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"
frombiodiv_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 andFALSE
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)