graphab_graph: Create a graph in the Graphab project

In graph4lg: Build Graphs for Landscape Genetics Analysis

Create a graph in the Graphab project

Description

The function creates a graph from a link set in a Graphab project

Usage

graphab_graph(
  proj_name,
  linkset = NULL,
  name = NULL,
  thr = NULL,
  cost_conv = FALSE,
  proj_path = NULL,
  alloc_ram = NULL
)

Arguments

proj_name	A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is. It can be created with graphab_project
linkset	(optional, default=NULL) A character string indicating the name of the link set used to create the graph. If linkset=NULL, every link set present in the project will be used to create a graph. Link sets can be created with graphab_link.
name	(optional, default=NULL) A character string indicating the name of the graph created. If name=NULL, a name will be created. If both linkset=NULL and name=NULL, then a graph will be created for every link set present in the project and a name will be created every time. In the latter case, a unique name cannot be specified. Link sets can be created with graphab_link.
thr	(optional, default=NULL) An integer or numeric value indicating the maximum distance associated with the links of the created graph. It allows users to create a pruned graph based on a distance threshold. Note that when the link set used has a planar topology, the graph is necessarily a pruned graph (not complete) and adding this threshold parameter can remove other links. When the link set has been created with cost-distances, the parameter is expressed in cost-distance units whereas when the link set is based upon Euclidean distances, the parameter is expressed in meters.
cost_conv	FALSE (default) or TRUE. Logical indicating whether numeric thr values are converted from cost-distance into Euclidean distance using a log-log linear regression. See also convert_cd function.
proj_path	(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().
alloc_ram	(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

Details

By default, intra-patch distances are considered for metric calculation. See more information in Graphab 2.8 manual: https://sourcesup.renater.fr/www/graphab/download/manual-2.8-en.pdf

Author(s)

P. Savary

Examples

## Not run: 
graphab_graph(proj_name = "grphb_ex",
              linkset = "lcp",
              name = "graph")

## End(Not run)

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