def _build_absorb(self, ids: Array) -> 'Absorb':
"""Build a function used to absorb fixed effects defined by columns of IDs."""
import pyhdfe
return Absorb(
pyhdfe.create(ids,
drop_singletons=False,
compute_degrees=False,
residualize_method=self._absorb_method,
options=self._absorb_options))
def __init__(self,
df,
target,
predictors,
ids,
cluster_ids=[],
drop_singletons=True):
"""
Args:
target (string): name of target variable
predictors (list of strings): names of predictors
ids (list of strings): names of variables to be absorbed
df (pandas Dataframe): dataframe containing referenced data
which includes target, predictors and ids
"""
self.df = df
self.algo = pyhdfe.create(ids=get_np_columns(df, ids),
cluster_ids=get_np_columns(df, cluster_ids),
drop_singletons=drop_singletons,
degrees_method='pairwise')
self.all_names = [target] + predictors
self.residualized = self.algo.residualize(
get_np_columns(df, [target] + predictors + cluster_ids))
self.formula = target + '~' + predictors[0]
for name in predictors[1:]:
self.formula = self.formula + '+' + name
self.formula = self.formula + '-1'
df_residualized = pd.DataFrame()
for i, name in enumerate(self.all_names):
df_residualized[name] = self.residualized[:, i]
y, X = dmatrices(self.formula,
data=df_residualized,
return_type='dataframe')
self.model = sm.OLS(y, X)
if cluster_ids == []:
self.model.df_resid = self.residualized.shape[0] - len(
predictors) - self.algo.degrees
else:
clusters = get_np_columns(
df, cluster_ids)[~self.algo._singleton_indices]
min_cluster_count = np.unique(clusters[:, 0]).shape[0]
for i in range(1, clusters.shape[1]):
current_count = np.unique(clusters[:, i]).shape[0]
if current_count < min_cluster_count:
min_cluster_count = current_count
self.model.df_resid = min_cluster_count - len(predictors)
def _build_absorb(
self, ids: Array) -> Callable[[Array], Tuple[Array, List[Error]]]:
"""Build a function used to absorb fixed effects defined by columns of IDs."""
import pyhdfe
# initialize the algorithm for repeated absorption
algorithm = pyhdfe.create(ids,
drop_singletons=False,
compute_degrees=False,
residualize_method=self._absorb_method,
options=self._absorb_options)
def absorb(matrix: Array) -> Tuple[Array, List[Error]]:
"""Handle any absorption errors."""
errors: List[Error] = []
try:
matrix = algorithm.residualize(matrix)
except Exception as exception:
errors.append(exceptions.AbsorptionError(exception))
return matrix, errors
return absorb
#del df_kappas, df_firm
# %%
#fe_var_cs = variables[['quarter']]
variables = df_merge_nas[[
'kappa', 'retail_share', 'lcap', 'marginsq', 'normalized_l2', 'big3',
'blackrock', 'vanguard', 'statestreet'
]]
fe_var_cs = df_merge_nas[['quarter_fe']]
fe_var_ts = df_merge_nas[['pair']]
fe_var_pa = df_merge_nas[['pair', 'quarter_fe']]
# keep even singletons; deal with them in the regression
tick()
alg_cs = pyhdfe.create(fe_var_cs, drop_singletons=False)
tock()
alg_ts = pyhdfe.create(fe_var_ts, drop_singletons=False)
tock()
alg_pa = pyhdfe.create(fe_var_pa, drop_singletons=False)
tock()
tick()
resid_cs = alg_cs.residualize(variables)
tock()
resid_ts = alg_ts.residualize(variables)
tock()
resid_pa = alg_pa.residualize(variables)
tock()
# %%
# million dates
df['pair_fe'] = df.groupby(['from', 'to']).ngroup()
df['quarter_fe'] = df.groupby(['quarter']).ngroup()
