pushViewport)
importFrom(grid,viewport)
importFrom(gridExtra,tableGrob)
importFrom(gridExtra,ttheme_default)
importFrom(mixtools,normalmixEM)
importFrom(moments,skewness)
importFrom(parallel,clusterEvalQ)
importFrom(parallel,clusterExport)
importFrom(parallel,parLapply)
importFrom(pracma,ceil)
importFrom(pracma,meshgrid)
importFrom(rgl,clear3d)
importFrom(rgl,par3d)
importFrom(rgl,polygon3d)
importFrom(rgl,registerSceneChange)
importFrom(rgl,renderRglwidget)
importFrom(rgl,rgl.bbox)
importFrom(rgl,rgl.bg)
importFrom(rgl,rgl.clear)
importFrom(rgl,rgl.close)
importFrom(rgl,rgl.cur)
importFrom(rgl,rgl.light)
importFrom(rgl,rgl.open)
importFrom(rgl,rgl.set)
importFrom(rgl,rgl.snapshot)
importFrom(rgl,rgl.surface)
importFrom(rgl,rgl.viewpoint)
importFrom(rgl,rglwidget)
importFrom(rgl,rglwidgetOutput)
importFrom(rgl,rotate3d)
importFrom(rgl,sceneChange)
importFrom(rgl,shade3d)
importFrom(rgl,terrain3d)
importFrom(rgl,translate3d)
importFrom(rgl,writeSTL)
importFrom(shiny,HTML)
importFrom(shiny,actionButton)
importFrom(shiny,downloadButton)
importFrom(shiny,downloadHandler)
importFrom(shiny,fileInput)
importFrom(shiny,h3)
importFrom(shiny,hr)
importFrom(shiny,htmlOutput)
importFrom(shiny,imageOutput)
importFrom(shiny,isolate)
importFrom(shiny,mainPanel)
importFrom(shiny,navbarMenu)
importFrom(shiny,navbarPage)
importFrom(shiny,observeEvent)
importFrom(shiny,plotOutput)
importFrom(shiny,radioButtons)
importFrom(shiny,reactive)
importFrom(shiny,reactiveValues)
importFrom(shiny,renderImage)
importFrom(shiny,renderPlot)
importFrom(shiny,renderTable)
importFrom(shiny,renderUI)
importFrom(shiny,shinyServer)
importFrom(shiny,shinyUI)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,sliderInput)
importFrom(shiny,tabPanel)
importFrom(shiny,tableOutput)
importFrom(shiny,uiOutput)
importFrom(shiny,updateSliderInput)
importFrom(shinyjs,disable)
importFrom(shinyjs,enable)
importFrom(shinyjs,useShinyjs)
importFrom(sp,"coordinates<-")
importFrom(sp,"proj4string<-")
importFrom(sp,CRS)
importFrom(sp,Polygon)
importFrom(sp,Polygons)
importFrom(sp,SpatialPoints)
importFrom(sp,SpatialPointsDataFrame)
importFrom(sp,SpatialPolygons)
importFrom(sp,coordinates)
importFrom(sp,is.projected)
importFrom(sp,over)
importFrom(sp,proj4string)
importFrom(sp,spDistsN1)
importFrom(sp,spplot)
importFrom(sp,surfaceArea)
importFrom(stats,coefficients)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,ks.test)
importFrom(stats,lm)
importFrom(stats,na.omit)
importFrom(stats,pnorm)
importFrom(stats,sd)
importFrom(stats,var)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_sub)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,installed.packages)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.table)
