suitable.habitat: Estimate a suitable habitat for a species from NEMO output

In MikkoVihtakari/SuitableHabitat: Estimate Habitat Spaces for Geographic Suitable Habitat Models

Description

Estimates suitable habitat for a species from European Modeling of the Ocean (NEMO) physical oceanography model output based on limitations set by temperature, salinity and bottom depth.

Usage

suitable.habitat(
  habitat.space,
  oceangr.model = NEMOdata,
  proj4 = "+init=epsg:3995",
  lat.lim = 40,
  res = 350,
  drop.crumbs = 30000,
  buffer.width = 15000,
  hexbins = 100,
  find.lim.factors = TRUE
)

Arguments

habitat.space	An object from the habitat.space function.
oceangr.model	A list of oceanographic model data. The format should follow that exemplified in the NEMOdata object.
proj4	Character argument specifying the proj4string (projection) for the smoothed polygon output.
lat.lim	Single numeric value defining a latitude value which is used to cut the model data.
res	Vertical and horizontal resolution of the smoothed polygon output. Setting this parameter makes the polygons more connected cutting corners in the raster based model.
drop.crumbs	Single numeric value specifying a threshold (area in km2) for small disconnected polygons which should be removed from the polygonized version of the suitable habitat. Set to 0 (or NA) to bypass the removal. Uses the drop_crumbs function.
buffer.width	Single numeric value defining the gBuffer parameter for the smoothing of polygon output.
hexbins	A number of (xbins) used for the hexagonization. See hexbin.
find.lim.factors	Logical indicating whether the function should which factors (if any) make the NEMO grid cell non-suitable habitat.

Details

The suitable habitat is estimated using the oceanographic model (oceangr.model) grid cells. The grid cell output are further manipulated using the rasterize.suitable.habitat, polygonize.suitable.habitat, and hexagonize.suitable.habitat functions.

The dimensions of NEMO input matrices must be equal.

Value

Returns a list containing suitable habitat estimates in following formats: 1) $raw: oceanographic model (oceangr.model) grid cells, 2) $raster: rasterized cells whose resolution is defined by the res with disconnected regions smaller than the drop.crumbs parameter removed (in km2), 3) $polygon: polygonized raster data, and 4) $hexagon: hexagonized raster data. See hexbin.

MikkoVihtakari/SuitableHabitat documentation built on Jan. 30, 2021, 12:50 a.m.