"""
=============================
Species distribution dataset
=============================
This dataset represents the geographic distribution of species.
The dataset is provided by Phillips et. al. (2006).
The two species are:
- `"Bradypus variegatus"
<http://www.iucnredlist.org/details/3038/0>`_ ,
the Brown-throated Sloth.
- `"Microryzomys minutus"
<http://www.iucnredlist.org/details/13408/0>`_ ,
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"
<http://rob.schapire.net/papers/ecolmod.pdf>`_ S. J. Phillips,
R. P. Anderson, R. E. Schapire - Ecological Modelling, 190:231-259, 2006.
Notes
-----
For an example of using this dataset, see
:ref:`examples/applications/plot_species_distribution_modeling.py
<sphx_glr_auto_examples_applications_plot_species_distribution_modeling.py>`.
"""
# Authors: Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Jake Vanderplas <vanderplas@astro.washington.edu>
#
# License: BSD 3 clause
import logging
from io import BytesIO
from numbers import Integral, Real
from os import PathLike, makedirs, remove
from os.path import exists
import joblib
import numpy as np
from ..utils import Bunch
from ..utils._param_validation import Interval, validate_params
from . import get_data_home
from ._base import RemoteFileMetadata, _fetch_remote, _pkl_filepath
# The original data can be found at:
# https://biodiversityinformatics.amnh.org/open_source/maxent/samples.zip
SAMPLES = RemoteFileMetadata(
filename="samples.zip",
url="https://ndownloader.figshare.com/files/5976075",
checksum="abb07ad284ac50d9e6d20f1c4211e0fd3c098f7f85955e89d321ee8efe37ac28",
)
# The original data can be found at:
# https://biodiversityinformatics.amnh.org/open_source/maxent/coverages.zip
COVERAGES = RemoteFileMetadata(
filename="coverages.zip",
url="https://ndownloader.figshare.com/files/5976078",
checksum="4d862674d72e79d6cee77e63b98651ec7926043ba7d39dcb31329cf3f6073807",
)
DATA_ARCHIVE_NAME = "species_coverage.pkz"
logger = logging.getLogger(__name__)
def _load_coverage(F, header_length=6, dtype=np.int16):
"""Load a coverage file from an open file object.
This will return a numpy array of the given dtype
"""
header = [F.readline() for _ in range(header_length)]
make_tuple = lambda t: (t.split()[0], float(t.split()[1]))
header = dict([make_tuple(line) for line in header])
M = np.loadtxt(F, dtype=dtype)
nodata = int(header[b"NODATA_value"])
if nodata != -9999:
M[nodata] = -9999
return M
def _load_csv(F):
"""Load csv file.
Parameters
----------
F : file object
CSV file open in byte mode.
Returns
-------
rec : np.ndarray
record array representing the data
"""
names = F.readline().decode("ascii").strip().split(",")
rec = np.loadtxt(F, skiprows=0, delimiter=",", dtype="S22,f4,f4")
rec.dtype.names = names
return rec
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)
@validate_params(
{
"data_home": [str, PathLike, None],
"download_if_missing": ["boolean"],
"n_retries": [Interval(Integral, 1, None, closed="left")],
"delay": [Interval(Real, 0.0, None, closed="neither")],
},
prefer_skip_nested_validation=True,
)
def fetch_species_distributions(
*,
data_home=None,
download_if_missing=True,
n_retries=3,
delay=1.0,
):
"""Loader for species distribution dataset from Phillips et. al. (2006).
Read more in the :ref:`User Guide <species_distribution_dataset>`.
Parameters
----------
data_home : str or path-like, default=None
Specify another download and cache folder for the datasets. By default
all scikit-learn data is stored in '~/scikit_learn_data' subfolders.
download_if_missing : bool, default=True
If False, raise an OSError if the data is not locally available
instead of trying to download the data from the source site.
n_retries : int, default=3
Number of retries when HTTP errors are encountered.
.. versionadded:: 1.5
delay : float, default=1.0
Number of seconds between retries.