# Regressions!
# We will need to absorb: do that first
# This is comically slow and uses 30+GB
var_list = [
'kappa', 'retail_share', 'lcap', 'marginsq', 'normalized_l2', 'big3',
'blackrock', 'vanguard', 'statestreet'
]
# Drop any missings
df2 = df[var_list + ['pair_fe', 'quarter_fe']].dropna()
alg_pa = pyhdfe.create(df2[['pair_fe', 'quarter_fe']].values,
drop_singletons=False)
resid_pa = alg_pa.residualize(df2[var_list].values)
# Perform Regressions
# no need for fixed effects because we've already residualized everything
# drop rows containing NAs
pd_vars = pd.DataFrame(resid_pa,
columns=[
'kappa', 'retail_share', 'lcap', 'marginsq',
'normalized_l2', 'big3', 'blackrock', 'vanguard',
'statestreet'
])
reg1 = smf.ols(formula='kappa ~ retail_share + lcap + marginsq + big3',
data=pd_vars).fit()
reg2 = smf.ols(
def _first_time_fit(
self,
use_cache: bool,
absorb_options: Optional[Dict[str, Union[bool, str, ArrayLike, None,
Dict[str, Any]]]],
method: str,
) -> None:
weights = (cast(Float64Array, self.weights.ndarray)
if self._is_weighted else None)
use_hdfe = weights is None and method in ("auto", "hdfe")
use_hdfe = use_hdfe and not self._absorb_inter.cont.shape[1]
use_hdfe = use_hdfe and not self._interaction_list
if not use_hdfe and method == "hdfe":
raise RuntimeError(
"HDFE has been set as the method but the model cannot be estimated "
"using HDFE. HDFE requires that the model is unweighted and that the "
"absorbed regressors include only fixed effects (dummy variables)."
)
areg = AbsorbingRegressor(
cat=self._absorb_inter.cat,
cont=self._absorb_inter.cont,
interactions=self._interaction_list,
weights=weights,
)
areg_constant = areg.has_constant
self._regressors = areg.regressors
self._num_params += areg.approx_rank
# Do not double count intercept-like terms
self._has_constant = self._has_constant_exog or areg_constant
self._num_params -= min(self._has_constant_exog, areg_constant)
self._regressors_hash = areg.hash
self._constant_absorbed = self._has_constant_exog and areg_constant
dep = self._dependent.ndarray
exog = cast(Float64Array, self._exog.ndarray)
root_w = sqrt(self._weight_data.ndarray)
dep = root_w * dep
exog = root_w * exog
denom = root_w.T @ root_w
mu_dep = (root_w.T @ dep) / denom
mu_exog = (root_w.T @ exog) / denom
absorb_options = {} if absorb_options is None else absorb_options
assert isinstance(self._regressors, sp.csc_matrix)
if self._regressors.shape[1] > 0:
if use_hdfe:
from pyhdfe import create
absorb_options["drop_singletons"] = False
algo = create(self._absorb_inter.cat, **absorb_options)
dep_exog = column_stack((dep, exog))
resids = algo.residualize(dep_exog)
dep_resid = resids[:, :1]
exog_resid = resids[:, 1:]
else:
self._regressors = preconditioner(self._regressors)[0]
dep_exog = column_stack((dep, exog))
resid = lsmr_annihilate(
self._regressors,
dep_exog,
use_cache,
self._regressors_hash,
**absorb_options,
)
dep_resid = resid[:, :1]
exog_resid = resid[:, 1:]
else:
dep_resid = dep
exog_resid = exog
if self._constant_absorbed:
dep_resid += root_w * mu_dep
exog_resid += root_w * mu_exog
if not self._drop_absorbed:
check_absorbed(exog_resid, self.exog.cols, exog)
else:
ncol = exog_resid.shape[1]
retain = not_absorbed(exog_resid)
if not retain:
raise ValueError(
"All columns in exog have been fully absorbed by the "
"included effects. This model cannot be estimated.")
