{
  "_id": "6a2531a24b233be198395ff2",
  "Package": "graph4lg",
  "Type": "Package",
  "Title": "Build Graphs for Landscape Genetics Analysis",
  "Version": "1.8.0",
  "Authors@R": "c(person(given = \"Paul\",\nfamily = \"Savary\",\nrole = c(\"aut\", \"cre\"),\nemail = \"psavary@protonmail.com\",\ncomment = c(ORCID = \"0000-0002-2104-9941\")),\nperson(given = \"Gilles\",\nfamily = \"Vuidel\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-6330-6136\")),\nperson(given = \"Tyler\",\nfamily = \"Rudolph\",\nrole = \"ctb\"),\nperson(given = \"Alexandrine\",\nfamily = \"Daniel\",\nrole = \"ctb\"))",
  "Maintainer": "Paul Savary <psavary@protonmail.com>",
  "Description": "Build graphs for landscape genetics analysis. This set of\nfunctions can be used to import and convert spatial and genetic\ndata initially in different formats, import landscape graphs\ncreated with 'GRAPHAB' software (Foltete et al., 2012)\n<doi:10.1016/j.envsoft.2012.07.002>, make diagnosis plots of\nisolation by distance relationships in order to choose how to\nbuild genetic graphs, create graphs with a large range of\npruning methods, weight their links with several genetic\ndistances, plot and analyse graphs, compare them with other\ngraphs. It uses functions from other packages such as\n'adegenet' (Jombart, 2008) <doi:10.1093/bioinformatics/btn129>\nand 'igraph' (Csardi et Nepusz, 2006) <https://igraph.org/>. It\nalso implements methods commonly used in landscape genetics to\ncreate graphs, described by Dyer et Nason (2004)\n<doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et\nFefferman (2017) <doi:10.1111/mec.14059>, and to analyse\ndistance data (van Strien et al., 2015)\n<doi:10.1038/hdy.2014.62>.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
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  "Packaged": {
    "Date": "2026-06-07 08:49:39 UTC",
    "User": "root"
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  "Author": "Paul Savary [aut, cre]\n(<https://orcid.org/0000-0002-2104-9941>), Gilles Vuidel [ctb]\n(<https://orcid.org/0000-0001-6330-6136>), Tyler Rudolph [ctb],\nAlexandrine Daniel [ctb]",
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  "Repository": "https://psavary3.r-universe.dev",
  "Date/Publication": "2023-01-30 13:00:05 UTC",
  "RemoteUrl": "https://github.com/cran/graph4lg",
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  "_created": "2026-06-07T08:49:39.000Z",
  "_published": "2026-06-07T08:53:54.042Z",
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  "_assets": [
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    "extra/citation.json",
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      "date": "2019-07-23"
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    {
      "version": "0.3.0",
      "date": "2020-03-19"
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  "_exports": [
    "add_nodes_attr",
    "check_merge",
    "compar_r_fisher",
    "compute_graph_modul",
    "compute_node_metric",
    "convert_cd",
    "deg2rad",
    "df_to_pw_mat",
    "dist_gc_hvs",
    "dist_gc_slc",
    "dist_gc_vicenty",
    "dist_great_circle",
    "dist_max_corr",
    "g_percol",
    "gen_graph_indep",
    "gen_graph_thr",
    "gen_graph_topo",
    "genepop_to_genind",
    "genind_to_genepop",
    "genind_to_structure",
    "get_graphab",
    "get_graphab_linkset",
    "get_graphab_linkset_cost",
    "get_graphab_metric",
    "get_graphab_raster_codes",
    "gini_coeff",
    "graph_modul_compar",
    "graph_node_compar",
    "graph_plan",
    "graph_plot_compar",
    "graph_to_df",
    "graph_to_shp",
    "graph_topo_compar",
    "graphab_capacity",
    "graphab_corridor",
    "graphab_graph",
    "graphab_interpol",
    "graphab_link",
    "graphab_metric",
    "graphab_modul",
    "graphab_pointset",
    "graphab_project",
    "graphab_project_desc",
    "graphab_to_igraph",
    "gstud_to_genind",
    "harm_mean",
    "kernel_param",
    "link_compar",
    "loci_to_genind",
    "mat_cost_dist",
    "mat_gen_dist",
    "mat_geo_dist",
    "mat_pw_dps",
    "mat_pw_fst",
    "mypalette",
    "patch_areas",
    "plot_graph_lg",
    "plot_w_hist",
    "pop_gen_index",
    "pop_rare_gen_index",
    "pw_mat_to_df",
    "reorder_mat",
    "sample_raster",
    "sc01",
    "scatter_dist",
    "scatter_dist_g",
    "structure_to_genind"
  ],
  "_datasets": [
    {
      "name": "data_ex_genind",
      "title": "data_ex_genind genetic dataset",
      "object": "data_ex_genind",
      "class": [
        "genind"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "data_ex_gstud",
