weights.Distance
— Distance based spatial weights¶
The weights.Distance
module provides for spatial weights defined
on distance relationships.
New in version 1.0.

class
pysal.weights.Distance.
KNN
(data, k=2, p=2, ids=None, radius=None, distance_metric='euclidean')[source]¶ Creates nearest neighbor weights matrix based on k nearest neighbors.
Parameters:  kdtree (object) – PySAL KDTree or ArcKDTree where KDtree.data is array (n,k) n observations on k characteristics used to measure distances between the n objects
 k (int) – number of nearest neighbors
 p (float) – Minkowski pnorm distance metric parameter: 1<=p<=infinity 2: Euclidean distance 1: Manhattan distance Ignored if the KDTree is an ArcKDTree
 ids (list) – identifiers to attach to each observation
Returns: w – instance Weights object with binary weights
Return type: Examples
>>> points = [(10, 10), (20, 10), (40, 10), (15, 20), (30, 20), (30, 30)] >>> kd = pysal.cg.kdtree.KDTree(np.array(points)) >>> wnn2 = pysal.KNN(kd, 2) >>> [1,3] == wnn2.neighbors[0] True
ids
>>> wnn2 = KNN(kd,2) >>> wnn2[0] {1: 1.0, 3: 1.0} >>> wnn2[1] {0: 1.0, 3: 1.0}
now with 1 rather than 0 offset
>>> wnn2 = KNN(kd, 2, ids=range(1,7)) >>> wnn2[1] {2: 1.0, 4: 1.0} >>> wnn2[2] {1: 1.0, 4: 1.0} >>> 0 in wnn2.neighbors False
Notes
Ties between neighbors of equal distance are arbitrarily broken.
See also
pysal.weights.W

classmethod
from_array
(array, **kwargs)[source]¶ Creates nearest neighbor weights matrix based on k nearest neighbors.
Parameters:  array (np.ndarray) – (n, k) array representing n observations on k characteristics used to measure distances between the n objects
 **kwargs (keyword arguments, see Rook) –
Returns: w – instance Weights object with binary weights
Return type: Examples
>>> points = [(10, 10), (20, 10), (40, 10), (15, 20), (30, 20), (30, 30)] >>> wnn2 = pysal.KNN.from_array(points, 2) >>> [1,3] == wnn2.neighbors[0] True
ids
>>> wnn2 = KNN.from_array(points,2) >>> wnn2[0] {1: 1.0, 3: 1.0} >>> wnn2[1] {0: 1.0, 3: 1.0}
now with 1 rather than 0 offset
>>> wnn2 = KNN.from_array(points, 2, ids=range(1,7)) >>> wnn2[1] {2: 1.0, 4: 1.0} >>> wnn2[2] {1: 1.0, 4: 1.0} >>> 0 in wnn2.neighbors False
Notes
Ties between neighbors of equal distance are arbitrarily broken.
See also
class: pysal.weights.KNN pysal.weights.W

classmethod
from_dataframe
(df, geom_col='geometry', ids=None, **kwargs)[source]¶ Make KNN weights from a dataframe.
Parameters:  df (pandas.dataframe) – a dataframe with a geometry column that can be used to construct a W object
 geom_col (string) – column name of the geometry stored in df
 ids (string or iterable) – if string, the column name of the indices from the dataframe if iterable, a list of ids to use for the W if None, df.index is used.
See also
class: pysal.weights.KNN pysal.weights.W