elif len(retain) < ncol:
drop = set(range(ncol)).difference(retain)
dropped = ", ".join([str(self.exog.cols[i]) for i in drop])
warnings.warn(
absorbing_warn_msg.format(absorbed_variables=dropped),
AbsorbingEffectWarning,
)
exog_resid = exog_resid[:, retain]
self._columns = [self._columns[i] for i in retain]
self._absorbed_dependent = DataFrame(
dep_resid,
index=self._dependent.pandas.index,
columns=self._dependent.pandas.columns,
)
self._absorbed_exog = DataFrame(exog_resid,
index=self._exog.pandas.index,
columns=self._columns)
#
######################################################################### PYHDFE TEST
# for a in list(enumerate(list(df))):
# print(a)
df_np = df.to_numpy()
# just a sanity check of straight forward regression
#print("ln_wage ~ hours_log")
#model = sm.OLS(get_np_columns(df, ['ln_wage'], False), get_np_columns(df, ['hours_log']))
#results = model.fit()
#print(results.summary())
algo = pyhdfe.create(get_np_columns(df, ['idcode', 'year'], False),
degrees_method='pairwise')
residualized = algo.residualize(get_np_columns(df, ['ln_wage', 'hours_log'], False))
print(algo.degrees)
import pdb; pdb.set_trace()
#model = sm.OLS(residualized[:,0], np.ones((residualized.shape[0], 1)))
model = sm.OLS(residualized[:,0], add_intercept(residualized[:, 1]))
#print(add_intercept(residualized[:,1])[:10])
ids = get_np_columns(df, ['idcode', 'year'], False)
df_kappas2['irat'] = df_kappas2['kappa'] / df_kappas2['cosine']
# Fixed Effects
df_kappas2['pair_fe'] = df_kappas2.groupby(['from', 'to']).ngroup()
df_kappas2['quarter_fe'] = df_kappas2.groupby(['quarter']).ngroup()
# Report the size of everything
print("N of Overall Dataframe:", len(df_kappas2))
print("N Quarter FE:", len(df_kappas2.quarter_fe.unique()))
print("N Pair FE:", len(df_kappas2.pair_fe.unique()))
# Take the logs of everything and get a NumPy array
variables = np.log(df_kappas2[['kappa', 'cosine', 'irat']]).values
# Use pyhdfe for high-dimensional fixed effects absorption
# This takes 13min on my iMac
resid_cs = pyhdfe.create(df_kappas2[['quarter_fe'
]].values).residualize(variables)
resid_ts = pyhdfe.create(df_kappas2[['pair_fe']].values).residualize(variables)
resid_pa = pyhdfe.create(df_kappas2[['pair_fe', 'quarter_fe'
]].values).residualize(variables)
# Do the Variance Decomposition for each case
tab_mat = np.vstack([
do_decomp(variables),
do_decomp(resid_cs),
do_decomp(resid_ts),
do_decomp(resid_pa)
]) * 100.0
table3 = pd.DataFrame(
tab_mat,
index=['Raw', 'Cross-Section', 'Time-Series', 'Panel'],
columns=['Overlapping Ownership', 'Relative IHHI', 'Covariance'])
def __init__(self,
df,
target,
predictors,
absorb_ids=[],
cluster_ids=[],
drop_singletons=True,
intercept=False):
"""Regression wrapper for PyHDFE.
Args:
df (pandas Dataframe): dataframe containing referenced data
which includes target, predictors and absorb and cluster.
target (string): name of target variable - the y in y = X*b + e.
predictors (string or list of strings): names of predictors, the X in y = X*b + e.
absorb_ids (string or list of strings): names of variables to be absorbed for fixed effects.
cluster_ids (string or list of strings): names of variables to be clustered on.
drop_singletons (bool): indicates whether to drop singleton groups. Defaults is True, same as stata. Setting to False is equivalent to passing keepsingletons to reghdfe.
"""
self.df = df
# in case user has not wrapped singular strings in a list
if isinstance(predictors, str):
predictors = [predictors]
if isinstance(absorb_ids, str):
absorb_ids = [absorb_ids]
if isinstance(cluster_ids, str):
cluster_ids = [cluster_ids]
