Kaggle competition: COVID19 Global Forecasting (Week 2)
<count_missing_values>
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import statsmodels.tsa.arima_model as arima
from sklearn.linear_model import LinearRegression
from sklearn import linear_model
df_all.isnull().sum().sort_values()<count_values>
warnings.filterwarnings('ignore')
 pd.set_option("display.max_rows", None, "display.max_columns", None )
df_all['edjefa'].value_counts()<count_values>
training_data_original = pd.read_csv('/kaggle/input/inputs-data/train_data.csv')
 training_data_original['Date'] = pd.to_datetime(training_data_original['Date'])
 training_data = training_data_original[training_data_original['Country_Region'] != 'Diamond Princess']
countries = training_data['Country_Region'].unique()
countries_main = ['China', 'US', 'Australia', 'Canada']
states = training_data['Province_State'].unique()
df_all['edjefe'].value_counts()<data_type_conversions>
state_metadata = pd.read_excel('/kaggle/input/external-data-source/states_data.xlsx')
 country_metadata = pd.read_excel('/kaggle/input/external-data-source/countries_data.xlsx' )
mapeamento = {'yes': 1, 'no': 0}
df_all['edjefa'] = df_all['edjefa'].replace(mapeamento ).astype(int)
 df_all['edjefe'] = df_all['edjefe'].replace(mapeamento ).astype(int )<count_values>
def data_preparation(training_data, countries, states, country_metadata, state_metadata, n_days_case,
n_days_fatal, min_num_cases = 2):
training_data_trun = training_data[training_data['ConfirmedCases'] >= min_num_cases]
conf_cases_dict = {}
fatal_dict = {}
for country in countries:
if country not in countries_main:
training_data_trun_loc = training_data_trun[(training_data_trun['Country_Region'] == country)&(pd.isnull(training_data_trun.Province_State)) ]
training_data_trun_loc = training_data_trun_loc.groupby(['Date'] ).sum()
training_data_trun_loc = training_data_trun_loc.sort_values(by = 'Date')
 if len(training_data_trun_loc['ConfirmedCases'].values)>= n_days_case:
conf_cases_dict[country] = training_data_trun_loc['ConfirmedCases'].values[:n_days_case] / country_metadata[country_metadata['Countries'] == country]['Population'].values[0]
if len(training_data_trun_loc['Fatalities'].values)>= n_days_fatal:
fatal_dict[country] = training_data_trun_loc['Fatalities'].values[:n_days_fatal]
for state in states:
training_data_trun_loc = training_data_trun[training_data_trun['Province_State'] == state]
training_data_trun_loc = training_data_trun_loc.groupby(['Date'] ).sum()
training_data_trun_loc = training_data_trun_loc.sort_values(by = 'Date')
 if len(training_data_trun_loc['ConfirmedCases'].values)>= n_days_case:
conf_cases_dict[state] = training_data_trun_loc['ConfirmedCases'].values[:n_days_case] / state_metadata[state_metadata['States'] == state]['Population'].values[0]
if len(training_data_trun_loc['Fatalities'].values)>= n_days_fatal:
fatal_dict[state] = training_data_trun_loc['Fatalities'].values[:n_days_fatal]
return pd.DataFrame(conf_cases_dict), pd.DataFrame(fatal_dict )
df_all['edjefe'].value_counts()<count_values>
def fts_training(input_df, rank = 3):
matrix = input_df.values
u, s, v = np.linalg.svd(matrix, full_matrices=False)
 scores = np.matmul(u[:, :rank], np.diag(s[:rank]))
pcs = v[:rank, :]
return scores, pcs
df_all['edjefa'].value_counts()<count_values>
def forecast_trajectories(training_data, countries, states, country_metadata,
state_metadata, loc = None, n_days_case = 30, n_days_fatal = 10,
forecast_days = 10, min_num_cases = 2, model_type = 'ARIMA',
components_modeling = True, rank = 3):
kf = KalmanFilter(initial_state_mean = np.zeros(rank ).tolist() , n_dim_obs = rank)
