├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── img │ ├── 2DVisualizer_Scaled.png │ ├── 3DVisualizer.png │ └── mully.png ├── mully-package.R ├── mully_constructor.R ├── mully_demo.R ├── mully_edge.R ├── mully_export.R ├── mully_import.R ├── mully_layer.R ├── mully_merge.R ├── mully_node.R └── mully_visualization.R ├── README.md ├── man ├── addEdge.Rd ├── addLayer.Rd ├── addNode.Rd ├── demo.Rd ├── exportCSV.Rd ├── getEdgeAttributes.Rd ├── getIDEdge.Rd ├── getIDNode.Rd ├── getLayer.Rd ├── getLayersCount.Rd ├── getNode.Rd ├── getNodeAttributes.Rd ├── importEdgesCSV.Rd ├── importGraphCSV.Rd ├── importLayersCSV.Rd ├── importNodesCSV.Rd ├── is.mully.Rd ├── isLayer.Rd ├── merge.Rd ├── mully-package.Rd ├── mully.Rd ├── plot.mully.Rd ├── plot3d.Rd ├── print.mully.Rd ├── removeEdge.Rd ├── removeLayer.Rd └── removeNode.Rd ├── merge.pdf ├── mully.Rcheck ├── 00_pkg_src │ └── mully │ │ ├── DESCRIPTION │ │ ├── NAMESPACE │ │ ├── R │ │ ├── mully-package.R │ │ ├── mully_constructor.R │ │ ├── mully_demo.R │ │ ├── mully_edge.R │ │ ├── mully_export.R │ │ ├── mully_import.R │ │ ├── mully_layer.R │ │ ├── mully_merge.R │ │ ├── mully_node.R │ │ └── mully_visualization.R │ │ ├── README.md │ │ ├── build │ │ └── vignette.rds │ │ ├── man │ │ ├── addEdge.Rd │ │ ├── addLayer.Rd │ │ ├── addNode.Rd │ │ ├── demo.Rd │ │ ├── exportCSV.Rd │ │ ├── getEdgeAttributes.Rd │ │ ├── getIDEdge.Rd │ │ ├── getIDNode.Rd │ │ ├── getLayer.Rd │ │ ├── getLayersCount.Rd │ │ ├── getNode.Rd │ │ ├── getNodeAttributes.Rd │ │ ├── importEdgesCSV.Rd │ │ ├── importGraphCSV.Rd │ │ ├── importLayersCSV.Rd │ │ ├── importNodesCSV.Rd │ │ ├── is.mully.Rd │ │ ├── isLayer.Rd │ │ ├── merge.Rd │ │ ├── mully-package.Rd │ │ ├── mully.Rd │ │ ├── plot.mully.Rd │ │ ├── plot3d.Rd │ │ ├── print.mully.Rd │ │ ├── removeEdge.Rd │ │ ├── removeLayer.Rd │ │ └── removeNode.Rd │ │ └── vignettes │ │ ├── mully-pdf.Rmd │ │ ├── mully-vignette.Rmd │ │ ├── mully.R │ │ └── mully.html ├── 00check.log ├── 00install.out ├── 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