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Code Summary

The following code is a data science script I've been working on that cross-validates a fixed effect model. I'm moving from R to Python and would appreciate feedback on the code below.

The code does the following:

  1. Split data into train and test using a custom function that groups/clusters the data

  2. Estimate a linear fixed effect model with train and test data

  3. Calculate RMSE and tstat to verify independence of residuals

  4. Prints RMSE, SE, and tstat from cross-validation exercise.

Note: the code downloads a remote data set, so the code can be run on its own.

Code

from urllib import request
from scipy import stats
import pandas as pd
import numpy as np
import statsmodels.api as sm

print("Defining functions......")

def main():
    """
    Estimate baseline and degree day regression.

    Returns:
        data.frame with RMSE, SE, and tstats
    """
    # Download remote from github
    print("Downloading custom data set from: ")
    print("https://github.com/johnwoodill/corn_yield_pred/raw/master/data/full_data.pickle")
    file_url = "https://github.com/johnwoodill/corn_yield_pred/raw/master/data/full_data.pickle"
    request.urlretrieve(file_url, "full_data.pickle")
    cropdat = pd.read_pickle("full_data.pickle")

    # Baseline WLS Regression Cross-Validation with FE and trends
    print("Estimating Baseline Regression")
    basedat = cropdat[['ln_corn_yield', 'trend', 'trend_sq', 'corn_acres']]
    fe_group = pd.get_dummies(cropdat.fips)
    regdat = pd.concat([basedat, fe_group], axis=1)
    base_rmse, base_se, base_tstat = felm_cv(regdat, cropdat['trend'])

    # Degree Day Regression Cross-Validation
    print("Estimating Degree Day Regression")
    dddat = cropdat[['ln_corn_yield', 'dday0_10C', 'dday10_30C', 'dday30C',
                     'prec', 'prec_sq', 'trend', 'trend_sq', 'corn_acres']]
    fe_group = pd.get_dummies(cropdat.fips)
    regdat = pd.concat([dddat, fe_group], axis=1)
    ddreg_rmse, ddreg_se, ddreg_tstat = felm_cv(regdat, cropdat['trend'])

    # Get results as data.frame
    fdat = {'Regression': ['Baseline', 'Degree Day',],
            'RMSE': [base_rmse, ddreg_rmse],
            'se': [base_se, ddreg_se],
            't-stat': [base_tstat, ddreg_tstat]}

    fdat = pd.DataFrame(fdat, columns=['Regression', 'RMSE', 'se', 't-stat'])

    # Calculate percentage change
    fdat['change'] = (fdat['RMSE'] - fdat['RMSE'].iloc[0])/fdat['RMSE'].iloc[0]
    return fdat


def felm_rmse(y_train, x_train, weights, y_test, x_test):
    """
    Estimate WLS from y_train, x_train, predict using x_test, calculate RMSE,
    and test whether residuals are independent.

    Arguments:
        y_train: Dep variable - Full or training data
        x_train: Covariates - Full or training data
        weights: Weights for WLS
        y_test: Dep variable - test data
        x_test: Covariates - test data

    Returns:
        Returns tuple with RMSE and tstat from ttest
    """
    # Fit model and get predicted values of test data
    mod = sm.WLS(y_train, x_train, weights=weights).fit()
    pred = mod.predict(x_test)

    #Get residuals from test data
    res = (y_test[:] - pred.values)

    # Calculate ttest to check residuals from test and train are independent
    t_stat = stats.ttest_ind(mod.resid, res, equal_var=False)[0]

    # Return RMSE and t-stat from ttest
    return (np.sqrt(np.mean(res**2)), t_stat)

def gc_kfold_cv(data, group, begin, end):
    """
    Custom group/cluster data split for cross-validation of panel data.
    (Ensure groups are clustered and train and test residuals are independent)

    Arguments:
        data:     data to filter with 'trend'
        group:    group to cluster
        begin:    start of cluster
        end:      end of cluster

    Return:
        Return test and train data for Group-by-Cluster Cross-validation method
    """
    # Get group data
    data = data.assign(group=group.values)

    # Filter test and train based on begin and end
    test = data[data['group'].isin(range(begin, end))]
    train = data[~data['group'].isin(range(begin, end))]

    # Return train and test
    dfs = {}
    tsets = [train, test]

    # Combine train and test to return dfs
    for i, val in enumerate([1, 2]):
        dfs[val] = tsets[i]

    return dfs

def felm_cv(regdata, group):
    """
    Cross-validate WLS FE model

    Arguments:
        regdata:  regression data
        group:    group fixed effect

    Returns:
        return mean RMSE, standard error, and mean tstat from ttest
    """
    # Loop through 1-31 years with 5 groups in test set and 26 train set
    #i = 1
    #j = False
    retrmse = []
    rettstat = []
    #for j, val in enumerate([1, 27]):
    for j in range(1, 28):
        # Get test and training data
        tset = gc_kfold_cv(regdata, group, j, j + 4)

        # Separate y_train, x_train, y_test, x_test, and weights
        y_train = tset[1].ln_corn_yield
        x_train = tset[1].drop(['ln_corn_yield', 'corn_acres'], 1)
        weights = tset[1].corn_acres
        y_test = tset[2].ln_corn_yield
        x_test = tset[2].drop(['ln_corn_yield', 'corn_acres'], 1)