.. versionadded:: 1.5
Returns
-------
data : :class:`~sklearn.utils.Bunch`
Dictionary-like object, with the following attributes.
coverages : array, shape = [14, 1592, 1212]
These represent the 14 features measured
at each point of the map grid.
The latitude/longitude values for the grid are discussed below.
Missing data is represented by the value -9999.
train : record array, shape = (1624,)
The training points for the data. Each point has three fields:
- train['species'] is the species name
- train['dd long'] is the longitude, in degrees
- train['dd lat'] is the latitude, in degrees
test : record array, shape = (620,)
The test points for the data. Same format as the training data.
Nx, Ny : integers
The number of longitudes (x) and latitudes (y) in the grid
x_left_lower_corner, y_left_lower_corner : floats
The (x,y) position of the lower-left corner, in degrees
grid_size : float
The spacing between points of the grid, in degrees
Notes
-----
This dataset represents the geographic distribution of species.
The dataset is provided by Phillips et. al. (2006).
The two species are:
- `"Bradypus variegatus"
<http://www.iucnredlist.org/details/3038/0>`_ ,
the Brown-throated Sloth.
- `"Microryzomys minutus"
<http://www.iucnredlist.org/details/13408/0>`_ ,
also known as the Forest Small Rice Rat, a rodent that lives in Peru,
Colombia, Ecuador, Peru, and Venezuela.
- For an example of using this dataset with scikit-learn, see
:ref:`examples/applications/plot_species_distribution_modeling.py
<sphx_glr_auto_examples_applications_plot_species_distribution_modeling.py>`.
References
----------
* `"Maximum entropy modeling of species geographic distributions"
<http://rob.schapire.net/papers/ecolmod.pdf>`_
S. J. Phillips, R. P. Anderson, R. E. Schapire - Ecological Modelling,
190:231-259, 2006.
Examples
--------
>>> from sklearn.datasets import fetch_species_distributions
>>> species = fetch_species_distributions()
>>> species.train[:5]
array([(b'microryzomys_minutus', -64.7 , -17.85 ),
(b'microryzomys_minutus', -67.8333, -16.3333),
(b'microryzomys_minutus', -67.8833, -16.3 ),
(b'microryzomys_minutus', -67.8 , -16.2667),
(b'microryzomys_minutus', -67.9833, -15.9 )],
dtype=[('species', 'S22'), ('dd long', '<f4'), ('dd lat', '<f4')])
"""
data_home = get_data_home(data_home)
if not exists(data_home):
makedirs(data_home)
# Define parameters for the data files. These should not be changed
# unless the data model changes. They will be saved in the npz file
# with the downloaded data.
extra_params = dict(
x_left_lower_corner=-94.8,
Nx=1212,
y_left_lower_corner=-56.05,
Ny=1592,
grid_size=0.05,
)
dtype = np.int16
archive_path = _pkl_filepath(data_home, DATA_ARCHIVE_NAME)
if not exists(archive_path):
if not download_if_missing:
raise OSError("Data not found and `download_if_missing` is False")
logger.info("Downloading species data from %s to %s" % (SAMPLES.url, data_home))
samples_path = _fetch_remote(
SAMPLES, dirname=data_home, n_retries=n_retries, delay=delay
)
with np.load(samples_path) as X: # samples.zip is a valid npz
for f in X.files:
fhandle = BytesIO(X[f])
if "train" in f:
train = _load_csv(fhandle)
if "test" in f:
test = _load_csv(fhandle)
remove(samples_path)
logger.info(
"Downloading coverage data from %s to %s" % (COVERAGES.url, data_home)
)
coverages_path = _fetch_remote(
COVERAGES, dirname=data_home, n_retries=n_retries, delay=delay
)
with np.load(coverages_path) as X: # coverages.zip is a valid npz
coverages = []
for f in X.files:
fhandle = BytesIO(X[f])
logger.debug(" - converting {}".format(f))
coverages.append(_load_coverage(fhandle))
coverages = np.asarray(coverages, dtype=dtype)
remove(coverages_path)
bunch = Bunch(coverages=coverages, test=test, train=train, **extra_params)
joblib.dump(bunch, archive_path, compress=9)
else:
bunch = joblib.load(archive_path)
return bunch