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Split 2D feature distributions into 3D ones

split_rast.Rd

Split 2D feature distributions into 3D ones

Usage

split_rast(biodiv_raster, depth_raster, breaks, biodiv_df, val_depth_range=TRUE,
sep_biodiv_df=",")

Arguments

biodiv_raster

SpatRaster object or folder path with 2D feature distributions as layers.

depth_raster

SpatRaster object or file path with elevation/bathymetric map.

breaks

Numeric vector defining the range of depth layers to use.

biodiv_df

data.frame or a file path (CSV, TXT, XLS, or XLSX) containing additional information about biodiversity features.

val_depth_range

No correction of the splitted 3D distributions based on depth range of the biodiversity features ("min_z" and "max_z" from biodiv_df) is needed.

sep_biodiv_df

The separator used in biodiv_df file, if biodiv_df is in path format.

Details

This function is used to convert 2D distributions of biodiversity features (rasters) into a 3D format. Here the biodiv_df can have the following column names (independently of their order and any other names are ignored):

  • "species_name": Mandatory column with the feature names, which must be the same with biodiv_raster.

  • "pelagic": Mandatory column about the features' behaviour. TRUE means that this feature is pelagic and FALSE means that this feature is benthic.

  • "min_z": Optional column about the minimum vertical range of features. NA values are translated as unlimited upward feature movement.

  • "max_z": Optional column about the maximum vertical range of features. NA values are translated as unlimited downward feature movement.

breaks must be in correspondence to depth_raster file. For example, if depth_raster has range \([10, -3000]\), then a breaks vector of c(0,-40,-200,-2000,-Inf) will create depth levels \([0,-40],\\ (-40,200], (-200, -2000], (-2000, -\infty)\) and set to NA cells with values greater than \(0\).

If val_depth_range = TRUE (default), then no correction is done and the depth range of the biodiversity features is derived from the corresponding feature distribution raster and so "min_z" and "max_z" are ignored. If val_depth_range = FALSE, then the function uses the minimum and maximum depth information provided in the biodiv_df, so as to remove feature occurrences outside their expected range.

Value

A list containing species distributions for each bathymetric layer, that are necessary for further 3D analysis. List names are indicating the depth levels.

Examples

biodiv_raster <- get_biodiv_raster()
depth_raster <- get_depth_raster()
data(biodiv_df)

# You can split features' 2D distributions into 3D ones and then run only 3D analysis
split_features <- split_rast(biodiv_raster,
                             depth_raster,
                             breaks = c(0, -40, -200, -2000, -Inf),
                             biodiv_df)