Package: graph4lg 1.8.0

graph4lg: Build Graphs for Landscape Genetics Analysis

Build graphs for landscape genetics analysis. This set of functions can be used to import and convert spatial and genetic data initially in different formats, import landscape graphs created with 'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>, make diagnosis plots of isolation by distance relationships in order to choose how to build genetic graphs, create graphs with a large range of pruning methods, weight their links with several genetic distances, plot and analyse graphs, compare them with other graphs. It uses functions from other packages such as 'adegenet' (Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi et Nepusz, 2006) <https://igraph.org/>. It also implements methods commonly used in landscape genetics to create graphs, described by Dyer et Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data (van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.

Authors:Paul Savary [aut, cre], Gilles Vuidel [ctb], Tyler Rudolph [ctb], Alexandrine Daniel [ctb]

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67 exports 3 stars 0.49 score 112 dependencies 45 scripts 436 downloads

Last updated 2 years agofrom:5de8af31ae. Checks:OK: 1 NOTE: 6. Indexed: yes.

Exports:add_nodes_attrcheck_mergecompar_r_fishercompute_graph_modulcompute_node_metricconvert_cddeg2raddf_to_pw_matdist_gc_hvsdist_gc_slcdist_gc_vicentydist_great_circledist_max_corrg_percolgen_graph_indepgen_graph_thrgen_graph_topogenepop_to_genindgenind_to_genepopgenind_to_structureget_graphabget_graphab_linksetget_graphab_linkset_costget_graphab_metricget_graphab_raster_codesgini_coeffgraph_modul_compargraph_node_compargraph_plangraph_plot_compargraph_to_dfgraph_to_shpgraph_topo_compargraphab_capacitygraphab_corridorgraphab_graphgraphab_interpolgraphab_linkgraphab_metricgraphab_modulgraphab_pointsetgraphab_projectgraphab_project_descgraphab_to_igraphgstud_to_genindharm_meankernel_paramlink_comparloci_to_genindmat_cost_distmat_gen_distmat_geo_distmat_pw_dpsmat_pw_fstmypalettepatch_areasplot_graph_lgplot_w_histpop_gen_indexpop_rare_gen_indexpw_mat_to_dfreorder_matsample_rastersc01scatter_distscatter_dist_gstructure_to_genind

Dependencies:abindade4adegenetapebase64encbootbslibcachemclassclassIntcliclustercolorspacecommonmarkcpp11crayonDBIdeldirdigestdplyre1071ecodistfansifarverfastmapfontawesomeforeignfsgastongdistancegenericsggplot2gluegoftestgtablegtoolshierfstathtmltoolshttpuvigraphisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepegaspermutepillarpixmappkgconfigplyrpolyclippromisesproxypurrrR6rappdirsrasterrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreshape2rlangrparts2sassscalessegmentedseqinrsfshinysourcetoolsspspatstat.dataspatstat.explorespatstat.geomspatstat.linnetspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrtensorterratibbletidyrtidyselectunitsutf8vctrsveganviridisLitewithrwkxtable