153 lines
4.6 KiB
Python
153 lines
4.6 KiB
Python
"""
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================================================
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Kernel Density Estimate of Species Distributions
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================================================
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This shows an example of a neighbors-based query (in particular a kernel
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density estimate) on geospatial data, using a Ball Tree built upon the
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Haversine distance metric -- i.e. distances over points in latitude/longitude.
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The dataset is provided by Phillips et. al. (2006).
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If available, the example uses
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`basemap <https://matplotlib.org/basemap/>`_
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to plot the coast lines and national boundaries of South America.
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This example does not perform any learning over the data
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(see :ref:`sphx_glr_auto_examples_applications_plot_species_distribution_modeling.py` for
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an example of classification based on the attributes in this dataset). It
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simply shows the kernel density estimate of observed data points in
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geospatial coordinates.
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The two species are:
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- `"Bradypus variegatus"
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<https://www.iucnredlist.org/species/3038/47437046>`_ ,
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the Brown-throated Sloth.
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- `"Microryzomys minutus"
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<http://www.iucnredlist.org/details/13408/0>`_ ,
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also known as the Forest Small Rice Rat, a rodent that lives in Peru,
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Colombia, Ecuador, Peru, and Venezuela.
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References
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----------
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* `"Maximum entropy modeling of species geographic distributions"
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<http://rob.schapire.net/papers/ecolmod.pdf>`_
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S. J. Phillips, R. P. Anderson, R. E. Schapire - Ecological Modelling,
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190:231-259, 2006.
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""" # noqa: E501
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# Author: Jake Vanderplas <jakevdp@cs.washington.edu>
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#
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# License: BSD 3 clause
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import matplotlib.pyplot as plt
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import numpy as np
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from sklearn.datasets import fetch_species_distributions
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from sklearn.neighbors import KernelDensity
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# if basemap is available, we'll use it.
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# otherwise, we'll improvise later...
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try:
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from mpl_toolkits.basemap import Basemap
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basemap = True
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except ImportError:
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basemap = False
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def construct_grids(batch):
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"""Construct the map grid from the batch object
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Parameters
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----------
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batch : Batch object
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The object returned by :func:`fetch_species_distributions`
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Returns
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-------
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(xgrid, ygrid) : 1-D arrays
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The grid corresponding to the values in batch.coverages
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"""
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# x,y coordinates for corner cells
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xmin = batch.x_left_lower_corner + batch.grid_size
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xmax = xmin + (batch.Nx * batch.grid_size)
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ymin = batch.y_left_lower_corner + batch.grid_size
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ymax = ymin + (batch.Ny * batch.grid_size)
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# x coordinates of the grid cells
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xgrid = np.arange(xmin, xmax, batch.grid_size)
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# y coordinates of the grid cells
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ygrid = np.arange(ymin, ymax, batch.grid_size)
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return (xgrid, ygrid)
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# Get matrices/arrays of species IDs and locations
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data = fetch_species_distributions()
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species_names = ["Bradypus Variegatus", "Microryzomys Minutus"]
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Xtrain = np.vstack([data["train"]["dd lat"], data["train"]["dd long"]]).T
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ytrain = np.array(
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[d.decode("ascii").startswith("micro") for d in data["train"]["species"]],
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dtype="int",
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)
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Xtrain *= np.pi / 180.0 # Convert lat/long to radians
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# Set up the data grid for the contour plot
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xgrid, ygrid = construct_grids(data)
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X, Y = np.meshgrid(xgrid[::5], ygrid[::5][::-1])
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land_reference = data.coverages[6][::5, ::5]
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land_mask = (land_reference > -9999).ravel()
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xy = np.vstack([Y.ravel(), X.ravel()]).T
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xy = xy[land_mask]
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xy *= np.pi / 180.0
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# Plot map of South America with distributions of each species
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fig = plt.figure()
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fig.subplots_adjust(left=0.05, right=0.95, wspace=0.05)
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for i in range(2):
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plt.subplot(1, 2, i + 1)
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# construct a kernel density estimate of the distribution
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print(" - computing KDE in spherical coordinates")
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kde = KernelDensity(
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bandwidth=0.04, metric="haversine", kernel="gaussian", algorithm="ball_tree"
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)
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kde.fit(Xtrain[ytrain == i])
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# evaluate only on the land: -9999 indicates ocean
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Z = np.full(land_mask.shape[0], -9999, dtype="int")
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Z[land_mask] = np.exp(kde.score_samples(xy))
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Z = Z.reshape(X.shape)
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# plot contours of the density
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levels = np.linspace(0, Z.max(), 25)
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plt.contourf(X, Y, Z, levels=levels, cmap=plt.cm.Reds)
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if basemap:
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print(" - plot coastlines using basemap")
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m = Basemap(
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projection="cyl",
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llcrnrlat=Y.min(),
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urcrnrlat=Y.max(),
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llcrnrlon=X.min(),
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urcrnrlon=X.max(),
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resolution="c",
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)
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m.drawcoastlines()
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m.drawcountries()
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else:
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print(" - plot coastlines from coverage")
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plt.contour(
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X, Y, land_reference, levels=[-9998], colors="k", linestyles="solid"
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)
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plt.xticks([])
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plt.yticks([])
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plt.title(species_names[i])
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plt.show()
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