Subset method for trophic_tbl

Description

Ensures that any subsetting or modification preserves the validity of the trophic table.

Usage

## S3 method for class 'trophic_tbl'
x[...]

Arguments

Value

A validated trophic_tbl object.

Add habitat zones to a Habitat object

Description

Add habitat zones to a Habitat object

Usage

add_habitat(hab, sf_data, weight = 1, ...)

Arguments

Value

A Habitat object with new geometries added as habitat

Add links to a trophic table

Description

Adds one or several directed links to a trophic_tbl object.

Usage

add_link(tbl, from, to, weight = 1)

Arguments

Details

The function performs several checks:

• from must be a scalar character string

• to must be a character vector

• Links must be unique

• Self-loops (from == to) are forbidden

• The resulting graph must remain acyclic

Value

A validated trophic_tbl object with the new links added.

Examples

net <- trophic() |>
  add_link("a", "b", weight = 1)

Add non-habitat zones to a Habitat object

Description

Add non-habitat zones to a Habitat object

Usage

add_nohabitat(hab, sf_data, ...)

Arguments

Value

A Habitat object with new geometries added as non-habitat

Compute dispersal or spread map (Generic Engine)

Description

Low-level function to apply spatial processing (Convolution or External algorithms) to a raster. It handles NA masking and method dispatch to Julia if necessary.

Usage

compute_dispersal(x, method = "convolution", options = list(), mask = NULL)

Arguments

Value

A SpatRaster object containing the dispersed values.

Create a 2D Gaussian motion kernel as a SpatRaster

Description

Create a 2D Gaussian motion kernel as a SpatRaster

Usage

compute_kernel(radius, GSD, size_std = 1.5)

Arguments

Value

A matrix defining the kernel

Compute trophic levels of nodes

Description

Determines the trophic level of each node in an acyclic directed graph.

Usage

compute_levels(edges)

Arguments

Value

A named numeric vector giving the trophic level of each node.

Disperse a species or variable over the landscape

Description

Applies a dispersal mechanism to a specific layer of the 'spacemodel' object. This function acts as a wrapper around compute_dispersal to handle the 'spacemodel' class structure.

Usage

dispersal(
  spacemodel,
  layer = 1,
  method = "convolution",
  method_option = list()
)

Arguments

Value

The spacemodel object with the specified layer updated with dispersed values.

See Also

compute_dispersal

Examples

## Not run: 
# 1. Convolution example
my_kernel <- matrix(1, nrow=3, ncol=3)
sm_updated <- dispersal(sm, layer = "Predator", method = "convolution",
                        method_option = list(kernel = my_kernel))

# 2. Omniscape example (requires Julia)
sm_updated <- dispersal(sm, layer = "Predator", method = "omniscape",
                        method_option = list(resistance = res_map, radius = 10))

## End(Not run)

Apply trophic flux from a resource layer

Description

Computes the contribution of a resource raster to a consumer layer using the normalized weight and a flux function stored in the trophic table.

Usage

flux(raster, intakes, from, to)

Arguments

Details

The function extracts the link corresponding to from -> to from the trophic table and applies:

1. the associated flux function to the raster values

2. the normalized weight of the link

An error is thrown if no such link exists.

Value

A raster object with transformed values.

Identify codes of departments intersecting a region of interest

Description

This function takes a region of interest (ROI) as an 'sf' or 'sfc' object and returns the codes of departments intersecting this region.

Usage

get_departements_for_roi(roi)

Arguments

Value

A character vector containing the codes of departments intersecting the region of interest.

Examples

library(sf)
roi <- sf::st_as_sfc(sf::st_bbox(
  c(xmin = 600000, ymin = 6600000, xmax = 650000, ymax = 6650000),
  crs = 2154)
)
departments <- get_departements_for_roi(roi)

Efficiently retrieve OCS GE data from a remote FlatGeobuf

Description

This function retrieves OCS GE (Land Cover) data for a specific Region of Interest (ROI) directly from a remote FlatGeobuf (.fgb) file hosted on a server (e.g., S3).

It leverages GDAL's virtual file system ('/vsicurl/') and the spatial indexing capabilities of FlatGeobuf to download only the data chunks intersecting the bounding box of the ROI, making it highly efficient for large datasets.

Usage

get_ocsge_data_fgb(roi, fgb_url)

Arguments

Details

The function performs the following steps:

1. Transforms the roi to Lambert-93 (EPSG:2154).

2. calculates the bounding box of the roi.