classmethod
from_shapefile
(filepath, **kwargs)[source]¶ Nearest neighbor weights from a shapefile.
Parameters:  data (string) – shapefile containing attribute data.
 k (int) – number of nearest neighbors
 p (float) – Minkowski pnorm distance metric parameter: 1<=p<=infinity 2: Euclidean distance 1: Manhattan distance
 ids (list) – identifiers to attach to each observation
 radius (float) – If supplied arc_distances will be calculated based on the given radius. p will be ignored.
Returns: w – instance; Weights object with binary weights.
Return type: Examples
Polygon shapefile
>>> wc=knnW_from_shapefile(pysal.examples.get_path("columbus.shp")) >>> "%.4f"%wc.pct_nonzero '4.0816' >>> set([2,1]) == set(wc.neighbors[0]) True >>> wc3=pysal.knnW_from_shapefile(pysal.examples.get_path("columbus.shp"),k=3) >>> set(wc3.neighbors[0]) == set([2,1,3]) True >>> set(wc3.neighbors[2]) == set([4,3,0]) True
1 offset rather than 0 offset
>>> wc3_1=knnW_from_shapefile(pysal.examples.get_path("columbus.shp"),k=3,idVariable="POLYID") >>> set([4,3,2]) == set(wc3_1.neighbors[1]) True >>> wc3_1.weights[2] [1.0, 1.0, 1.0] >>> set([4,1,8]) == set(wc3_1.neighbors[2]) True
Point shapefile
>>> w=knnW_from_shapefile(pysal.examples.get_path("juvenile.shp")) >>> w.pct_nonzero 1.1904761904761905 >>> w1=knnW_from_shapefile(pysal.examples.get_path("juvenile.shp"),k=1) >>> "%.3f"%w1.pct_nonzero
Notes
Ties between neighbors of equal distance are arbitrarily broken.
See also
pysal.weights.KNN
,pysal.weights.W

reweight
(k=None, p=None, new_data=None, new_ids=None, inplace=True)[source]¶ Redo KNearest Neighbor weights construction using given parameters
Parameters:  new_data (np.ndarray) – an array containing additional data to use in the KNN weight
 new_ids (list) – a list aligned with new_data that provides the ids for each new observation
 inplace (bool) – a flag denoting whether to modify the KNN object in place or to return a new KNN object
 k (int) – number of nearest neighbors
 p (float) – Minkowski pnorm distance metric parameter: 1<=p<=infinity 2: Euclidean distance 1: Manhattan distance Ignored if the KDTree is an ArcKDTree
Returns:  A copy of the object using the new parameterization, or None if the
 object is reweighted in place.

class
pysal.weights.Distance.
Kernel
(data, bandwidth=None, fixed=True, k=2, function='triangular', eps=1.0000001, ids=None, diagonal=False)[source]¶ Spatial weights based on kernel functions.
Parameters:  data (array) – (n,k) or KDTree where KDtree.data is array (n,k) n observations on k characteristics used to measure distances between the n objects
 bandwidth (float) – or arraylike (optional) the bandwidth for the kernel.
 fixed (binary) – If true then . If false then bandwidth is adaptive across observations.
 k (int) – the number of nearest neighbors to use for determining bandwidth. For fixed bandwidth, where is a vector of knearest neighbor distances (the distance to the kth nearest neighbor for each observation). For adaptive bandwidths,
 diagonal (boolean) – If true, set diagonal weights = 1.0, if false (default), diagonals weights are set to value according to kernel function.
 function ({'triangular','uniform','quadratic','quartic','gaussian'}) –
kernel function defined as follows with
triangular
uniform
quadratic
quartic
gaussian
 eps (float) – adjustment to ensure knn distance range is closed on the knnth observations

