Source code for statsmodels.tools.tools

"""
Utility functions models code
"""
import numpy as np
import pandas as pd
import scipy.linalg

from statsmodels.tools.data import _is_using_pandas
from statsmodels.tools.validation import array_like


def asstr2(s):
    if isinstance(s, str):
        return s
    elif isinstance(s, bytes):
        return s.decode('latin1')
    else:
        return str(s)


def _make_dictnames(tmp_arr, offset=0):
    """
    Helper function to create a dictionary mapping a column number
    to the name in tmp_arr.
    """
    col_map = {}
    for i, col_name in enumerate(tmp_arr):
        col_map[i + offset] = col_name
    return col_map


def drop_missing(Y, X=None, axis=1):
    """
    Returns views on the arrays Y and X where missing observations are dropped.

    Y : array_like
    X : array_like, optional
    axis : int
        Axis along which to look for missing observations.  Default is 1, ie.,
        observations in rows.

    Returns
    -------
    Y : ndarray
        All Y where the
    X : ndarray

    Notes
    -----
    If either Y or X is 1d, it is reshaped to be 2d.
    """
    Y = np.asarray(Y)
    if Y.ndim == 1:
        Y = Y[:, None]
    if X is not None:
        X = np.array(X)
        if X.ndim == 1:
            X = X[:, None]
        keepidx = np.logical_and(~np.isnan(Y).any(axis),
                                 ~np.isnan(X).any(axis))
        return Y[keepidx], X[keepidx]
    else:
        keepidx = ~np.isnan(Y).any(axis)
        return Y[keepidx]


# TODO: needs to better preserve dtype and be more flexible
# ie., if you still have a string variable in your array you do not
# want to cast it to float
# TODO: add name validator (ie., bad names for datasets.grunfeld)
def categorical(data, col=None, dictnames=False, drop=False):
    """
    Construct a dummy matrix from categorical variables

    .. deprecated:: 0.12

       Use pandas.get_dummies instead.

    Parameters
    ----------
    data : array_like
        An array, Series or DataFrame.  This can be either a 1d vector of
        the categorical variable or a 2d array with the column specifying
        the categorical variable specified by the col argument.
    col : {str, int, None}
        If data is a DataFrame col must in a column of data. If data is a
        Series, col must be either the name of the Series or None. For arrays,
        `col` can be an int that is the (zero-based) column index
        number.  `col` can only be None for a 1d array.  The default is None.
    dictnames : bool, optional
        If True, a dictionary mapping the column number to the categorical
        name is returned.  Used to have information about plain arrays.
    drop : bool
        Whether or not keep the categorical variable in the returned matrix.

    Returns
    -------
    dummy_matrix : array_like
        A matrix of dummy (indicator/binary) float variables for the
        categorical data.
    dictnames :  dict[int, str], optional
        Mapping between column numbers and categorical names.

    Notes
    -----
    This returns a dummy variable for *each* distinct variable.  If a
    a DaataFrame is provided, the names for the new variable is the
    old variable name - underscore - category name.  So if the a variable
    'vote' had answers as 'yes' or 'no' then the returned array would have to
    new variables-- 'vote_yes' and 'vote_no'.  There is currently
    no name checking.

    Examples
    --------
    >>> import numpy as np
    >>> import statsmodels.api as sm

    Univariate examples

    >>> import string
    >>> string_var = [string.ascii_lowercase[0:5],
    ...               string.ascii_lowercase[5:10],
    ...               string.ascii_lowercase[10:15],
    ...               string.ascii_lowercase[15:20],
    ...               string.ascii_lowercase[20:25]]
    >>> string_var *= 5
    >>> string_var = np.asarray(sorted(string_var))
    >>> design = sm.tools.categorical(string_var, drop=True)

    Or for a numerical categorical variable

    >>> instr = np.floor(np.arange(10,60, step=2)/10)
    >>> design = sm.tools.categorical(instr, drop=True)

    With a structured array

    >>> num = np.random.randn(25,2)
    >>> struct_ar = np.zeros((25,1),
    ...                      dtype=[('var1', 'f4'),('var2', 'f4'),
    ...                             ('instrument','f4'),('str_instr','a5')])
    >>> struct_ar['var1'] = num[:,0][:,None]
    >>> struct_ar['var2'] = num[:,1][:,None]
    >>> struct_ar['instrument'] = instr[:,None]
    >>> struct_ar['str_instr'] = string_var[:,None]
    >>> design = sm.tools.categorical(struct_ar, col='instrument', drop=True)