 conf_cases_df, fatal_df = data_preparation(training_data, countries, states,
country_metadata, state_metadata,
n_days_case = n_days_case,
n_days_fatal = n_days_case,
min_num_cases = min_num_cases)
 pred_countries = conf_cases_df.columns.tolist()
pred_countries_fatal = fatal_df.columns.tolist()
conf_cases_exog_df, fatal_exog_df = data_preparation(training_data, countries, states,
country_metadata, state_metadata,
n_days_case = n_days_case + forecast_days,
n_days_fatal = n_days_case + forecast_days,
min_num_cases = min_num_cases)
 scores_exog, pcs_exog = fts_training(conf_cases_exog_df, rank = rank)
 if len(scores_exog)> 0:
scores_exog = kf.em(scores_exog ).smooth(scores_exog)[0]
scores, pcs = fts_training(conf_cases_df, rank = rank)
 forecasted_scores = []
idx = 0
for score in scores.T:
if components_modeling:
exog = scores_exog[:n_days_case, idx] if len(scores_exog)> 0 else None
pred_exog = scores_exog[n_days_case:, idx] if len(scores_exog)> 0 else None
y = score
else:
exog = scores_exog[:n_days_case, :] if len(scores_exog)> 0 else None
pred_exog = scores_exog[n_days_case:, :] if len(scores_exog)> 0 else None
y = conf_cases_df[loc].values
try:
model = arima.ARIMA(endog = y, exog = exog, order =(4, 1, 0)).fit(
 seasonal = False,
trace = False,
method = 'css',
solver = 'bfgs',
error_action = 'ignore',
setpwise_fit = True,
warn_convergence = True,
disp = False)
 except:
try:
model = arima.ARIMA(endog = y, exog = exog, order =(3, 1, 0)).fit(
 seasonal = False,
trace = False,
method = 'css',
solver = 'bfgs',
error_action = 'ignore',
setpwise_fit = True,
warn_convergence = True,
disp = False)
 except:
try:
model = arima.ARIMA(endog = y, exog = exog, order =(2, 1, 0)).fit(
 seasonal = False,
trace = False,
method = 'css',
solver = 'bfgs',
error_action = 'ignore',
setpwise_fit = True,
warn_convergence = True,
disp = False)
 except:
model = arima.ARIMA(endog = y, exog = exog, order =(1, 0, 0)).fit(
 seasonal = False,
trace = False,
method = 'css',
solver = 'bfgs',
error_action = 'ignore',
setpwise_fit = True,
warn_convergence = True,
disp = False)
 if not components_modeling:
pred_traj = model.forecast(steps = forecast_days,
alpha = 0.001,
exog = pred_exog)[0]
break
else:
forecasted_scores.append(model.forecast(steps = forecast_days,
alpha = 0.001,
exog = pred_exog)[0].tolist())
 idx = idx + 1
if components_modeling:
pred_traj = np.matmul(np.array(forecasted_scores ).T, pcs)
 pred_traj_df = pd.DataFrame(pred_traj, columns = pred_countries)
 for loc in pred_countries:
if loc in country_metadata['Countries'].values.tolist() :
pred_traj_df[loc] = country_metadata[country_metadata['Countries']
== loc]['Population'].values[0] * pred_traj_df[loc]
if loc in state_metadata['States'].values.tolist() :
pred_traj_df[loc] = state_metadata[state_metadata['States']
== loc]['Population'].values[0] * pred_traj_df[loc]
else:
pred_traj_df = pd.DataFrame()
if loc in countries:
pred_traj_df[loc] = country_metadata[country_metadata['Countries']
== loc]['Population'].values[0] * pred_traj
elif loc in states:
pred_traj_df[loc] = state_metadata[state_metadata['States']
== loc]['Population'].values[0] * pred_traj
fatal_scores_exog, fatal_pcs_exog = fts_training(fatal_exog_df, rank = rank)
 if len(fatal_pcs_exog)> 0:
fatal_scores_exog = kf.em(fatal_scores_exog ).smooth(fatal_scores_exog)[0]
fatal_scores, fatal_pcs = fts_training(fatal_df, rank = rank)
 forecasted_fatal_scores = []
idx = 0
for fatal_score in fatal_scores.T:
if components_modeling:
exog = fatal_scores_exog[:n_days_fatal, idx] if len(fatal_scores_exog)> 0 else None
pred_exog = fatal_scores_exog[n_days_fatal:, idx] if len(fatal_scores_exog)> 0 else None
y = fatal_score
else:
