import_from_asnr: Import network from asnr package Bansal lab's Animal Social...

In R-KenK/SimuNet: Network Simulation Framework, with a Zest of Empiricism

Description

Import network from asnr package Bansal lab's Animal Social Network Repository

Usage

import_from_asnr(
  class = NULL,
  species = NULL,
  network = NULL,
  url = NULL,
  output = c("graph", "adjacency"),
  type = c("both", "upper", "lower"),
  ...,
  default_prefix = "https://raw.githubusercontent.com/bansallab/asnr/master/Networks/",
  full.path = NULL
)

Arguments

class	character scalar. Phylogenetic class folder of the network to import (e.g. "Aves","Mammalia",etc.). Supports partial matching.
species	character scalar. species folder of the network to import (e.g. "Aves","Mammalia",etc.). Needs to match the beginning of the folder's name Supports partial matching.
network	character scalar. Optional if the folder contains only one .graphml file. Otherwise the .graphml file name to import. Supports partial matching.
url	character scalar. Optional if argument class and species (and network in the case of several graphml in one folder). URL of the .graphml file to import.
output	character scalar. Either "graph" for an igraph graph object, or "adjacency" for an adjacency matrix
type	character scalar. One of "both", "upper", and "lower". In the case of undirected network, "upper" or "lower" should probably be preferred.
...	additional argument. Useful to pass a asnr.df argument to construct_full.path.
default_prefix	character scalar. URL "prefix" used to retrieve the graphml file from github.
full.path	character scalar. Optional, can be used to input directly an URL to a graphml file.

Value

According to output, either a igraph object or an adjacency matrix.

Examples

 ## Not run: 
   import_from_asnr("Aves","cowbird")
   # partial matching works, but at the moment not case insensitive
   import_from_asnr("Amph","frog",output = "adj")
   # Users can also copy-paste a `.graphml`'s URL
   # link split into two for line length reason. User can directly copy paste full links, however
   import_from_asnr(
     url = paste0(
       "https://github.com/bansallab/asnr/blob/master/Networks/Reptilia/",
       "lizard_proximity_weighted/weighted_network_social_T_rugosa.graphml"
     )
   )
   # To avoid multiple get querries and longer computation time, users can first
   # load a `asnr.df` data frame by calling once the `asnr_network_df` function
   asnr.df <- asnr_network_df()
   import_from_asnr("Amph","frog",output = "adj",asnr.df = asnr.df)
 
## End(Not run)

R-KenK/SimuNet documentation built on Oct. 22, 2021, 1:27 a.m.