graphab_to_igraph: Create landscape graphs from Graphab link set

In graph4lg: Build Graphs for Landscape Genetics Analysis

Create landscape graphs from Graphab link set

Description

The function creates a landscape graph from a link set created with Graphab software or different functions of this package and converts it into a graph object of class igraph. The graph has weighted links and is undirected. Nodes attributes present in the Graphab project are included, including connectivity metrics when computed

Usage

graphab_to_igraph(
  proj_name,
  linkset,
  nodes = "patches",
  weight = "cost",
  proj_path = NULL,
  fig = FALSE,
  crds = FALSE
)

Arguments

proj_name	A character string indicating the project name. It is also the name of the directory in which proj_name.xml file is found. By default, 'proj_name' is searched into the current working directory
linkset	A character string indicating the name of the linkset used to create the graph links. The linkset must have been created previously (see the function graphab_link). It can be complete or planar. The graph is given the topology of the selected link set.
nodes	A character string indicating whether the nodes of the created graph are given all the attributes or metrics computed in Graphab or only those specific to a given graph previously created with graphab_graph It can be: nodes = "patches"(default): all the attributes and metrics of the habitat patches are included as node attributes in igraph object. nodes = "graph_name"(default): only the metrics of the habitat patches computed from the graph 'graph_name' created with graphab_graph are included as node attributes in igraph object, along with some basic patch attributes.
weight	A character string ("euclid" or "cost") indicating whether to weight the links with Euclidean distance or cost-distance (default) values.
proj_path	(optional) A character string indicating the path to the directory that contains the project directory ('proj_name'). By default, 'proj_name' is searched into the current working directory
fig	Logical (default = FALSE) indicating whether to plot a figure of the resulting spatial graph. The figure is plotted using function plot_graph_lg. The plotting can be long if the graph has many nodes and links.
crds	Logical (default = FALSE) indicating whether to create an object of class data.frame with the node centroid spatial coordinates. Such a data.frame has 3 columns: 'ID', 'x', 'y'.

Value

A graph object of class igraph (if crds = FALSE) or a list of objects: a graph object of class igraph and a data.frame with the nodes spatial coordinates (if crds = TRUE).

Author(s)

P. Savary

References

\insertRef

foltete2012softwaregraph4lg

Examples

## Not run: 
proj_path <- system.file('extdata',package='graph4lg')
proj_name <- "grphb_ex"
linkset <- "lkst1"
nodes <- "graph"
graph <- graphab_to_igraph(proj_name = proj_name,
                           linkset = "lkst1",
                           nodes = "graph",
                           links = links,
                           weights = "cost",
                           proj_path = proj_path,
                           crds = FALSE,
                           fig = FALSE)
                           
## End(Not run)

graph4lg documentation built on Feb. 16, 2023, 5:43 p.m.