    Or

    >>> design2 = sm.tools.categorical(struct_ar, col='str_instr', drop=True)
    """
    import warnings
    warnings.warn(
        "categorical is deprecated. Use pandas Categorical to represent "
        "categorical data and can get_dummies to construct dummy arrays. "
        "It will be removed after release 0.13.",
        FutureWarning
    )
    # TODO: add a NameValidator function
    if isinstance(col, (list, tuple)):
        if len(col) == 1:
            col = col[0]
        else:
            raise ValueError("Can only convert one column at a time")
    if (not isinstance(data, (pd.DataFrame, pd.Series)) and
            not isinstance(col, (str, int)) and
            col is not None):
        raise TypeError('col must be a str, int or None')

    # Pull out a Series from a DataFrame if provided
    if isinstance(data, pd.DataFrame):
        if col is None:
            raise TypeError('col must be a str or int when using a DataFrame')
        elif col not in data:
            raise ValueError('Column \'{0}\' not found in data'.format(col))
        data = data[col]
        # Set col to None since we not have a Series
        col = None

    if isinstance(data, pd.Series):
        if col is not None and data.name != col:
            raise ValueError('data.name does not match col '
                             '\'{0}\''.format(col))
        data_cat = pd.Categorical(data)
        dummies = pd.get_dummies(data_cat)
        col_map = {i: cat for i, cat in enumerate(data_cat.categories) if
                   cat in dummies}
        if not drop:
            dummies.columns = list(dummies.columns)
            dummies = pd.concat([dummies, data], axis=1)
        if dictnames:
            return dummies, col_map
        return dummies
    # Catch array_like for an error
    elif not isinstance(data, np.ndarray):
        raise NotImplementedError("array_like objects are not supported")
    else:
        if isinstance(col, int):
            offset = data.shape[1]          # need error catching here?
            tmp_arr = np.unique(data[:, col])
            tmp_dummy = (tmp_arr[:, np.newaxis] == data[:, col]).astype(float)
            tmp_dummy = tmp_dummy.swapaxes(1, 0)
            if drop is True:
                offset -= 1
                data = np.delete(data, col, axis=1).astype(float)
            data = np.column_stack((data, tmp_dummy))
            if dictnames is True:
                col_map = _make_dictnames(tmp_arr, offset)
                return data, col_map
            return data
        elif col is None and np.squeeze(data).ndim == 1:
            tmp_arr = np.unique(data)
            tmp_dummy = (tmp_arr[:, None] == data).astype(float)
            tmp_dummy = tmp_dummy.swapaxes(1, 0)
            if drop is True:
                if dictnames is True:
                    col_map = _make_dictnames(tmp_arr)
                    return tmp_dummy, col_map
                return tmp_dummy
            else:
                data = np.column_stack((data, tmp_dummy))
                if dictnames is True:
                    col_map = _make_dictnames(tmp_arr, offset=1)
                    return data, col_map
                return data
        else:
            raise IndexError("The index %s is not understood" % col)