weights
¶ dict – Dictionary keyed by id with a list of weights for each neighbor

neighbors
¶ dict – of lists of neighbors keyed by observation id

bandwidth
¶ array – array of bandwidths
Examples
>>> points=[(10, 10), (20, 10), (40, 10), (15, 20), (30, 20), (30, 30)] >>> kw=Kernel(points) >>> kw.weights[0] [1.0, 0.500000049999995, 0.4409830615267465] >>> kw.neighbors[0] [0, 1, 3] >>> kw.bandwidth array([[ 20.000002], [ 20.000002], [ 20.000002], [ 20.000002], [ 20.000002], [ 20.000002]]) >>> kw15=Kernel(points,bandwidth=15.0) >>> kw15[0] {0: 1.0, 1: 0.33333333333333337, 3: 0.2546440075000701} >>> kw15.neighbors[0] [0, 1, 3] >>> kw15.bandwidth array([[ 15.], [ 15.], [ 15.], [ 15.], [ 15.], [ 15.]])
Adaptive bandwidths user specified
>>> bw=[25.0,15.0,25.0,16.0,14.5,25.0] >>> kwa=Kernel(points,bandwidth=bw) >>> kwa.weights[0] [1.0, 0.6, 0.552786404500042, 0.10557280900008403] >>> kwa.neighbors[0] [0, 1, 3, 4] >>> kwa.bandwidth array([[ 25. ], [ 15. ], [ 25. ], [ 16. ], [ 14.5], [ 25. ]])
Endogenous adaptive bandwidths
>>> kwea=Kernel(points,fixed=False) >>> kwea.weights[0] [1.0, 0.10557289844279438, 9.99999900663795e08] >>> kwea.neighbors[0] [0, 1, 3] >>> kwea.bandwidth array([[ 11.18034101], [ 11.18034101], [ 20.000002 ], [ 11.18034101], [ 14.14213704], [ 18.02775818]])
Endogenous adaptive bandwidths with Gaussian kernel
>>> kweag=Kernel(points,fixed=False,function='gaussian') >>> kweag.weights[0] [0.3989422804014327, 0.2674190291577696, 0.2419707487162134] >>> kweag.bandwidth array([[ 11.18034101], [ 11.18034101], [ 20.000002 ], [ 11.18034101], [ 14.14213704], [ 18.02775818]])
Diagonals to 1.0
>>> kq = Kernel(points,function='gaussian') >>> kq.weights {0: [0.3989422804014327, 0.35206533556593145, 0.3412334260702758], 1: [0.35206533556593145, 0.3989422804014327, 0.2419707487162134, 0.3412334260702758, 0.31069657591175387], 2: [0.2419707487162134, 0.3989422804014327, 0.31069657591175387], 3: [0.3412334260702758, 0.3412334260702758, 0.3989422804014327, 0.3011374490937829, 0.26575287272131043], 4: [0.31069657591175387, 0.31069657591175387, 0.3011374490937829, 0.3989422804014327, 0.35206533556593145], 5: [0.26575287272131043, 0.35206533556593145, 0.3989422804014327]} >>> kqd = Kernel(points, function='gaussian', diagonal=True) >>> kqd.weights {0: [1.0, 0.35206533556593145, 0.3412334260702758], 1: [0.35206533556593145, 1.0, 0.2419707487162134, 0.3412334260702758, 0.31069657591175387], 2: [0.2419707487162134, 1.0, 0.31069657591175387], 3: [0.3412334260702758, 0.3412334260702758, 1.0, 0.3011374490937829, 0.26575287272131043], 4: [0.31069657591175387, 0.31069657591175387, 0.3011374490937829, 1.0, 0.35206533556593145], 5: [0.26575287272131043, 0.35206533556593145, 1.0]}

classmethod
from_array
(array, **kwargs)[source]¶ Construct a Kernel weights from an array. Supports all the same options as
pysal.weights.Kernel
See also
pysal.weights.Kernel
,pysal.weights.W

classmethod
from_dataframe
(df, geom_col='geometry', ids=None, **kwargs)[source]¶ Make Kernel weights from a dataframe.
Parameters:  df (pandas.dataframe) – a dataframe with a geometry column that can be used to construct a W object
 geom_col (string) – column name of the geometry stored in df
 ids (string or iterable) – if string, the column name of the indices from the dataframe if iterable, a list of ids to use for the W if None, df.index is used.
See also
pysal.weights.Kernel
,pysal.weights.W

classmethod
from_shapefile
(filepath, idVariable=None, **kwargs)[source]¶ Kernel based weights from shapefile
Parameters:  shapefile (string) – shapefile name with shp suffix
 idVariable (string) – name of column in shapefile’s DBF to use for ids
Returns: Return type: Kernel Weights Object
See also
pysal.weights.Kernel
,pysal.weights.W

