.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/applications/plot_species_distribution_modeling.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code or to run this example in your browser via JupyterLite or Binder .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_applications_plot_species_distribution_modeling.py: ============================= Species distribution modeling ============================= Modeling species' geographic distributions is an important problem in conservation biology. In this example, we model the geographic distribution of two South American mammals given past observations and 14 environmental variables. Since we have only positive examples (there are no unsuccessful observations), we cast this problem as a density estimation problem and use the :class:`~sklearn.svm.OneClassSVM` as our modeling tool. The dataset is provided by Phillips et. al. (2006). If available, the example uses `basemap `_ to plot the coast lines and national boundaries of South America. 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 ---------- * `"Maximum entropy modeling of species geographic distributions" `_ S. J. Phillips, R. P. Anderson, R. E. Schapire - Ecological Modelling, 190:231-259, 2006. .. GENERATED FROM PYTHON SOURCE LINES 38-249 .. image-sg:: /auto_examples/applications/images/sphx_glr_plot_species_distribution_modeling_001.png :alt: bradypus variegatus, microryzomys minutus :srcset: /auto_examples/applications/images/sphx_glr_plot_species_distribution_modeling_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none ________________________________________________________________________________ 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: 6.73s | .. code-block:: Python # Authors: Peter Prettenhofer # Jake Vanderplas # # 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() .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 6.886 seconds) .. _sphx_glr_download_auto_examples_applications_plot_species_distribution_modeling.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/scikit-learn/scikit-learn/main?urlpath=lab/tree/notebooks/auto_examples/applications/plot_species_distribution_modeling.ipynb :alt: Launch binder :width: 150 px .. container:: lite-badge .. image:: images/jupyterlite_badge_logo.svg :target: ../../lite/lab/?path=auto_examples/applications/plot_species_distribution_modeling.ipynb :alt: Launch JupyterLite :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_species_distribution_modeling.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_species_distribution_modeling.py ` .. include:: plot_species_distribution_modeling.recommendations .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_