Merge remote-tracking branch 'upstream/master'

hpc/mrollier-calibration_full-pandemic.py → hpc/mrollier-calibration-full_pandemic.py

@@ -288,8 +288,7 @@
                'refusal' : [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]})
 
 # time-dependent seasonality parameters in seasonality_function
-params.update({'season_factor' : 1,
-               'amplitude' : 0.1,
+params.update({'amplitude' : 0.1,
                'peak_shift' : 0})
 
 
@@ -310,7 +309,9 @@
                                                    'place' : mobility_function,
                                                    'N_vacc' : vaccination_function, 
                                                    'alpha' : VOC_function,
-                                                   'season_factor' : seasonality_function})
+                                                   'beta_R' : seasonality_function,
+                                                   'beta_U': seasonality_function,
+                                                   'beta_M': seasonality_function})
 
 
 
@@ -345,7 +346,7 @@
     # PSO settings
     processes = int(os.getenv('SLURM_CPUS_ON_NODE', mp.cpu_count()))
     sys.stdout.flush()
-    multiplier = 10
+    multiplier = 2
     maxiter = maxiter_PSO
     popsize = multiplier*processes
 
@@ -428,104 +429,6 @@
         print(f"Run time PSO: {day}d{hour}h{minute:02}m{second:02}s")
     sys.stdout.flush()
 
-
-    # ------------------
-    # Setup MCMC sampler
-    # ------------------
-
-    # NOTE: actually, I don't think running the MCMC is necessary for job==R0?
-
-    # Define priors
-    log_prior_fcn = [prior_uniform, prior_uniform, prior_uniform]
-    log_prior_fcn_args = bounds[1:]
-    # Perturbate PSO estimate
-    pars = ['beta_R', 'beta_U', 'beta_M']
-    pert = [0.02, 0.02, 0.02]
-    ndim, nwalkers, pos = perturbate_PSO(theta[1:], pert, multiplier=processes, bounds=log_prior_fcn_args, verbose=False)
-
-    # Manually overwrite the number of walkers (12 times 14 is too much man!)
-    nwalkers = processes * 4
-
-    # Set up the sampler backend if needed
-    if backend:
-        filename = f'{spatial_unit}_backend_{run_date}'
-        backend = emcee.backends.HDFBackend(results_folder+filename)
-        backend.reset(nwalkers, ndim)
-
-    # Labels for traceplots
-    labels = ['$\\beta^R$', '$\\beta^U$', '$\\beta^M$']
-    # Arguments of chosen objective function
-    objective_fcn = objective_fcns.log_probability
-    objective_fcn_args = (model, log_prior_fcn, log_prior_fcn_args, data, states, pars)
-    objective_fcn_kwargs = {'weights':weights, 'draw_fcn':None, 'samples':{}, 'start_date':start_calibration, \
-                            'warmup':warmup, 'dist':'poisson', 'poisson_offset':poisson_offset, 'agg':agg}
-
-
-    print('\n2) Markov-Chain Monte-Carlo sampling')
-    print('~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n')
-    print(f'Using {processes} cores for {ndim} parameters, in {nwalkers} chains.\n')
-    sys.stdout.flush()
-
-
-    # ----------------
-    # Run MCMC sampler
-    # ----------------
-
-    # Print autocorrelation and traceplot every print_n'th iteration
-    sampler = run_MCMC(pos, max_n, print_n, labels, objective_fcn, objective_fcn_args, \
-                       objective_fcn_kwargs, backend, spatial_unit, run_date, job, progress=progress, agg=agg)
-
-
-    # ---------------
-    # Process results
-    # ---------------
-
-    thin = 1
-    try:
-        autocorr = sampler.get_autocorr_time()
-        thin = max(1,int(0.5 * np.min(autocorr)))
-        print(f'Convergence: the chain is longer than 50 times the intergrated autocorrelation time.\nPreparing to save samples with thinning value {thin}.')
-        sys.stdout.flush()
-    except:
-        print('Warning: The chain is shorter than 50 times the integrated autocorrelation time.\nUse this estimate with caution and run a longer chain! Saving all samples (thinning=1).\n')
-        sys.stdout.flush()
-
-    # Print runtime in hours
-    final_time = datetime.datetime.now()
-    runtime = (final_time - intermediate_time)
-    totalMinute, second = divmod(runtime.seconds, 60)
-    hour, minute = divmod(totalMinute, 60)
-    day = runtime.days
-    if day == 0:
-        print(f"Run time MCMC: {hour}h{minute:02}m{second:02}s")
-    else:
-        print(f"Run time MCMC: {day}d{hour}h{minute:02}m{second:02}s")
-    sys.stdout.flush()
-
-    print('\n3) Sending samples to dictionary')
-    sys.stdout.flush()
-
-    flat_samples = sampler.get_chain(discard=0,thin=thin,flat=True)
-    samples_dict = {}
-    for count,name in enumerate(pars):
-        samples_dict[name] = flat_samples[:,count].tolist()
-
-    samples_dict.update({
-        'warmup' : warmup,
-        'start_date_R0' : start_calibration,
-        'end_date_R0' : end_calibration,
-        'n_chains_R0': int(nwalkers)
-    })
-
-    json_file = f'{samples_path}{str(spatial_unit)}_{run_date}.json'
-    with open(json_file, 'w') as fp:
-        json.dump(samples_dict, fp)
-
-    print('DONE!')
-    print(f'SAMPLES DICTIONARY SAVED IN "{json_file}"')
-    print('-----------------------------------------------------------------------------------------------------------------------------------\n')
-    sys.stdout.flush()
-
     # Work is done
     sys.exit()
 
