R/gather_interactions_for_species.R

In r4atlantis/ratlantis: R package for developing, executing, and assessing Atlantis ecosystem models

#' gather_interactions_for_species function
#'
#' This function aids in gathering data on species interactions that may be useful
#' in constructing functional groups and diet matrices
#' @param species_list_location where is species list located,defaults to working directory
#' @param species_list_csv name of csv file with the following column headers:
#' Genus, species,common_name.  functional_group may also be included.
#' @param map_location location of shape file used to create bgm, defaults to working
#' directory
#' @param map_name name of map used for bgm creation; can be produced by rbgmeriser
#' function or created manually, defaults to file created by rbgmeriser
#' @param bbox_coordinates (optional) bounding box (in EPSG:4326 decimal degrees, defining
#' "left, bottom, right, top" of bounding box) in which you wish for information
#' on interactions.  If these are not supplied code uses provided map to determine
#' bounding boxes
#' @keywords biology prm, functional groups,
#' @details This function aids in gathering data on species interactions that may
#' be useful in constructing functional groups and diet matrices.  User submits
#' a list of potential species to be included in the model (may include potential
#' functional groupings). The code gathers data on species from rglobi.
#' @export

gather_interactions_for_species <- function(species_list_location = getwd(), species_list_csv,
                                            map_location =  getwd(), map_name = "map_for_bgmeriser",
                                            bbox_coordinates){
  #read in the species_list
  species_input <- read.csv(paste(species_list_location, "/", species_list_csv, sep=""),
                                 header=T)
  if ("Genus" %!in% names(species_input) |
        "species" %!in% names(species_input) |
        "common_name" %!in% names(species_input)){
      stop(message = "Species list needs all of the following columns: Genus,  species, common_name")
      }
  #add scientific name for matching
  species_input$scientific_name <- paste (species_input$Genus, species_input$species,
                                         sep = " ")
  species_input$scientific_name_underscore <- paste (species_input$Genus, species_input$species,
                                    sep = "_")

  #species interactions using rglobi
  if (missing(bbox_coordinates)){
    map_area <- rgdal::readOGR(map_location, layer=map_name)
    bbox_coordinates <- c(map_area@bbox[1,1], map_area@bbox[2,1], map_area@bbox[1,2],
                          map_area@bbox[2,2])
  }
  species_interactions <- rglobi::get_interactions_in_area( bbox=bbox_coordinates)

  return (species_interactions)

}