# TODO: add an axis argument to this for sysreg
[docs]def add_constant(data, prepend=True, has_constant='skip'): """ Add a column of ones to an array. Parameters ---------- data : array_like A column-ordered design matrix. prepend : bool If true, the constant is in the first column. Else the constant is appended (last column). has_constant : str {'raise', 'add', 'skip'} Behavior if ``data`` already has a constant. The default will return data without adding another constant. If 'raise', will raise an error if any column has a constant value. Using 'add' will add a column of 1s if a constant column is present. Returns ------- array_like The original values with a constant (column of ones) as the first or last column. Returned value type depends on input type. Notes ----- When the input is a pandas Series or DataFrame, the added column's name is 'const'. """ if _is_using_pandas(data, None): from statsmodels.tsa.tsatools import add_trend return add_trend(data, trend='c', prepend=prepend, has_constant=has_constant) # Special case for NumPy x = np.asarray(data) ndim = x.ndim if ndim == 1: x = x[:, None] elif x.ndim > 2: raise ValueError('Only implemented for 2-dimensional arrays') is_nonzero_const = np.ptp(x, axis=0) == 0 is_nonzero_const &= np.all(x != 0.0, axis=0) if is_nonzero_const.any(): if has_constant == 'skip': return x elif has_constant == 'raise': if ndim == 1: raise ValueError("data is constant.") else: columns = np.arange(x.shape[1]) cols = ",".join([str(c) for c in columns[is_nonzero_const]]) raise ValueError(f"Column(s) {cols} are constant.") x = [np.ones(x.shape[0]), x] x = x if prepend else x[::-1] return np.column_stack(x)
[docs]def isestimable(c, d): """ True if (Q, P) contrast `c` is estimable for (N, P) design `d`. From an Q x P contrast matrix `C` and an N x P design matrix `D`, checks if the contrast `C` is estimable by looking at the rank of ``vstack([C,D])`` and verifying it is the same as the rank of `D`. Parameters ---------- c : array_like A contrast matrix with shape (Q, P). If 1 dimensional assume shape is (1, P). d : array_like The design matrix, (N, P). Returns ------- bool True if the contrast `c` is estimable on design `d`. Examples -------- >>> d = np.array([[1, 1, 1, 0, 0, 0], ... [0, 0, 0, 1, 1, 1], ... [1, 1, 1, 1, 1, 1]]).T >>> isestimable([1, 0, 0], d) False >>> isestimable([1, -1, 0], d) True """ c = array_like(c, 'c', maxdim=2) d = array_like(d, 'd', ndim=2) c = c[None, :] if c.ndim == 1 else c if c.shape[1] != d.shape[1]: raise ValueError('Contrast should have %d columns' % d.shape[1]) new = np.vstack([c, d]) if np.linalg.matrix_rank(new) != np.linalg.matrix_rank(d): return False return True
def pinv_extended(x, rcond=1e-15): """ Return the pinv of an array X as well as the singular values used in computation. Code adapted from numpy. """ x = np.asarray(x) x = x.conjugate() u, s, vt = np.linalg.svd(x, False) s_orig = np.copy(s) m = u.shape[0] n = vt.shape[1] cutoff = rcond * np.maximum.reduce(s) for i in range(min(n, m)): if s[i] > cutoff: s[i] = 1./s[i] else: s[i] = 0. res = np.dot(np.transpose(vt), np.multiply(s[:, np.core.newaxis], np.transpose(u))) return res, s_orig
[docs]def recipr(x): """ Reciprocal of an array with entries less than or equal to 0 set to 0. Parameters ---------- x : array_like The input array. Returns ------- ndarray The array with 0-filled reciprocals. """ x = np.asarray(x) out = np.zeros_like(x, dtype=np.float64) nans = np.isnan(x.flat) pos = ~nans pos[pos] = pos[pos] & (x.flat[pos] > 0) out.flat[pos] = 1.0 / x.flat[pos] out.flat[nans] = np.nan return out
[docs]def recipr0(x): """ Reciprocal of an array with entries less than 0 set to 0. Parameters ---------- x : array_like The input array. Returns ------- ndarray The array with 0-filled reciprocals. """ x = np.asarray(x) out = np.zeros_like(x, dtype=np.float64) nans = np.isnan(x.flat) non_zero = ~nans non_zero[non_zero] = non_zero[non_zero] & (x.flat[non_zero] != 0) out.flat[non_zero] = 1.0 / x.flat[non_zero] out.flat[nans] = np.nan return out
[docs]def clean0(matrix): """ Erase columns of zeros: can save some time in pseudoinverse. Parameters ---------- matrix : ndarray The array to clean. Returns ------- ndarray The cleaned array. """ colsum = np.add.reduce(matrix**2, 0) val = [matrix[:, i] for i in np.flatnonzero(colsum)] return np.array(np.transpose(val))
