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graph4lg  

Build Graphs for Landscape Genetics Analysis
View on CRAN: Click here


Download and install graph4lg package within the R console
Install from CRAN:
install.packages("graph4lg")

Install from Github:
library("remotes")
install_github("cran/graph4lg")

Install by package version:
library("remotes")
install_version("graph4lg", "1.8.0")



Attach the package and use:
library("graph4lg")
Maintained by
Paul Savary
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-07-23
Latest Update: 2023-01-30
Description:
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) , 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) and 'igraph' (Csardi et Nepusz, 2006) . It also implements methods commonly used in landscape genetics to create graphs, described by Dyer et Nason (2004) and Greenbaum et Fefferman (2017) , and to analyse distance data (van Strien et al., 2015) .
How to cite:
Paul Savary (2019). graph4lg: Build Graphs for Landscape Genetics Analysis. R package version 1.8.0, https://cran.r-project.org/web/packages/graph4lg. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.1.1 (2019-07-23 11:30), 0.2.0 (2019-12-12 11:40), 0.3.0 (2020-03-19 08:40), 0.5.0 (2020-05-04 10:30), 1.0.0 (2020-07-22 09:10), 1.0.1 (2020-09-28 09:20), 1.2.0 (2021-03-16 16:20), 1.4.0 (2022-03-08 09:40), 1.6.0 (2022-05-18 15:50)
Other packages that cited graph4lg R package
View graph4lg citation profile
Other R packages that graph4lg depends, imports, suggests or enhances
Complete documentation for graph4lg
Functions, R codes and Examples using the graph4lg R package
Some associated functions: add_nodes_attr . check_merge . compar_r_fisher . compute_graph_modul . compute_node_metric . convert_cd . data_ex_genind . data_ex_gstud . data_ex_loci . data_simul_genind . data_tuto . 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 . pts_pop_ex . pts_pop_simul . pw_mat_to_df . reorder_mat . sample_raster . sc01 . scatter_dist . scatter_dist_g . structure_to_genind . 
Some associated R codes: add_nodes_attr.R . aux_25_09.R . check_merge.R . compar_r_fisher.R . compute_graph_modul.R . compute_node_metric.R . convert_cd.R . data.R . df_to_pw_mat.R . dist_great_circle.R . dist_max_corr.R . g_percol.R . gen_graph_indep.R . gen_graph_thr.R . gen_graph_topo.R . genepop_to_genind.R . genind_to_genepop.R . genind_to_structure.R . get_graphab.R . get_graphab_linkset.R . get_graphab_linkset_cost.R . get_graphab_metric.R . get_graphab_raster_codes.R . graph_modul_compar.R . graph_node_compar.R . graph_plan.R . graph_plot_compar.R . graph_to_df.R . graph_to_shp.R . graph_topo_compar.R . graphab_capacity.R . graphab_corridor.R . graphab_graph.R . graphab_interpol.R . graphab_link.R . graphab_metric.R . graphab_modul.R . graphab_pointset.R . graphab_project.R . graphab_project_desc.R . graphab_to_igraph.R . gstud_to_genind.R . internal_functions.R . kernel_param.R . link_compar.R . loci_to_genind.R . mat_cost_dist.R . mat_gen_dist.R . mat_geo_dist.R . mat_pw_dps.R . mat_pw_fst.R . other_objects.R . plot_graph_lg.R . plot_w_hist.R . pop_gen_index.R . pop_rare_gen_index.R . pw_mat_to_df.R . reorder_mat.R . sample_raster.R . scatter_dist.R . scatter_dist_g.R . structure_to_genind.R .  Full graph4lg package functions and examples
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