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Kernel Density Estimate of Species Distributions

This shows an example of a neighbors-based query (in particular a kernel density estimate) on geospatial data, using a Ball Tree built upon the Haversine distance metric – i.e. distances over points in latitude/longitude. The dataset is provided by Phillips et. al. (2006) [1]. If available, the example uses basemap to plot the coast lines and national boundaries of South America.

This example does not perform any learning over the data (see Species distribution modeling for an example of classification based on the attributes in this dataset). It simply shows the kernel density estimate of observed data points in geospatial coordinates.

The two species are:

“Bradypus variegatus” , the Brown-throated Sloth.
“Microryzomys minutus” , also known as the Forest Small Rice Rat, a rodent that lives in Peru, Colombia, Ecuador, Peru, and Venezuela.

References

Bradypus Variegatus, Microryzomys Minutus

- computing KDE in spherical coordinates
- plot coastlines from coverage
- computing KDE in spherical coordinates
- plot coastlines from coverage

# Authors: The scikit-learn developers
# SPDX-License-Identifier: BSD-3-Clause

import matplotlib.pyplot as plt
import numpy as np

from sklearn.datasets import fetch_species_distributions
from sklearn.neighbors import KernelDensity

# if basemap is available, we'll use it.
# otherwise, we'll improvise later...
try:
    from mpl_toolkits.basemap import Basemap

    basemap = True
except ImportError:
    basemap = False


def construct_grids(batch):
    """Construct the map grid from the batch object

    Parameters
    ----------
    batch : Batch object
        The object returned by :func:`fetch_species_distributions`

    Returns
    -------
    (xgrid, ygrid) : 1-D arrays
        The grid corresponding to the values in batch.coverages
    """
    # x,y coordinates for corner cells
    xmin = batch.x_left_lower_corner + batch.grid_size
    xmax = xmin + (batch.Nx * batch.grid_size)
    ymin = batch.y_left_lower_corner + batch.grid_size
    ymax = ymin + (batch.Ny * batch.grid_size)

    # x coordinates of the grid cells
    xgrid = np.arange(xmin, xmax, batch.grid_size)
    # y coordinates of the grid cells
    ygrid = np.arange(ymin, ymax, batch.grid_size)

    return (xgrid, ygrid)


# Get matrices/arrays of species IDs and locations
data = fetch_species_distributions()
species_names = ["Bradypus Variegatus", "Microryzomys Minutus"]

Xtrain = np.vstack([data["train"]["dd lat"], data["train"]["dd long"]]).T
ytrain = np.array(
    [d.decode("ascii").startswith("micro") for d in data["train"]["species"]],
    dtype="int",
)
Xtrain *= np.pi / 180.0  # Convert lat/long to radians

# Set up the data grid for the contour plot
xgrid, ygrid = construct_grids(data)
X, Y = np.meshgrid(xgrid[::5], ygrid[::5][::-1])
land_reference = data.coverages[6][::5, ::5]
land_mask = (land_reference > -9999).ravel()

xy = np.vstack([Y.ravel(), X.ravel()]).T
xy = xy[land_mask]
xy *= np.pi / 180.0

# Plot map of South America with distributions of each species
fig = plt.figure()
fig.subplots_adjust(left=0.05, right=0.95, wspace=0.05)

for i in range(2):
    plt.subplot(1, 2, i + 1)

    # construct a kernel density estimate of the distribution
    print(" - computing KDE in spherical coordinates")
    kde = KernelDensity(
        bandwidth=0.04, metric="haversine", kernel="gaussian", algorithm="ball_tree"
    )
    kde.fit(Xtrain[ytrain == i])

    # evaluate only on the land: -9999 indicates ocean
    Z = np.full(land_mask.shape[0], -9999, dtype="int")
    Z[land_mask] = np.exp(kde.score_samples(xy))
    Z = Z.reshape(X.shape)

    # plot contours of the density
    levels = np.linspace(0, Z.max(), 25)
    plt.contourf(X, Y, Z, levels=levels, cmap=plt.cm.Reds)

    if basemap:
        print(" - plot coastlines using basemap")
        m = Basemap(
            projection="cyl",
            llcrnrlat=Y.min(),
            urcrnrlat=Y.max(),
            llcrnrlon=X.min(),
            urcrnrlon=X.max(),
            resolution="c",
        )
        m.drawcoastlines()
        m.drawcountries()
    else:
        print(" - plot coastlines from coverage")
        plt.contour(
            X, Y, land_reference, levels=[-9998], colors="k", linestyles="solid"
        )
        plt.xticks([])
        plt.yticks([])

    plt.title(species_names[i])

plt.show()

Total running time of the script: (0 minutes 3.677 seconds)

Related examples

Species distribution modeling

Kernel Density Estimation

SGD: Weighted samples

Simple 1D Kernel Density Estimation

© 2007–2026 The scikit-learn developers
Licensed under the 3-clause BSD License.
https://scikit-learn.org/1.9/auto_examples/neighbors/plot_species_kde.html