exog = fatal_scores_exog[:n_days_fatal, :] if len(fatal_scores_exog)> 0 else None
pred_exog = fatal_scores_exog[n_days_fatal:, :] if len(fatal_scores_exog)> 0 else None
y = fatal_df[loc].values
try:
model = arima.ARIMA(endog = y, exog = exog, order =(4, 1, 0)).fit(
 seasonal = False,
trace = False,
method = 'css',
solver = 'bfgs',
error_action = 'ignore',
setpwise_fit = True,
warn_convergence = True,
disp = False)
 except:
try:
model = arima.ARIMA(endog = y, exog = exog, order =(3, 1, 0)).fit(
 seasonal = False,
trace = False,
method = 'css',
solver = 'bfgs',
error_action = 'ignore',
setpwise_fit = True,
warn_convergence = True,
disp = False)
 except:
try:
model = arima.ARIMA(endog = y, exog = exog, order =(2, 1, 0)).fit(
 seasonal = False,
trace = False,
method = 'css',
solver = 'bfgs',
error_action = 'ignore',
setpwise_fit = True,
warn_convergence = True,
disp = False)
 except:
model = arima.ARIMA(endog = y, exog = exog, order =(1, 0, 0)).fit(
 seasonal = False,
trace = False,
method = 'css',
solver = 'bfgs',
error_action = 'ignore',
setpwise_fit = True,
warn_convergence = True,
disp = False)
 if not components_modeling:
fatal_pred_traj = model.forecast(steps = forecast_days,
alpha = 0.001,
exog = pred_exog)[0]
break
else:
forecasted_fatal_scores.append(model.forecast(steps = forecast_days,
alpha = 0.001,
exog = pred_exog)[0].tolist())
 idx = idx + 1
if components_modeling:
fatal_pred_traj = np.matmul(np.array(forecasted_fatal_scores ).T, fatal_pcs)
 fatal_pred_traj_df = pd.DataFrame(fatal_pred_traj, columns = pred_countries_fatal)
 else:
fatal_pred_traj_df = pd.DataFrame()
if loc in countries:
fatal_pred_traj_df[loc] = country_metadata[country_metadata['Countries']
== loc]['Population'].values[0] * fatal_pred_traj
elif loc in states:
fatal_pred_traj_df[loc] = state_metadata[state_metadata['States']
== loc]['Population'].values[0] * fatal_pred_traj
return pred_traj_df, fatal_pred_traj_df
df_all['dependency'].value_counts().sort_values()<data_type_conversions>
pred_traj_df, fatal_pred_traj_df = forecast_trajectories(training_data, countries, states, country_metadata, state_metadata,
loc = 'New York', n_days_case = 55, n_days_fatal = 55,
forecast_days = 33, rank = 3, min_num_cases = 2,
components_modeling = True )
df_all['dependency'] = df_all['dependency'].replace(mapeamento ).astype(float )<count_values>
def generate_prediction(test_data, training_data, countries_main, countries, states, min_num_cases):
for country in countries:
print(country)
 if country not in countries_main and country not in excl_list:
test_loc_df = test_data[(test_data['Country_Region'] == country)&(pd.isnull(test_data.Province_State)) ].reset_index()
train_loc_df = training_data[(training_data['Country_Region'] == country)&(pd.isnull(training_data.Province_State)) ].reset_index()
test_start = test_loc_df['Date'][0]
test_end = test_loc_df['Date'][len(test_loc_df)- 1]
train_end = train_loc_df['Date'][len(train_loc_df)- 1]
test_loc_df.loc[(( test_loc_df['Date'] >= test_start)) &(test_loc_df['Date'] <= train_end), 'ConfirmedCases'] = train_loc_df[(train_loc_df['Date'] >= test_start)&(train_loc_df['Date'] <= train_end)]['ConfirmedCases'].values
test_loc_df.loc[(( test_loc_df['Date'] >= test_start)) &(test_loc_df['Date'] <= train_end), 'Fatalities'] = train_loc_df[(train_loc_df['Date'] >= test_start)&(train_loc_df['Date'] <= train_end)]['Fatalities'].values
effective_df = train_loc_df[train_loc_df['ConfirmedCases'] >= min_num_cases]
forecast_days = int(( test_end - train_end ).days)
 if len(effective_df)> 0:
effective_train_start = train_loc_df[train_loc_df['ConfirmedCases'] >= min_num_cases].reset_index() ['Date'][0]