      "title": "data_ex_gstud genetic dataset",
      "object": "data_ex_gstud",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "POP",
        "LOCUS-1",
        "LOCUS-2",
        "LOCUS-3",
        "LOCUS-4",
        "LOCUS-5",
        "LOCUS-6",
        "LOCUS-7",
        "LOCUS-8",
        "LOCUS-9",
        "LOCUS-10",
        "LOCUS-11",
        "LOCUS-12",
        "LOCUS-13",
        "LOCUS-14",
        "LOCUS-15",
        "LOCUS-16",
        "LOCUS-17",
        "LOCUS-18",
        "LOCUS-19",
        "LOCUS-20"
      ],
      "rows": 200,
      "table": true,
      "tojson": false
    },
    {
      "name": "data_ex_loci",
      "title": "data_ex_loci genetic dataset",
      "object": "data_ex_loci",
      "class": [
        "loci",
        "data.frame"
      ],
      "fields": [
        "population",
        "LOCUS-1",
        "LOCUS-2",
        "LOCUS-3",
        "LOCUS-4",
        "LOCUS-5",
        "LOCUS-6",
        "LOCUS-7",
        "LOCUS-8",
        "LOCUS-9",
        "LOCUS-10",
        "LOCUS-11",
        "LOCUS-12",
        "LOCUS-13",
        "LOCUS-14",
        "LOCUS-15",
        "LOCUS-16",
        "LOCUS-17",
        "LOCUS-18",
        "LOCUS-19",
        "LOCUS-20"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "data_simul_genind",
      "title": "data_simul_genind genetic dataset",
      "object": "data_simul_genind",
      "class": [
        "genind"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "data_tuto",
      "title": "data_tuto : data used to generate the vignette",
      "object": "data_tuto",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pts_pop_ex",
      "title": "pts_pop_ex : details on simulated populations",
      "object": "pts_pop_ex",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "x",
        "y"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "pts_pop_simul",
      "title": "pts_pop_simul : details on simulated populations",
      "object": "pts_pop_simul",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "x",
        "y"
      ],
      "rows": 50,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_nodes_attr",
      "title": "Add attributes to the nodes of a graph",
      "topics": [
        "add_nodes_attr"
      ]
    },
    {
      "page": "compute_graph_modul",
      "title": "Compute modules from a graph by maximising modularity",
      "topics": [
        "compute_graph_modul"
      ]
    },
    {
      "page": "compute_node_metric",
      "title": "Compute graph-theoretic metrics from a graph at the node level",
      "topics": [
        "compute_node_metric"
      ]
    },
    {
      "page": "convert_cd",
      "title": "Fit a model to convert cost-distances into Euclidean distances",
      "topics": [
        "convert_cd"
      ]
    },
    {
      "page": "data_ex_genind",
      "title": "data_ex_genind genetic dataset",
      "topics": [
        "data_ex_genind"
      ]
    },
    {
      "page": "data_ex_gstud",
      "title": "data_ex_gstud genetic dataset",
      "topics": [
        "data_ex_gstud"
      ]
    },
    {
      "page": "data_ex_loci",
      "title": "data_ex_loci genetic dataset",
      "topics": [
        "data_ex_loci"
      ]
    },
    {
      "page": "data_simul_genind",
      "title": "data_simul_genind genetic dataset",
      "topics": [
        "data_simul_genind"
      ]
    },
    {
      "page": "data_tuto",
      "title": "data_tuto : data used to generate the vignette",
      "topics": [
        "data_tuto"
      ]
    },
    {
      "page": "df_to_pw_mat",
      "title": "Convert an edge-list data.frame into a pairwise matrix",
      "topics": [
        "df_to_pw_mat"
      ]
    },
    {
      "page": "dist_max_corr",
      "title": "Compute the distance at which the correlation between genetic distance and landscape distance is maximal",
      "topics": [
        "dist_max_corr"
      ]
    },
    {
      "page": "g_percol",
      "title": "Prune a graph using the 'percolation threshold' method",
      "topics": [
        "g_percol"
      ]
    },
    {
      "page": "gen_graph_indep",
      "title": "Create an independence graph of genetic differentiation from genetic data of class genind",
      "topics": [
        "gen_graph_indep"
      ]
    },
    {
      "page": "gen_graph_thr",
      "title": "Create a graph of genetic differentiation using a link weight threshold",
      "topics": [
        "gen_graph_thr"
      ]
    },
    {
      "page": "gen_graph_topo",
      "title": "Create a graph of genetic differentiation with a specific topology",
