gather_habitat_for_species: gather_habitat_for_species function

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

Description

This function aids in gathering data on species occurence that may be useful in constructing functional groups and diet matrices

Usage

gather_habitat_for_species(species_list_location = getwd(), species_list_csv,
  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_list_location	where is species list located; defaults to working director
species_list_csv	name of csv file with the following column headers: Genus, species,common_name. functional_group may also be included.
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 potential habitat types to be included in the model. defaults to full list avaialble from Fishbase

Details

This function aids in gathering data on species occurrence 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 rgbif and rfishbase.

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