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Extract a composition matrix of communities and nodes

get_node_site_matrix.Rd

Extract a composition matrix of communities and nodes

Usage

get_node_site_matrix(simulation_path, save = FALSE, output_file = NULL)

Arguments

simulation_path

A string indicating the path from the root directory to the simulation results from gen3sis. Each folder must be separated by a forward slash "/"

save

Logical. If FALSE (default), the list with the results won't be saved in your machine

output_file

A string indicating the path where the output of this function will be saved. If NULL (default), and if save is TRUE the output will be saved in the directory root

Value

A list with four components:

  • node_site_matrixA matrix containing the sites in the rows and the nodes of the tree in the columns

  • treeA phylo object with the species produced in the simulation process. The nodes were renamed from the original phylogeny

  • nameIndexGuideA data frame with node information

  • coordinatesA data frame with coordinate information for the sites in node_site_matrix

Examples

if (FALSE) { # \dontrun{
# Load node-site matrix from gen3sis simulation
result <- get_node_site_matrix(
  simulation_path = "path/to/simulation",
  save = TRUE,
  output_file = "output/node_site_data.rds"
)
} # }