from io import BytesIO import os from zipfile import ZipFile import pandas as pd import requests from aif360.sklearn.datasets.utils import standardize_dataset # cache location DATA_HOME_DEFAULT = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', 'data', 'raw') MEPS_URL = "https://meps.ahrq.gov/mepsweb/data_files/pufs" PROMPT = """ By using this function you acknowledge the responsibility for reading and abiding by any copyright/usage rules and restrictions as stated on the MEPS web site (https://meps.ahrq.gov/data_stats/data_use.jsp). Continue [y/n]? > """ def fetch_meps(panel, *, accept_terms=None, data_home=None, cache=True, usecols=['REGION', 'AGE', 'SEX', 'RACE', 'MARRY', 'FTSTU', 'ACTDTY', 'HONRDC', 'RTHLTH', 'MNHLTH', 'HIBPDX', 'CHDDX', 'ANGIDX', 'MIDX', 'OHRTDX', 'STRKDX', 'EMPHDX', 'CHBRON', 'CHOLDX', 'CANCERDX', 'DIABDX', 'JTPAIN', 'ARTHDX', 'ARTHTYPE', 'ASTHDX', 'ADHDADDX', 'PREGNT', 'WLKLIM', 'ACTLIM', 'SOCLIM', 'COGLIM', 'DFHEAR42', 'DFSEE42', 'ADSMOK42', 'PCS42', 'MCS42', 'K6SUM42', 'PHQ242', 'EMPST', 'POVCAT', 'INSCOV'], dropcols=None, numeric_only=False, dropna=True): """Load the Medical Expenditure Panel Survey (MEPS) dataset. Note: For descriptions of the dataset features, see the `data codebook `_. Args: panel ({19, 20, 21}): Panel number (only 19, 20, and 21 are currently supported). accept_terms (bool, optional): Bypass terms prompt. Note: by setting this to ``True``, you acknowledge responsibility for reading and accepting the MEPS usage terms. data_home (string, optional): Specify another download and cache folder for the datasets. By default all AIF360 datasets are stored in 'aif360/sklearn/data/raw' subfolders. cache (bool): Whether to cache downloaded datasets. usecols (single label or list-like, optional): Feature column(s) to keep. All others are dropped. dropcols (single label or list-like, optional): Feature column(s) to drop. numeric_only (bool): Drop all non-numeric feature columns. dropna (bool): Drop rows with NAs. Returns: namedtuple: Tuple containing X and y for the MEPS dataset accessible by index or name. """ if panel not in {19, 20, 21}: raise ValueError("only panels 19, 20, and 21 are currently supported.") fname = 'h192' if panel == 21 else 'h181' cache_path = os.path.join(data_home or DATA_HOME_DEFAULT, fname + '.csv') if cache and os.path.isfile(cache_path): df = pd.read_csv(cache_path) else: # skip prompt if user chooses accept = accept_terms or input(PROMPT) if accept != 'y' and accept != True: raise PermissionError("Terms not agreed.") rawz = requests.get(os.path.join(MEPS_URL, fname + 'ssp.zip')).content with ZipFile(BytesIO(rawz)) as zf: with zf.open(fname + '.ssp') as ssp: df = pd.read_sas(ssp, format='xport') # TODO: does this cause any differences? # reduce storage size df = df.apply(pd.to_numeric, errors='ignore', downcast='integer') if cache: os.makedirs(os.path.dirname(cache_path), exist_ok=True) df.to_csv(cache_path, index=None) # restrict to correct panel df = df[df['PANEL'] == panel] # change all 15s to 16s if panel == 21 yr = 16 if panel == 21 else 15 # non-Hispanic Whites are marked as WHITE; all others as NON-WHITE df['RACEV2X'] = (df['HISPANX'] == 2) & (df['RACEV2X'] == 1) # rename all columns that are panel/round-specific df = df.rename(columns={ 'FTSTU53X': 'FTSTU', 'ACTDTY53': 'ACTDTY', 'HONRDC53': 'HONRDC', 'RTHLTH53': 'RTHLTH', 'MNHLTH53': 'MNHLTH', 'CHBRON53': 'CHBRON', 'JTPAIN53': 'JTPAIN', 'PREGNT53': 'PREGNT', 'WLKLIM53': 'WLKLIM', 'ACTLIM53': 'ACTLIM', 'SOCLIM53': 'SOCLIM', 'COGLIM53': 'COGLIM', 'EMPST53': 'EMPST', 'REGION53': 'REGION', 'MARRY53X': 'MARRY', 'AGE53X': 'AGE', f'POVCAT{yr}': 'POVCAT', f'INSCOV{yr}': 'INSCOV', f'PERWT{yr}F': 'PERWT', 'RACEV2X': 'RACE'}) df.loc[df.AGE < 0, 'AGE'] = None # set invalid ages to NaN cat_cols = ['REGION', 'SEX', 'RACE', 'MARRY', 'FTSTU', 'ACTDTY', 'HONRDC', 'RTHLTH', 'MNHLTH', 'HIBPDX', 'CHDDX', 'ANGIDX', 'MIDX', 'OHRTDX', 'STRKDX', 'EMPHDX', 'CHBRON', 'CHOLDX', 'CANCERDX', 'DIABDX', 'JTPAIN', 'ARTHDX', 'ARTHTYPE', 'ASTHDX', 'ADHDADDX', 'PREGNT', 'WLKLIM', 'ACTLIM', 'SOCLIM', 'COGLIM', 'DFHEAR42', 'DFSEE42', 'ADSMOK42', 'PHQ242', 'EMPST', 'POVCAT', 'INSCOV', # NOTE: education tracking seems to have changed between panels. 'EDUYRDG' # was used for panel 19, 'EDUCYR' and 'HIDEG' were used for panels 20 & 21. # User may change usecols to include these manually. 'EDUCYR', 'HIDEG'] if panel == 19: cat_cols += ['EDUYRDG'] for col in cat_cols: df[col] = df[col].astype('category') thresh = 0 if col in ['REGION', 'MARRY', 'ASTHDX'] else -1 na_cats = [c for c in df[col].cat.categories if c < thresh] df[col] = df[col].cat.remove_categories(na_cats) # set NaN cols to NaN df['SEX'] = df['SEX'].cat.rename_categories({1: 'Male', 2: 'Female'}) df['RACE'] = df['RACE'].cat.rename_categories({False: 'Non-White', True: 'White'}) df['RACE'] = df['RACE'].cat.reorder_categories(['Non-White', 'White'], ordered=True) # Compute UTILIZATION, binarize it to 0 (< 10) and 1 (>= 10) cols = [f'OBTOTV{yr}', f'OPTOTV{yr}', f'ERTOT{yr}', f'IPNGTD{yr}', f'HHTOTD{yr}'] util = df[cols].sum(axis=1) df['UTILIZATION'] = pd.cut(util, [min(util)-1, 10, max(util)+1], right=False, labels=['< 10 Visits', '>= 10 Visits'])#['low', 'high']) return standardize_dataset(df, prot_attr='RACE', target='UTILIZATION', sample_weight='PERWT', usecols=usecols, dropcols=dropcols, numeric_only=numeric_only, dropna=dropna)