create_functional_groups: create_functional_groups function

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

Description

This function uses data to suggest functional (focus) groups for an Atlantis model

Usage

create_functional_groups(species_data_location = getwd(), species_info_csv,
  bathymetry_levels, map_location = getwd(), map_name = "map_for_bgmeriser",
  habitat_list = c("Intertidal", "Sublittoral", "Caves", "Oceanic",
  "Epipelagic", "Mesopelagic", "Bathypelagic", "Abyssopelagic", "Hadopelagic",
  "Estuaries", "Mangroves", "MarshesSwamps", "Stream", "Lakes", "Benthos",
  "Sessile", "Demersal", "Pelagic", "Endofauna", "Megabenthos", "Meiobenthos",
  "SoftBottom", "Sand", "Coarse", "Fine", "Level", "Sloping", "Silt", "Mud",
  "Ooze", "HardBottom", "Rocky", "Rubble", "SeaGrassBeds", "BedsBivalve",
  "BedsRock", "CoralReefs", "DropOffs", "ReefFlats", "Lagoons",
  "DeepWaterCorals"))

Arguments

species_data_location	where csv file with species data is located (defaults to working directory).
species_info_csv	name of csv file with the following column headers (all provided by merging "gather" functions (gather_groups_for_species, gather_data_for_species, gather_habitat_for_species): "Genus" "species" "family" "order" "class" "superclass" "phylum" "Trophic level information" One of the following for trophic level: TrophicLevel (developed by user),FoodTroph (from gather_data_for_species), or DietTroph (from gather_data_for_species). These will be averaged. min_depth highest depth at which a species is found; assumes fishbase style, with depths positive max_depth lowest depth at which a species is found; assumes fishbase style, with depths positive
bathymetry_levels	(also used in rbgmeriser function)
map_location	location of shape file used to create bgm; defaults to working directory
map_name	name of map used for bgm creation; can be produced by rbgmeriser function or created manually; defaults to map_for_bgmeriser (produced by rbgmeriser function)
habitat_list	(optional) list of habitat types to be included in the model (see gather_habitat_for_species for default list and potential options)

Details

This function uses provided information to suggest functional group classification for Atlantis models. Species are separated based on taxonomy, depth, habitat, and trophic-level groupings. Given the available information, this focuses mostly on fish. For depth placement, one of the following must be provided: bathymetry_levels OR map_location and map_name

jsgosnell/ratlantis documentation built on May 20, 2019, 2:08 a.m.