self.target = target
self.predictors = predictors
self.absorb_ids = absorb_ids
self.cluster_ids = cluster_ids
self.drop_singletons = drop_singletons
# names of all features involved in regression
self.all_names = [target] + predictors
# We construct a formula here to feed it into OLS
# We do this to make the output prettier and give each coefficient
# meaningful names (otherwise the regression coefficients are named x1, x2 etc.)
self.formula = target + '~' + predictors[0]
for name in predictors[1:]:
self.formula = self.formula + '+' + name
# if there's stuff to be absorbed
if absorb_ids:
# Intercept term is redundant in fixed effects
self.formula = self.formula + '-1'
self.algo = pyhdfe.create(ids=get_np_columns(df, absorb_ids),
cluster_ids=get_np_columns(
df, cluster_ids),
drop_singletons=drop_singletons,
degrees_method='pairwise')
# self.residualized contains features adjusted for fixed effects
# (i.e. means subtracted, singleton groups dropped etc.)
self.data = self.algo.residualize(
get_np_columns(df, [target] + predictors))
else:
# otherwise just get np columns as is
self.data = get_np_columns(df, self.all_names)
if not intercept:
self.formula = self.formula + '-1'
df_data = pd.DataFrame()
for i, name in enumerate(self.all_names):
df_data[name] = self.data[:, i]
y, X = dmatrices(self.formula, data=df_data, return_type='dataframe')
# now We prepare the cluster groups if they exist
# We do this here rather than later in fit() since it can be convenient to have
# access to these groups as early as possible
# if not empty
self.model = sm.OLS(y, X)
if bool(self.cluster_ids):
# numpy array of group data
self.groups_np = get_np_columns(self.df, self.cluster_ids)
if bool(self.absorb_ids):
# number of groups - already calculated by pyhdfe so We're just retrieving the value
n_groups = self.algo._groups_list[0].group_count
# get numpy representation of cluster groups
# and remove singleton groups (if fixed effects were used)
self.groups_np = self.groups_np[~self.algo._singleton_indices]
min_cluster_count = np.unique(self.groups_np[:, 0]).shape[0]
for i in range(1, self.groups_np.shape[1]):
current_count = np.unique(self.groups_np[:, i]).shape[0]
if current_count < min_cluster_count:
min_cluster_count = current_count
self.min_cluster_count = min_cluster_count
self.model.df_resid = min_cluster_count - len(
self.predictors) + 1
self.model._df_resid = self.model.df_resid
##print(res.summary)
#
######################################################################### PYHDFE TEST
for a in list(enumerate(list(df))):
print(a)
df_np = df.to_numpy()
# just a sanity check of straight forward regression
#print("ln_wage ~ hours_log")
#model = sm.OLS(get_np_columns(df, ['ln_wage'], False), get_np_columns(df, ['hours_log']))
#results = model.fit()
#print(results.summary())
algo = pyhdfe.create(get_np_columns(df, ['idcode', 'year'], False))
residualized = algo.residualize(
get_np_columns(df, ['ln_wage', 'hours_log'], False))
#model = sm.OLS(residualized[:,0], add_intercept(residualized[:,1]))
#ln_wage ~ hours_log, absorb(year)
# OLS Regression Results
#==============================================================================
#Dep. Variable: y R-squared: 0.005
#Model: OLS Adj. R-squared: 0.005
#Method: Least Squares F-statistic: 69.95
#Date: Sat, 05 Dec 2020 Prob (F-statistic): 6.67e-17
#Time: 13:04:23 Log-Likelihood: -8305.1
#No. Observations: 13452 AIC: 1.661e+04
#Df Residuals: 13450 BIC: 1.663e+04
#Df Model: 1
import pyhdfe
from utils import add_intercept, get_np_columns
from sklearn.datasets import load_boston
# details about dataset can be found at https://www.kaggle.com/crawford/80-cereals
df = pd.read_csv('/home/abom/Downloads/dataset_cereal/cereal.csv')
print(list(df))
#results = smf.ols(formula='rating ~ fat + protein + carbo + sugars', data=df).fit()
#print(results.summary())
print(get_np_columns(df, ['cups'], False)[:10])
algo = pyhdfe.create(get_np_columns(df, ['shelf'], False))
# OLS Regression Results
# ==============================================================================
# Dep. Variable: y R-squared: 0.759
# Model: OLS Adj. R-squared: 0.745
# Method: Least Squares F-statistic: 56.55
# Date: Mon, 07 Dec 2020 Prob (F-statistic): 1.71e-21
# Time: 09:15:25 Log-Likelihood: -252.82
# No. Observations: 77 AIC: 515.6
# Df Residuals: 72 BIC: 527.4
# Df Model: 4
# Covariance Type: nonrobust
# ==============================================================================
# coef std err t P>|t| [0.025 0.975]
# ------------------------------------------------------------------------------