      "topics": [
        "gen_graph_topo"
      ]
    },
    {
      "page": "genepop_to_genind",
      "title": "Convert a GENEPOP file into a genind object",
      "topics": [
        "genepop_to_genind"
      ]
    },
    {
      "page": "genind_to_genepop",
      "title": "Convert a genind object into a GENEPOP file",
      "topics": [
        "genind_to_genepop"
      ]
    },
    {
      "page": "get_graphab",
      "title": "Download Graphab if not present on the user's machine",
      "topics": [
        "get_graphab"
      ]
    },
    {
      "page": "get_graphab_linkset",
      "title": "Get linkset computed in the Graphab project",
      "topics": [
        "get_graphab_linkset"
      ]
    },
    {
      "page": "get_graphab_linkset_cost",
      "title": "Get cost values associated with a linkset in a Graphab project",
      "topics": [
        "get_graphab_linkset_cost"
      ]
    },
    {
      "page": "get_graphab_metric",
      "title": "Get metrics computed at the node in the Graphab project",
      "topics": [
        "get_graphab_metric"
      ]
    },
    {
      "page": "get_graphab_raster_codes",
      "title": "Get unique raster codes from a Graphab project",
      "topics": [
        "get_graphab_raster_codes"
      ]
    },
    {
      "page": "graph_modul_compar",
      "title": "Compare the partition into modules of two graphs",
      "topics": [
        "graph_modul_compar"
      ]
    },
    {
      "page": "graph_node_compar",
      "title": "Compare the local properties of the nodes from two graphs",
      "topics": [
        "graph_node_compar"
      ]
    },
    {
      "page": "graph_plan",
      "title": "Create a graph with a minimum planar graph topology",
      "topics": [
        "graph_plan"
      ]
    },
    {
      "page": "graph_plot_compar",
      "title": "Visualize the topological differences between two spatial graphs on a map",
      "topics": [
        "graph_plot_compar"
      ]
    },
    {
      "page": "graph_to_df",
      "title": "Convert a graph into a edge list data.frame",
      "topics": [
        "graph_to_df"
      ]
    },
    {
      "page": "graph_to_shp",
      "title": "Export a spatial graph to shapefile layers",
      "topics": [
        "graph_to_shp"
      ]
    },
    {
      "page": "graph_topo_compar",
      "title": "Compute an index comparing graph topologies",
      "topics": [
        "graph_topo_compar"
      ]
    },
    {
      "page": "graphab_capacity",
      "title": "Computes custom capacities of patches in the Graphab project",
      "topics": [
        "graphab_capacity"
      ]
    },
    {
      "page": "graphab_corridor",
      "title": "Computes corridors from least-cost paths already computed in the Graphab project",
      "topics": [
        "graphab_corridor"
      ]
    },
    {
      "page": "graphab_graph",
      "title": "Create a graph in the Graphab project",
      "topics": [
        "graphab_graph"
      ]
    },
    {
      "page": "graphab_interpol",
      "title": "Creates a raster with interpolated connectivity metric values from metrics already computed in the Graphab project",
      "topics": [
        "graphab_interpol"
      ]
    },
    {
      "page": "graphab_link",
      "title": "Create a link set in the Graphab project",
      "topics": [
        "graphab_link"
      ]
    },
    {
      "page": "graphab_metric",
      "title": "Compute connectivity metrics from a graph in the Graphab project",
      "topics": [
        "graphab_metric"
      ]
    },
    {
      "page": "graphab_modul",
      "title": "Create modules from a graph in the Graphab project",
      "topics": [
        "graphab_modul"
      ]
    },
    {
      "page": "graphab_pointset",
      "title": "Add a point set to the Graphab project",
      "topics": [
        "graphab_pointset"
      ]
    },
    {
      "page": "graphab_project",
      "title": "Create a Graphab project",
      "topics": [
        "graphab_project"
      ]
    },
    {
      "page": "graphab_project_desc",
      "title": "Describe the objects of a Graphab project",
      "topics": [
        "graphab_project_desc"
      ]
    },
    {
      "page": "graphab_to_igraph",
      "title": "Create landscape graphs from Graphab link set",
      "topics": [
        "graphab_to_igraph"
      ]
    },
    {
      "page": "gstud_to_genind",
      "title": "Convert a file from 'gstudio' or 'popgraph' into a genind object",
      "topics": [
        "gstud_to_genind"
      ]
    },
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