n_days_case = int(( train_end - effective_train_start ).days)+ 1
pred_df, fatal_pred_df = forecast_trajectories(training_data, countries, states,
country_metadata, state_metadata, loc = country,
n_days_case = n_days_case, n_days_fatal = n_days_case,
forecast_days = forecast_days, min_num_cases = min_num_cases,
rank = 3)
 test_loc_df.loc[test_loc_df['Date'] > train_end, 'ConfirmedCases'] = np.maximum.accumulate(pred_df[country].values ).astype(int)
 test_data.loc[(test_data['Country_Region'] == country)&(pd.isnull(test_data.Province_State)) , 'ConfirmedCases'] = test_loc_df['ConfirmedCases'].values
test_loc_df.loc[test_loc_df['Date'] > train_end, 'Fatalities'] = np.maximum.accumulate(fatal_pred_df[country].values ).astype(int)
 test_data.loc[(test_data['Country_Region'] == country)&(pd.isnull(test_data.Province_State)) , 'Fatalities'] = test_loc_df['Fatalities'].values
for state in states:
print(state)
 if str(state)not in excl_list:
test_loc_df = test_data[(test_data['Province_State'] == state)].reset_index()
train_loc_df = training_data[(training_data['Province_State'] == state)].reset_index()
test_start = test_loc_df['Date'][0]
test_end = test_loc_df['Date'][len(test_loc_df)- 1]
train_end = train_loc_df['Date'][len(train_loc_df)- 1]
test_loc_df.loc[(( test_loc_df['Date'] >= test_start)) &(test_loc_df['Date'] <= train_end), 'ConfirmedCases'] = train_loc_df[(train_loc_df['Date'] >= test_start)&(train_loc_df['Date'] <= train_end)]['ConfirmedCases'].values
test_loc_df.loc[(( test_loc_df['Date'] >= test_start)) &(test_loc_df['Date'] <= train_end), 'Fatalities'] = train_loc_df[(train_loc_df['Date'] >= test_start)&(train_loc_df['Date'] <= train_end)]['Fatalities'].values
effective_df = train_loc_df[train_loc_df['ConfirmedCases'] >= min_num_cases]
forecast_days = int(( test_end - train_end ).days)
 if len(effective_df)> 0:
effective_train_start = train_loc_df[train_loc_df['ConfirmedCases'] >= min_num_cases].reset_index() ['Date'][0]
n_days_case = int(( train_end - effective_train_start ).days)+ 1
pred_df, fatal_pred_df = forecast_trajectories(training_data, countries, states,
country_metadata, state_metadata, loc = state,
n_days_case = n_days_case, n_days_fatal = n_days_case,
forecast_days = forecast_days, min_num_cases = min_num_cases,
rank = 3)
 test_loc_df.loc[test_loc_df['Date'] > train_end, 'ConfirmedCases'] = np.maximum.accumulate(pred_df[state].values ).astype(int)
 test_data.loc[test_data['Province_State'] == state, 'ConfirmedCases'] = test_loc_df['ConfirmedCases'].values
test_loc_df.loc[test_loc_df['Date'] > train_end, 'Fatalities'] = np.maximum.accumulate(fatal_pred_df[state].values ).astype(int)
 test_data.loc[test_data['Province_State'] == state, 'Fatalities'] = test_loc_df['Fatalities'].values
return test_data
df_all['dependency'].value_counts()<count_missing_values>
test_data = pd.read_csv('/kaggle/input/inputs-data/test_data.csv')
 test_data['Date'] = pd.to_datetime(test_data['Date'] )
df_all['dependency'].isnull().sum()<count_missing_values>
test_data['ConfirmedCases'] = None
test_data['Fatalities'] = None
df_all.isnull().sum().sort_values()<count_values>
excl_list = ['Hubei', 'Belize', 'Chad', 'Eritrea', 'Grenada', 'Guinea-Bissau', 'Holy See',
'Laos', 'Libya', 'Mali', 'Mozambique', 'Saint Kitts and Nevis', 'Somalia',
'Syria', 'nan', 'Saint Barthelemy', 'Virgin Islands', 'Montserrat',
'Congo(Brazzaville)', 'Gabon', 'Guinea', 'Guyana', 'Haiti', 'Namibia',
'Saint Lucia', 'Seychelles', 'Curacao', 'Cayman Islands']
df_all['Target'].value_counts()<count_missing_values>
predictions = generate_prediction(test_data, training_data, countries_main, countries, states, min_num_cases = 10 )
