AFM

Package: AFM
Type: Package
Version: 1.2.1
Date: 2016-04-10
Title: Atomic Force Microscope Image Analysis
Authors@R: c(person("Mathieu", "Beauvais", role = c("aut", "cre"), email = "beauvais.escp@gmail.com"),person("Irma", "Liascukiene", role = "aut"),person("Jessem", "Landoulsi", role = "aut"))
Author: Mathieu Beauvais [aut, cre],
Irma Liascukiene [aut],
Jessem Landoulsi [aut]
Maintainer: Mathieu Beauvais <beauvais.escp@gmail.com>
Description: Provides Atomic Force Microscope images analysis such as Power
Spectrum Density, roughness against lengthscale, variogram and variance,
fractal dimension and scale. The AFM images can be exported to STL format for 3D
printing.
NeedsCompilation: no
Repository: CRAN
License: AGPL-3
Depends: R (>= 3.1.3)
Imports: data.table (>= 1.9.6), stringr (>= 1.0.0), gstat (>=
1.0-26), fractaldim (>= 0.8-4), rgl (>= 0.95.1367), pracma (>=
1.8.6), fftwtools (>= 0.9-7), grid (>= 3.1.3), gridExtra (>=
2.0.0), moments (>= 0.14), ggplot2 (>= 1.0.1), sp (>= 1.2-0), png (>=
0.1-7), plyr (>= 1.8.3), igraph (>= 1.0.1), methods (>= 3.1.3),
shiny (>= 0.12.2), shinyjs (>= 0.4.0), rglwidget (>= 0.1.1434)
Collate: 'AFM3DPrinter.R' 'AFMFractalDimensionAnalyser.R' 'AFMImage.R'
'AFMNetworksAnalyser.R' 'AFMPSDAnalyser.R'
'AFMVariogramAnalyser.R' 'AFMImageAnalyser.R'
'AFMReportMaker.R' 'pkgname.R' 'runAFMApp.R'
RoxygenNote: 5.0.1
Packaged: 2016-04-11 17:39:43 UTC; nobody
Date/Publication: 2016-04-12 00:57:04

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'AFM' ...
** package 'AFM' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'AFM'
    finding HTML links ... done
    AFM                                     html  
    finding level-2 HTML links ... done

    AFMFractalDimensionAnalyser-getFractalDimensions
                                            html  
Rd warning: /tmp/RtmpFQ8ZDS/R.INSTALL5484148f6c96/AFM/man/AFMFractalDimensionAnalyser-getFractalDimensions.Rd:18: missing file link 'fd.estim.method'
    AFMImage-class                          html  
    AFMImage-extractAFMImage                html  
    AFMImage-importFromNanoscope            html  
    AFMImage-sampleAFMImage                 html  
    AFMImage-saveOnDisk                     html  
    AFMImage-simplifyAFMImage               html  
    AFMImage3DModelAnalysis-class           html  
    AFMImageAnalyser-class-initialize       html  
    AFMImageAnalyser-class                  html  
    AFMImageFractalDimensionMethod-class    html  
    AFMImageFractalDimensionsAnalysis-class
                                            html  
    AFMImageNetworksAnalysis-class          html  
    AFMImageOfAluminiumInterface            html  
    AFMImageOfNormallyDistributedHeights    html  
    AFMImageOfOnePeak                       html  
    AFMImageOfRegularPeaks                  html  
    AFMImagePSDAnalysis-class               html  
    AFMImageVariogramAnalyser-calculateDirectionalVariograms
                                            html  
    AFMImageVariogramAnalyser-calculateOmnidirectionalVariogram
                                            html  
    AFMImageVariogramAnalyser-getAutomaticWidthForVariogramCalculation
                                            html  
    AFMImageVariogramAnalysis-class         html  
    AFMImageVariogramAnalysis-evaluateVariogramModels-method
                                            html  
    AFMImageVariogramAnalysis-getDTModelEvaluation-method
                                            html  
    AFMImageVariogramAnalysis-getDTModelSillRange-method
                                            html  
    AFMImageVariogramAnalysis-updateProgress-method
                                            html  
    AFMImageVariogramModel-class            html  
    AFMVariogramAnalyser-getSpplotFromAFMImage
                                            html  
    AFMVariogramAnalyser-saveSpplotFromAFMImage
                                            html  
    PSD1DAgainstFrequency-methods           html  
    PSD2DAgainstFrequency-methods           html  
    RoughnessByLengthScale-methods          html  
    analyse                                 html  
    calculate3DModel-methods                html  
    calculateIgraph                         html  
    calculateNetworkSkeleton                html  
    calculateNetworks-methods               html  
    canBeRemoved                            html  
    checkIsotropy                           html  
    checkNormality                          html  
    displayIn3D                             html  
    existsEdge                              html  
    exportToSTL                             html  
    generateAFMImageReport                  html  
    generateCheckReport                     html  
    generateReport                          html  
    generateReportFromNanoscopeImageDirectory
                                            html  
    getBresenham2DSegment                   html  
    getCoordinatesFromVertexId              html  
    getListOfDiameters                      html  
    getNetworkGridLayout                    html  
    getNyquistSpatialFrequency-methods      html  
    getPaddedAFMImage                       html  
    getRoughnessParameters-methods          html  
    getSurroundingVertexesList              html  
    getTopologyAFMImage                     html  
    getVertexId                             html  
    gridIgraphPlot                          html  
    isAdjacentToBetterVertex                html  
    performAllPSDCalculation                html  
    printVariogramModelEvaluations          html  
    putAnalysisOnDisk-methods               html  
    putImagesFromAnalysisOnDisk             html  
    runAFMApp                               html  
    shiftFFT2D                              html  
    shiftedPSDuv                            html  
    totalRMSRoughness                       html  
** building package indices
** testing if installed package can be loaded
* DONE (AFM)
Making 'packages.html' ... done