3. Uses sf::st_read with a WKT filter to fetch only relevant features from the remote file.

4. Applies a precise geometric intersection ('st_intersection') to clip the data to the exact shape of the roi.

Value

An sf object containing the OCS GE polygons intersected by the ROI, projected in Lambert-93 (EPSG:2154).

Note

This function requires a working internet connection and GDAL support for the FlatGeobuf driver and network capabilities (vsicurl).

Examples

## Not run: 
  library(sf)

  # 1. Define a Region of Interest (ROI)
  # Example: A small bounding box in France
  my_roi <- st_as_sf(data.frame(
    lon = c(2.3, 2.4, 2.4, 2.3, 2.3),
    lat = c(48.8, 48.8, 48.9, 48.9, 48.8)
  ), coords = c("lon", "lat"), crs = 4326)

  # 2. URL to the remote FlatGeobuf file
  # (Replace with the actual URL of your OCS GE bucket)
  url_fgb <- "https://example.com/data/ocsge_grand_est.fgb"

  # 3. Fetch data
  ocsge_data <- get_ocsge_data_fgb(roi = my_roi, fgb_url = url_fgb)

  # 4. Check result
  print(ocsge_data)
  plot(st_geometry(ocsge_data))

## End(Not run)

Create a Habitat object

Description

Create a spatial Habitat object based on an optional sf data.frame. If no geometry is provided, creates an empty Habitat object. The object has columns:

• habitat: logical, TRUE/FALSE

• weight: numeric

• geometry: sfc geometry

Usage

habitat(geometry = NULL, habitat = NULL, weight = NULL)

Arguments

Value

An object of class habitat, inheriting from sf and data.frame.

Examples

library(sf)

# Empty habitat
h <- habitat()
h

# Habitat with geometries
geom <- st_sfc(
  st_point(c(0, 0)),
  st_point(c(1, 1)),
  crs = 4326
)

hab <- habitat(
  geometry = geom,
  habitat = c(TRUE, FALSE),
  weight = c(0.8, 0)
)
hab

Create a raster from a habitat object

Description

Create a raster from a habitat object

Usage

habitat_raster(ground_raster, habitat)

Arguments

Value

SpatRaster (weight and NA in nogo)

Constructor for Intake Parameters

Description

Creates and configures the trophic flux table with a simplified syntax.

Usage

intake(x, ..., default = NULL, normalize = TRUE)

Arguments

Value

A 'trophic_tbl' with a configured 'flux' column.

Test if a directed graph is cyclic

Description

Implements Kahn's algorithm to detect cycles in a directed graph.

Usage

is_cyclic(df)

Arguments

Value

Logical. TRUE if the graph contains at least one cycle.

Examples

df <- data.frame(from=c("A","B"), to=c("B","A"))
is_cyclic(df)

load raster file from internal data

Description

A raster of the (example).

Usage

load_raster_extdata(path_name)

Arguments

Format

An object 'SpatRaster' (package terra).

Value

A SpatRaster object

Source

Internal data package.

See Also

rast

Get resource layers for a given trophic layer

Description

Returns the upstream neighbors (prey/resources) of a given layer in a trophic graph.

Usage

lower_neighbors(trophic_tbl, layer)

Arguments

Value

A character vector of names of layers that are resources for layer.

Normalize weights of a trophic table

Description

Adds a new column normalized_weight to a trophic_tbl object so that, for each target node (to), the sum of incoming weights equals 1.

Usage

normalize_weights(tbl)

Arguments

Details

For every unique value in the to elements of the link column, the function divides each corresponding weight by the total weight of all links pointing to that same node.

Nodes with no incoming links are left unchanged.

Value

A trophic_tbl object with an additional column normalized_weight.

Examples

net <- trophic() |>
  add_link("a", "b", weight = 2) |>
  add_link("c", "b", weight = 3)

net_norm <- normalize_weights(net)

SF object defining very simplified OCS-GE soil cover metaleurop

Description

Simple feature collection with 9 features and 11 fields. Projected CRS: RGF93 v1 / Lambert-93.

Usage

data(ocsge_metaleurop)

Format

An object of class sf (inherits from data.frame) with 9 rows and 12 columns.

Examples

data(ocsge_metaleurop)

Valued weight between OCSGE layer and species

Description

Valued weight between OCSGE layer and species

Usage

data(ocsge_species_dict)

Format

An object of class data.frame with 13090 rows and 6 columns.

Examples

data(ocsge_species_dict)

Plot a trophic table

Description

Creates a simple graphical representation of a trophic network using ggplot2.

