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graph4lg

Overview

The goal of graph4lg is to make easier the construction and analysis of genetic and landscape graphs in landscape genetics studies (hence the name graph4lg). The package allows to weight the links and to prune the graphs by several ways. To our knowledge, it is the first software which enables to create genetic graphs with such a large variety of parameters. Besides, it allows to carry out preliminary analyses of the spatial pattern of genetic differentiation in order to choose the best genetic distance and pruning method in every context. Lastly, it makes possible the comparison of two spatial graphs sharing the same nodes.

Installation

You can install the released version of graph4lg from CRAN with:

install.packages("graph4lg")

Example

The package includes a tutorial with examples showing why and how to use each of the included functions. The package also includes data sets in order to test the functions.

More complete tutorials in English or French language are available for more details.

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Version

Install

install.packages('graph4lg')

Monthly Downloads

516

Version

1.8.0

License

GPL-2

Maintainer

Paul Savary

Last Published

January 30th, 2023

Functions in graph4lg (1.8.0)

genind_to_structure

Convert a genind object into a STRUCTURE file

Create a graph of genetic differentiation using a link weight threshold

Create a graph of genetic differentiation with a specific topology

Download Graphab if not present on the user's machine

genind_to_genepop

Convert a genind object into a GENEPOP file

get_graphab_linkset_cost

Get cost values associated with a linkset in a Graphab project

genepop_to_genind

Convert a GENEPOP file into a genind object

get_graphab_linkset

Get linkset computed in the Graphab project

graph_modul_compar

Compare the partition into modules of two graphs

Compute Gini coefficient from a numeric vector

graph_node_compar

Compare the local properties of the nodes from two graphs

Create a graph with a minimum planar graph topology

Convert a graph into a edge list data.frame

graph_plot_compar

Visualize the topological differences between two spatial graphs on a map

get_graphab_raster_codes

Get unique raster codes from a Graphab project

get_graphab_metric

Get metrics computed at the node in the Graphab project

graph_topo_compar

Compute an index comparing graph topologies

Export a spatial graph to shapefile layers

dist_gc_vicenty

Calculate the Great-Circle distance between two points using the Vincenty inverse formula for ellipsoids (vicenty)

Create a link set in the Graphab project

gstud_to_genind

Convert a file from gstudio or popgraph into a genind object

graphab_capacity

Computes custom capacities of patches in the Graphab project

Create a graph in the Graphab project

graphab_to_igraph

Create landscape graphs from Graphab link set

Compute connectivity metrics from a graph in the Graphab project

graphab_corridor

Computes corridors from least-cost paths already computed in the Graphab project

Create modules from a graph in the Graphab project

graphab_project_desc

Describe the objects of a Graphab project

Convert a loci object into a genind object

graphab_interpol

Creates a raster with interpolated connectivity metric values from metrics already computed in the Graphab project

graphab_project

Create a Graphab project

Compute a pairwise FST matrix between populations

Compute Euclidean geographic distances between points

graphab_pointset

Add a point set to the Graphab project

Compute a pairwise genetic distance matrix between populations using Bowcock et al. (1994) formula

Compare two link sets created in a Graphab project

Vector of custom colors

pts_pop_simul : details on simulated populations

Reorder the rows and columns of a symmetric matrix

Compute dispersal kernel parameters

Sample points or patches on a categorical raster layer

Compute the harmonic mean of a numeric vector

Plot scatterplots of genetic distance vs landscape distance

Plot histograms of link weights

Compute population-level genetic indices

Compute a pairwise matrix of genetic distances between populations

Compute cost distances between points on a raster

pop_rare_gen_index

Compute population-level rarefied genetic indices with ADZE software

Scaling function

pts_pop_ex : details on simulated populations

Plot scatterplots of distances to visualize the graph pruning intensity

structure_to_genind

Convert a file in STRUCTURE format into a genind object

Extract patch areas from a categorical raster

Convert a pairwise matrix into an edge-list data.frame

Add attributes to the nodes of a graph

data_ex_genind genetic dataset

compute_node_metric

Compute graph-theoretic metrics from a graph at the node level

compute_graph_modul

Compute modules from a graph by maximising modularity

Fit a model to convert cost-distances into Euclidean distances

Check whether the option 'nomerge' was used when building the landscape graph with Graphab

data_ex_loci genetic dataset

compar_r_fisher

Compare two correlation coefficients obtained from different sample sizes

data_ex_gstud genetic dataset

data_simul_genind

data_simul_genind genetic dataset

Compute the distance at which the correlation between genetic distance and landscape distance is maximal

Convert an edge-list data.frame into a pairwise matrix

dist_great_circle

Compute the Great Circle distance between two points

Calculate the Great-Circle distance between two points using the Spherical Law of Cosines (slc)

Calculate the Great-Circle distance between two points using the Harversine formula (hvs)

gen_graph_indep

Create an independence graph of genetic differentiation from genetic data of class genind

Prune a graph using the 'percolation threshold' method

data_tuto : data used to generate the vignette

Convert degrees to radians