[docs]def fullrank(x, r=None): """ Return an array whose column span is the same as x. Parameters ---------- x : ndarray The array to adjust, 2d. r : int, optional The rank of x. If not provided, determined by `np.linalg.matrix_rank`. Returns ------- ndarray The array adjusted to have full rank. Notes ----- If the rank of x is known it can be specified as r -- no check is made to ensure that this really is the rank of x. """ if r is None: r = np.linalg.matrix_rank(x) v, d, u = np.linalg.svd(x, full_matrices=False) order = np.argsort(d) order = order[::-1] value = [] for i in range(r): value.append(v[:, order[i]]) return np.asarray(np.transpose(value)).astype(np.float64)
[docs]def unsqueeze(data, axis, oldshape): """ Unsqueeze a collapsed array. Parameters ---------- data : ndarray The data to unsqueeze. axis : int The axis to unsqueeze. oldshape : tuple[int] The original shape before the squeeze or reduce operation. Returns ------- ndarray The unsqueezed array. Examples -------- >>> from numpy import mean >>> from numpy.random import standard_normal >>> x = standard_normal((3,4,5)) >>> m = mean(x, axis=1) >>> m.shape (3, 5) >>> m = unsqueeze(m, 1, x.shape) >>> m.shape (3, 1, 5) >>> """ newshape = list(oldshape) newshape[axis] = 1 return data.reshape(newshape)
def nan_dot(A, B): """ Returns np.dot(left_matrix, right_matrix) with the convention that nan * 0 = 0 and nan * x = nan if x != 0. Parameters ---------- A, B : ndarray """ # Find out who should be nan due to nan * nonzero should_be_nan_1 = np.dot(np.isnan(A), (B != 0)) should_be_nan_2 = np.dot((A != 0), np.isnan(B)) should_be_nan = should_be_nan_1 + should_be_nan_2 # Multiply after setting all nan to 0 # This is what happens if there were no nan * nonzero conflicts C = np.dot(np.nan_to_num(A), np.nan_to_num(B)) C[should_be_nan] = np.nan return C def maybe_unwrap_results(results): """ Gets raw results back from wrapped results. Can be used in plotting functions or other post-estimation type routines. """ return getattr(results, '_results', results) class Bunch(dict): """ Returns a dict-like object with keys accessible via attribute lookup. Parameters ---------- *args Arguments passed to dict constructor, tuples (key, value). **kwargs Keyword agument passed to dict constructor, key=value. """ def __init__(self, *args, **kwargs): super(Bunch, self).__init__(*args, **kwargs) self.__dict__ = self def _ensure_2d(x, ndarray=False): """ Parameters ---------- x : ndarray, Series, DataFrame or None Input to verify dimensions, and to transform as necesary ndarray : bool Flag indicating whether to always return a NumPy array. Setting False will return an pandas DataFrame when the input is a Series or a DataFrame. Returns ------- out : ndarray, DataFrame or None array or DataFrame with 2 dimensiona. One dimensional arrays are returned as nobs by 1. None is returned if x is None. names : list of str or None list containing variables names when the input is a pandas datatype. Returns None if the input is an ndarray. Notes ----- Accepts None for simplicity """ if x is None: return x is_pandas = _is_using_pandas(x, None) if x.ndim == 2: if is_pandas: return x, x.columns else: return x, None elif x.ndim > 2: raise ValueError('x mst be 1 or 2-dimensional.') name = x.name if is_pandas else None if ndarray: return np.asarray(x)[:, None], name else: return pd.DataFrame(x), name def matrix_rank(m, tol=None, method="qr"): """ Matrix rank calculation using QR or SVD Parameters ---------- m : array_like A 2-d array-like object to test tol : float, optional The tolerance to use when testing the matrix rank. If not provided an appropriate value is selected. method : {"ip", "qr", "svd"} The method used. "ip" uses the inner-product of a normalized version of m and then computes the rank using NumPy's matrix_rank. "qr" uses a QR decomposition and is the default. "svd" defers to NumPy's matrix_rank. Returns ------- int The rank of m. Notes ----- When using a QR factorization, the rank is determined by the number of elements on the leading diagonal of the R matrix that are above tol in absolute value. """ m = array_like(m, "m", ndim=2) if method == "ip": m = m[:, np.any(m != 0, axis=0)] m = m / np.sqrt((m ** 2).sum(0)) m = m.T @ m return np.linalg.matrix_rank(m, tol=tol, hermitian=True) elif method == "qr": r, = scipy.linalg.qr(m, mode="r") abs_diag = np.abs(np.diag(r)) if tol is None: tol = abs_diag[0] * m.shape[1] * np.finfo(float).eps return int((abs_diag > tol).sum()) else: return np.linalg.matrix_rank(m, tol=tol)