物种分布建模#

对物种的地理分布进行建模是保护生物学中的一个重要问题。在本例中，我们根据过去的观察结果和 14 个环境变量，对两种南美哺乳动物的地理分布进行建模。由于我们只有正样本（没有不成功的观察结果），因此我们将此问题视为密度估计问题，并使用 OneClassSVM 作为我们的建模工具。该数据集由 Phillips 等人 (2006) 提供。如果可用，该示例使用 basemap 绘制南美洲的海岸线和国界。

这两种物种是

“Bradypus variegatus”，褐喉树懒。

“Microryzomys minutus”，也称为森林小稻鼠，一种生活在秘鲁、哥伦比亚、厄瓜多尔、秘鲁和委内瑞拉的啮齿动物。

参考文献#

“物种地理分布的最大熵建模” S. J. Phillips, R. P. Anderson, R. E. Schapire - 生态建模，190:231-259, 2006。

bradypus variegatus, microryzomys minutus

________________________________________________________________________________
Modeling distribution of species 'bradypus variegatus'
 - fit OneClassSVM ... done.
 - plot coastlines from coverage
 - predict species distribution

 Area under the ROC curve : 0.868443
________________________________________________________________________________
Modeling distribution of species 'microryzomys minutus'
 - fit OneClassSVM ... done.
 - plot coastlines from coverage
 - predict species distribution

 Area under the ROC curve : 0.993919

time elapsed: 11.35s

# Authors: Peter Prettenhofer <[email protected]>
#          Jake Vanderplas <[email protected]>
#
# License: BSD 3 clause

from time import time

import matplotlib.pyplot as plt
import numpy as np

from sklearn import metrics, svm
from sklearn.datasets import fetch_species_distributions
from sklearn.utils import Bunch

# 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)


def create_species_bunch(species_name, train, test, coverages, xgrid, ygrid):
    """Create a bunch with information about a particular organism

    This will use the test/train record arrays to extract the
    data specific to the given species name.
    """
    bunch = Bunch(name=" ".join(species_name.split("_")[:2]))
    species_name = species_name.encode("ascii")
    points = dict(test=test, train=train)

    for label, pts in points.items():
        # choose points associated with the desired species
        pts = pts[pts["species"] == species_name]
        bunch["pts_%s" % label] = pts

        # determine coverage values for each of the training & testing points
        ix = np.searchsorted(xgrid, pts["dd long"])
        iy = np.searchsorted(ygrid, pts["dd lat"])
        bunch["cov_%s" % label] = coverages[:, -iy, ix].T

    return bunch


def plot_species_distribution(
    species=("bradypus_variegatus_0", "microryzomys_minutus_0")
):
    """
    Plot the species distribution.
    """
    if len(species) > 2:
        print(
            "Note: when more than two species are provided,"
            " only the first two will be used"
        )

    t0 = time()

    # Load the compressed data
    data = fetch_species_distributions()

    # Set up the data grid
    xgrid, ygrid = construct_grids(data)

    # The grid in x,y coordinates
    X, Y = np.meshgrid(xgrid, ygrid[::-1])

    # create a bunch for each species
    BV_bunch = create_species_bunch(
        species[0], data.train, data.test, data.coverages, xgrid, ygrid
    )
    MM_bunch = create_species_bunch(
        species[1], data.train, data.test, data.coverages, xgrid, ygrid
    )

    # background points (grid coordinates) for evaluation
    np.random.seed(13)
    background_points = np.c_[
        np.random.randint(low=0, high=data.Ny, size=10000),
        np.random.randint(low=0, high=data.Nx, size=10000),
    ].T

    # We'll make use of the fact that coverages[6] has measurements at all
    # land points.  This will help us decide between land and water.
    land_reference = data.coverages[6]

    # Fit, predict, and plot for each species.
    for i, species in enumerate([BV_bunch, MM_bunch]):
        print("_" * 80)
        print("Modeling distribution of species '%s'" % species.name)

        # Standardize features
        mean = species.cov_train.mean(axis=0)
        std = species.cov_train.std(axis=0)
        train_cover_std = (species.cov_train - mean) / std

        # Fit OneClassSVM
        print(" - fit OneClassSVM ... ", end="")
        clf = svm.OneClassSVM(nu=0.1, kernel="rbf", gamma=0.5)
        clf.fit(train_cover_std)
        print("done.")

        # Plot map of South America
        plt.subplot(1, 2, i + 1)
        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([])

        print(" - predict species distribution")

        # Predict species distribution using the training data
        Z = np.ones((data.Ny, data.Nx), dtype=np.float64)

        # We'll predict only for the land points.
        idx = np.where(land_reference > -9999)
        coverages_land = data.coverages[:, idx[0], idx[1]].T

        pred = clf.decision_function((coverages_land - mean) / std)
        Z *= pred.min()
        Z[idx[0], idx[1]] = pred

        levels = np.linspace(Z.min(), Z.max(), 25)
        Z[land_reference == -9999] = -9999

        # plot contours of the prediction
        plt.contourf(X, Y, Z, levels=levels, cmap=plt.cm.Reds)
        plt.colorbar(format="%.2f")

        # scatter training/testing points
        plt.scatter(
            species.pts_train["dd long"],
            species.pts_train["dd lat"],
            s=2**2,
            c="black",
            marker="^",
            label="train",
        )
        plt.scatter(
            species.pts_test["dd long"],
            species.pts_test["dd lat"],
            s=2**2,
            c="black",
            marker="x",
            label="test",
        )
        plt.legend()
        plt.title(species.name)
        plt.axis("equal")

        # Compute AUC with regards to background points
        pred_background = Z[background_points[0], background_points[1]]
        pred_test = clf.decision_function((species.cov_test - mean) / std)
        scores = np.r_[pred_test, pred_background]
        y = np.r_[np.ones(pred_test.shape), np.zeros(pred_background.shape)]
        fpr, tpr, thresholds = metrics.roc_curve(y, scores)
        roc_auc = metrics.auc(fpr, tpr)
        plt.text(-35, -70, "AUC: %.3f" % roc_auc, ha="right")
        print("\n Area under the ROC curve : %f" % roc_auc)

    print("\ntime elapsed: %.2fs" % (time() - t0))


plot_species_distribution()
plt.show()

脚本总运行时间：（0 分 11.520 秒）