Usage

## S3 method for class 'trophic_tbl'
plot(x, shift = TRUE, ...)

Arguments

Details

Nodes are positioned according to their trophic level:

• The y-axis represents trophic levels

• Nodes of the same level are placed on the same horizontal line

• The x-axis positions are assigned sequentially (0, 1, 2, ...)

Directed links are drawn from lower to higher trophic levels using arrows.

Value

A ggplot object.

Examples

net <- trophic() |>
  add_link("a", "b") |>
  add_link("b", "c")

plot(net)

Create a RasterStack from a list of rasters and names

Description

This function creates a 'SpatRaster' stack from a list of rasters and assigns unique names to each layer.

Usage

raster_stack(raster_list, names = NULL)

Arguments

Details

The function checks that the length of 'raster_list' matches the length of 'names', and that all names are unique. If not, it stops with an error.

Value

A SpatRaster object with named layers.

Examples

# Example with terra rasters
library(terra)
r1 <- rast(nrows=10, ncols=10, vals=1:100)
r2 <- rast(nrows=10, ncols=10, vals=101:200)
raster_stack(list(r1, r2), c("layer1", "layer2"))

Nomenclature of OCS-GE soil cover

Description

Nomenclature of OCS-GE soil cover

Usage

data(ref_ocsge)

Format

An object of class data.frame with 14 rows and 4 columns.

Examples

data(ref_ocsge)

SF object defining ROI metaleurop

Description

Simple feature collection with 1 feature and 1 field. Geodetic CRS: WGS 84.

Usage

data(roi_metaleurop)

Format

An object of class sf (inherits from data.frame) with 1 rows and 2 columns.

Examples

data(roi_metaleurop)

DataBase of collected MicroMammals species

Description

DataBase of collected MicroMammals species

Usage

data(sf_micromammals)

Format

An object of class sf (inherits from tbl_df, tbl, data.frame) with 1426 rows and 27 columns.

Examples

data(sf_micromammals)

Create a spacemodel object

Description

Constructor for the 'spacemodel' class. This function combines spatial data (a raster stack) and ecological data (a trophic table) into a single object used for modelling.

Usage

spacemodel(raster_stack, trophic_tbl)

Arguments

Details

The function performs several checks to ensure data consistency:

• Verifies that raster_stack is a SpatRaster.

• Verifies that trophic_tbl is a trophic_tbl object.

• Ensures the number of raster layers matches the number of levels in the trophic table.

• Ensures that the names of the raster layers match the names in the trophic table.

Value

A SpatRaster object with the following additional attributes:

• trophic_tbl: The trophic_tbl object passed as input.

• spacemodel: A logical flag set to TRUE, indicating this raster is part of a spacemodel.

See Also

rast, trophic_tbl

Transfer (food, contaminant) across trophic levels

Description

Computes the transfer through a trophic network from lower to higher trophic levels using spatial spreading and intake functions.

Usage

transfer(
  spacemodel,
  kernels,
  intakes = NULL,
  exposure_weighting = "local",
  verbose = FALSE
)

Arguments

Details

The function processes layers in ascending trophic order, as defined by the level attribute of the trophic table.

For each layer:

1. Resources (lower neighbors) are identified.

2. Concentration from each resource is spatially spread using spread().

3. Intake is computed using intake().

4. Contributions from all resources are summed.

The function assumes that intake weights are already normalized so that, for each consumer, the sum of contributions from all resources equals 1.

Value

A named 'spacemodel' object as a list of spatial layers representing values after transfer.

Create a trophic table

Description

Creates a data.frame of class trophic_tbl designed to store trophic links. Can be initialized empty or from an existing data.frame.

Usage

trophic(data = NULL, from = NULL, to = NULL, weight = NULL)

Arguments

Value

An object of class trophic_tbl.

Examples

# 1. Empty initialization (pipe style)
net <- trophic() |>
  add_link("sol", "sp1")

# 2. Initialization from data.frame
df_raw <- data.frame(src = c("A", "A"), target = c("B", "C"), w = c(2, 5))
net_from_df <- trophic(df_raw, from = "src", to = "target", weight = "w")

Validate a trophic table

Description

Internal function used to ensure that a trophic_tbl object respects all structural constraints.

Usage

validate_trophic_tbl(df)

Arguments

Details

The function checks that:

• All links are unique

• No self-loops are present

• The graph is acyclic

It also computes and updates the trophic level attribute.

Value

A validated trophic_tbl object.