class
pysal.weights.Distance.
DistanceBand
(data, threshold, p=2, alpha=1.0, binary=True, ids=None, build_sp=True, silent=False)[source]¶ Spatial weights based on distance band.
Parameters:  data (array) – (n,k) or KDTree where KDtree.data is array (n,k) n observations on k characteristics used to measure distances between the n objects
 threshold (float) – distance band
 p (float) – Minkowski pnorm distance metric parameter: 1<=p<=infinity 2: Euclidean distance 1: Manhattan distance
 binary (boolean) – If true w_{ij}=1 if d_{i,j}<=threshold, otherwise w_{i,j}=0 If false wij=dij^{alpha}
 alpha (float) – distance decay parameter for weight (default 1.0) if alpha is positive the weights will not decline with distance. If binary is True, alpha is ignored
 ids (list) – values to use for keys of the neighbors and weights dicts
 build_sp (boolean) – True to build sparse distance matrix and false to build dense distance matrix; significant speed gains may be obtained dending on the sparsity of the of distance_matrix and threshold that is applied
 silent (boolean) – By default PySAL will print a warning if the dataset contains any disconnected observations or islands. To silence this warning set this parameter to True.

weights
¶ dict – of neighbor weights keyed by observation id

neighbors
¶ dict – of neighbors keyed by observation id
Examples
>>> points=[(10, 10), (20, 10), (40, 10), (15, 20), (30, 20), (30, 30)] >>> wcheck = pysal.W({0: [1, 3], 1: [0, 3], 2: [], 3: [0, 1], 4: [5], 5: [4]}) WARNING: there is one disconnected observation (no neighbors) Island id: [2] >>> w=DistanceBand(points,threshold=11.2) WARNING: there is one disconnected observation (no neighbors) Island id: [2] >>> pysal.weights.util.neighbor_equality(w, wcheck) True >>> w=DistanceBand(points,threshold=14.2) >>> wcheck = pysal.W({0: [1, 3], 1: [0, 3, 4], 2: [4], 3: [1, 0], 4: [5, 2, 1], 5: [4]}) >>> pysal.weights.util.neighbor_equality(w, wcheck) True
inverse distance weights
>>> w=DistanceBand(points,threshold=11.2,binary=False) WARNING: there is one disconnected observation (no neighbors) Island id: [2] >>> w.weights[0] [0.10000000000000001, 0.089442719099991588] >>> w.neighbors[0] [1, 3] >>>
gravity weights
>>> w=DistanceBand(points,threshold=11.2,binary=False,alpha=2.) WARNING: there is one disconnected observation (no neighbors) Island id: [2] >>> w.weights[0] [0.01, 0.0079999999999999984]
Notes
This was initially implemented running scipy 0.8.0dev (in epd 6.1). earlier versions of scipy (0.7.0) have a logic bug in scipy/sparse/dok.py so serge changed line 221 of that file on saldev to fix the logic bug.

classmethod
from_array
(array, threshold, **kwargs)[source]¶ Construct a DistanceBand weights from an array. Supports all the same options as
pysal.weights.DistanceBand
See also
pysal.weights.DistanceBand
,pysal.weights.W

classmethod
from_dataframe
(df, threshold, geom_col='geometry', ids=None, **kwargs)[source]¶ Make DistanceBand weights from a dataframe.
Parameters:  df (pandas.dataframe) – a dataframe with a geometry column that can be used to construct a W object
 geom_col (string) – column name of the geometry stored in df
 ids (string or iterable) – if string, the column name of the indices from the dataframe if iterable, a list of ids to use for the W if None, df.index is used.
See also
pysal.weights.DistanceBand
,pysal.weights.W

classmethod
from_shapefile
(filepath, threshold, idVariable=None, **kwargs)[source]¶ Distanceband based weights from shapefile
Parameters:  shapefile (string) – shapefile name with shp suffix
 idVariable (string) – name of column in shapefile’s DBF to use for ids
Returns: Return type: Kernel Weights Object
See also
class: pysal.weights.DistanceBand class: pysal.weights.W