        # Get RMSE and tstat from train and test data
        inrmse, t_stat = felm_rmse(y_train, x_train, weights, y_test, x_test)

        # Append RMSE and tstats to return
        retrmse.append(inrmse)
        rettstat.append(t_stat)

        # If end of loop return mean RMSE, s.e., and tstat
        if j == 27:
            return (np.mean(retrmse), np.std(retrmse), np.mean(t_stat))

if __name__ == "__main__":
    RDAT = main()
    print(RDAT)

    # print results
    print("---Results--------------------------------------------")
    print("Baseline: ", round(RDAT.iloc[0, 1], 2), "(RMSE)",
          round(RDAT.iloc[0, 2], 2), "(se)",
          round(RDAT.iloc[0, 1], 3), "(t-stat)")
    print("Degree Day: ", round(RDAT.iloc[1, 1], 2), "(RMSE)",
          round(RDAT.iloc[0, 2], 2), "(se)",
          round(RDAT.iloc[1, 3], 2), "(t-stat)")
    print("------------------------------------------------------")
    print("% Change from Baseline: ", round(RDAT.iloc[1, 4], 4)*100, "%")
    print("------------------------------------------------------")
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A first analysis. Once I have more time, I'll try to look in what happens with the data exactly, these are some remarks are about the general code quality:

pickle

from the python documentation:

Warning

The pickle module is not secure against erroneous or maliciously constructed data. Never unpickle data received from an untrusted or unauthenticated source.

If this is partially processed data, another intermediary format like feather or parquet or so might be more appropriate

Functions

I would make even more functions, instead of cramming everything into the main

actually, almost everywhere where you do a print('<doing this>'), I would make a different functions - fetch_data - baseline_regression`` -degree_day` - ...

caching

Instead of downloading the file each time you do the analysis, you might try to cache it

dataframe indexing

sometimes you use df['<key>'], sometimes df.<key>. Try to be consistent

return values

in gc_kfold_cv you use 5 lines to put the result in a dictionary, with 1 and 2 as keys. Simpler would be to return a tuple test, train or a dict {'test': test, 'train': train}

keyword arguments

in tset[2].drop(['ln_corn_yield', 'corn_acres'], 1), the significance of the 1 is unclear, so better use axis=1 or axis='columns'

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In general looks great and clean the code, I saw just a couple of things that looked strange, marked with ##!##:

def gc_kfold_cv(data, group, begin, end):
    """
    Custom group/cluster data split for cross-validation of panel data.
    (Ensure groups are clustered and train and test residuals are independent)

    Arguments:
        data:     data to filter with 'trend'
        group:    group to cluster
        begin:    start of cluster
        end:      end of cluster

    Return:
        Return test and train data for Group-by-Cluster Cross-validation method
    """
    # Get group data
    data = data.assign(group=group.values)

    # Filter test and train based on begin and end
    test = data[data['group'].isin(range(begin, end))]
    train = data[~data['group'].isin(range(begin, end))]

    # Return train and test
    dfs = {}
    tsets = [train, test]

    # Combine train and test to return dfs
    ##!## In the felm_cv method you already had changed
    ##!## the definition of the loop, here you can do the same.
    for val in range(2):  
        dfs[val + 1] = tsets[val]

    return dfs

def felm_cv(regdata, group):
    """
    Cross-validate WLS FE model

    Arguments:
        regdata:  regression data
        group:    group fixed effect

    Returns:
        return mean RMSE, standard error, and mean tstat from ttest
    """
    # Loop through 1-31 years with 5 groups in test set and 26 train set
    #i = 1
    #j = False
    retrmse = []
    rettstat = []
    #for j, val in enumerate([1, 27]):
    for j in range(1, 28):
        # Get test and training data
        tset = gc_kfold_cv(regdata, group, j, j + 4)

        # Separate y_train, x_train, y_test, x_test, and weights
        y_train = tset[1].ln_corn_yield
        x_train = tset[1].drop(['ln_corn_yield', 'corn_acres'], 1)
        weights = tset[1].corn_acres
        y_test = tset[2].ln_corn_yield
        x_test = tset[2].drop(['ln_corn_yield', 'corn_acres'], 1)

        # Get RMSE and tstat from train and test data
        inrmse, t_stat = felm_rmse(y_train, x_train, weights, y_test, x_test)

        # Append RMSE and tstats to return
        retrmse.append(inrmse)
        rettstat.append(t_stat)

        # If end of loop return mean RMSE, s.e., and tstat
        ##!## If you want to do something at the end of a loop, you 
        ##!## just need to write the code outside it (One indentation level lower)
    return (np.mean(retrmse), np.std(retrmse), np.mean(t_stat))
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  • \$\begingroup\$ Great, thank you. Good point on the last loop. How do you feel about include __main__ in data science scripts like this? If I'm not loading it as a module is it ok to leave it off? \$\endgroup\$ – Amstell Aug 28 '18 at 14:00
  • \$\begingroup\$ If you are sure that you will never call it as a module you "could", but it is good practice and styling to leave it like this. \$\endgroup\$ – ImanolUr Aug 29 '18 at 8:04

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