df_all[df_all['parentesco1'] == 1]['v2a1'].isnull().sum()<count_values>
missing_countries = predictions[(predictions.ConfirmedCases.isnull())&(pd.isnull(predictions.Province_State)) ]['Country_Region'].unique().tolist()
missing_states = predictions[(predictions.ConfirmedCases.isnull())&(pd.notnull(predictions.Province_State)) ]['Province_State'].unique().tolist()
df_all['v2a1'].value_counts()<count_missing_values>
def fill_excl_pred(predictions, training_data_original, test_data):
for country in missing_countries:
print(country)
 pred_loc_df = predictions[predictions['Country_Region'] == country]
train_loc_df = training_data_original[training_data_original['Country_Region'] == country]
series_comf_cases = train_loc_df['ConfirmedCases'].values
series_fatal = train_loc_df['Fatalities'].values
test_start = test_data[test_data['Country_Region'] == country]['Date'].values[0]
series_comf_cases_test = training_data_original[(training_data_original['Country_Region'] == country)&(training_data_original['Date'] >= test_start)]['ConfirmedCases']
series_fatal_test = training_data_original[(training_data_original['Country_Region'] == country)&(training_data_original['Date'] >= test_start)]['Fatalities']
if len(series_comf_cases)> 0:
regressor = LinearRegression()
regressor.fit(np.arange(len(series_comf_cases_test)).reshape(-1, 1), series_comf_cases_test)
 comf_cases_pred = regressor.predict(np.arange(10, 40 ).reshape(-1, 1))
regressor.fit(np.arange(len(series_fatal_test)).reshape(-1, 1), series_fatal_test)
 fatal_pred = regressor.predict(np.arange(10, 40 ).reshape(-1, 1))
else:
comf_cases_pred = []
fatal_pred = []
conf_cases_loc = np.concatenate(( series_comf_cases_test, comf_cases_pred), axis=0)
 fatal_loc = np.concatenate(( series_fatal_test, fatal_pred), axis=0)
 predictions.loc[predictions['Country_Region'] == country, 'ConfirmedCases'] = conf_cases_loc.astype(int)
 predictions.loc[predictions['Country_Region'] == country, 'Fatalities'] = fatal_loc.astype(int)
 for state in missing_states:
print(state)
 pred_loc_df = predictions[predictions['Province_State'] == state]
train_loc_df = training_data_original[training_data_original['Province_State'] == state]
series_comf_cases = train_loc_df['ConfirmedCases'].values
series_fatal = train_loc_df['Fatalities'].values
test_start = test_data[test_data['Province_State'] == state]['Date'].values[0]
series_comf_cases_test = training_data_original[(training_data_original['Province_State'] == state)&(training_data_original['Date'] >= test_start)]['ConfirmedCases']
series_fatal_test = training_data[(training_data_original['Province_State'] == state)&(training_data_original['Date'] >= test_start)]['Fatalities']
regressor = LinearRegression()
regressor.fit(np.arange(len(series_comf_cases_test)).reshape(-1, 1), series_comf_cases_test)
 comf_cases_pred = regressor.predict(np.arange(10, 40 ).reshape(-1, 1))
regressor.fit(np.arange(len(series_fatal_test)).reshape(-1, 1), series_fatal_test)
 fatal_pred = regressor.predict(np.arange(10, 40 ).reshape(-1, 1))
conf_cases_loc = np.concatenate(( series_comf_cases_test, comf_cases_pred), axis=0)
 fatal_loc = np.concatenate(( series_fatal_test, fatal_pred), axis=0)
 predictions.loc[predictions['Province_State'] == state, 'ConfirmedCases'] = conf_cases_loc.astype(int)
 predictions.loc[predictions['Province_State'] == state, 'Fatalities'] = fatal_loc.astype(int)
 return predictions
df_all['v2a1'].isnull().sum()<count_values>
prediction_final = fill_excl_pred(predictions, training_data_original, test_data )
df_all['v18q'].value_counts()<count_missing_values>
predictions_csv = pd.DataFrame()
<count_values><EOS> 
predictions_csv.to_csv('submission.csv', index = False )