@@ -543,17 +446,17 @@
 
     # Start of calibration
     start_calibration = '2020-03-02'
-    # Last datapoint used to calibrate infectivity, compliance and effectivity 
+    # Last datapoint used to calibrate infectivity, compliance and effectivity
     if not args.enddate:
-        end_calibration = '2021-08-27'
+        end_calibration = df_sciensano.index.max().strftime("%m-%d-%Y")
     else:
         end_calibration = str(args.enddate)
     # Spatial unit: depesnds on aggregation
     spatial_unit = f'{agg}_full-pandemic_{job}_{signature}'
 
     # PSO settings
     processes = int(os.getenv('SLURM_CPUS_ON_NODE', mp.cpu_count()))
-    multiplier = 1 # 10
+    multiplier = 2 # 10
     maxiter = maxiter_PSO
     popsize = multiplier*processes
 

src/covid19model/data/mobility.py

@@ -83,7 +83,7 @@ def get_apple_mobility_data(update=True):
 
     return df_apple
 
-def get_google_mobility_data(update=True, plot=False, filename_plot=None):
+def get_google_mobility_data(update=True, provincial=False, plot=False, filename_plot=None):
     """Download Google Community mobility report data
 
     This function downloads, formats and returns the available Belgian Google Community mobility report data.
@@ -94,6 +94,8 @@ def get_google_mobility_data(update=True, plot=False, filename_plot=None):
     update : boolean (default True)
         True if you want to update the data,
         False if you want to read only previously saved data
+    provincial : boolean (default False)
+        True to return the google mobility data per province (10 provinces + Brussels)
     plot : boolean (default False)
         If True, return a preformatted plot of the data
     filename_viz: string
@@ -103,15 +105,20 @@ def get_google_mobility_data(update=True, plot=False, filename_plot=None):
     Returns
     -----------
     data : pandas.DataFrame
-        DataFrame with the google mobility data on daily basis. The following columns
-        are returned:
+        DataFrame with the google mobility data on daily basis. The following columns are returned:
 
         - retail_recreation : Mobility trends for places such as restaurants, cafés, shopping centres, theme parks, museums, libraries and cinemas.
         - grocery : Mobility trends for places such as grocery shops, food warehouses, farmers markets, specialty food shops and pharmacies.
         - parks: Mobility trends for places such as local parks, national parks, public beaches, marinas, dog parks, plazas and public gardens.
         - transport: Mobility trends for places that are public transport hubs, such as underground, bus and train stations.
         - work: Mobility trends for places of work.
         - residential: Mobility trends for places of residence.
+    
+        If provincial data is requested the resulting dataframe has a pandas multiindex containing two levels: 1) date and 2) region.
+        To access multi-indexed data, use the 'loc' method: df.loc[(index_val_1, index_val_2), column_name].
+        F.i. df[('2020-03-15', 'Brussels'), :] returns the mobility reductions on March 15th, 2020 in Brussels.
+        To access the entries corresponding to an entire index level (f.i. all dates), use the slice method.
+        F.i. df[(slice(None), 'Brussels'),:] returns the mobility reductions in Brussels on all possible dates
 
     Notes
     ----------
@@ -137,6 +144,7 @@ def get_google_mobility_data(update=True, plot=False, filename_plot=None):
     abs_dir = os.path.dirname(__file__)
     dtypes = {'sub_region_1': str, 'sub_region_2': str}
 
+    # Update data if necessary
     if update:
         # download raw data
         df = pd.read_csv(url, parse_dates=['date'], dtype=dtypes)
@@ -152,36 +160,58 @@ def get_google_mobility_data(update=True, plot=False, filename_plot=None):
             '../../../data/raw/mobility/google/google_community_mobility_data_BE.csv'),
             parse_dates=['date'], dtype=dtypes)
 
-    # Extract values
-    data=df[df['sub_region_1'].isnull().values]
-
-    # Assign data to output variables
+    # Map column names
     variable_mapping = {
-        'retail_and_recreation_percent_change_from_baseline': 'retail_recreation',
-        'grocery_and_pharmacy_percent_change_from_baseline': 'grocery',
-        'parks_percent_change_from_baseline': 'parks',
-        'transit_stations_percent_change_from_baseline': 'transport',
-        'workplaces_percent_change_from_baseline': 'work',
-        'residential_percent_change_from_baseline': 'residential'
+    'retail_and_recreation_percent_change_from_baseline': 'retail_recreation',
+    'grocery_and_pharmacy_percent_change_from_baseline': 'grocery',
+    'parks_percent_change_from_baseline': 'parks',
+    'transit_stations_percent_change_from_baseline': 'transport',
+    'workplaces_percent_change_from_baseline': 'work',
+    'residential_percent_change_from_baseline': 'residential'
     }
-    data = data.rename(columns=variable_mapping)
-    data = data.set_index("date")
-    data.index.freq = 'D'
-    data = data[list(variable_mapping.values())]
+    df = df.rename(columns=variable_mapping)
+
+    if provincial == True:
+        # Extract region names and append Brussels
+        regions = list(df['sub_region_2'].dropna().unique())
+        regions.insert(0,'Brussels')
+        # Build multiindex dataframe
+        iterables = [df['date'].unique(), regions]
+        index = pd.MultiIndex.from_product(iterables, names=["date", "region"])
+        new_df = pd.DataFrame(index=index, columns=list(variable_mapping.values()))
+        # Loop over regions
+        for region in regions:
+            if region == 'Brussels':
+                new_df.loc[(slice(None),region),:] = df.loc[(df['sub_region_1'] == 'Brussels')][list(variable_mapping.values())].values
+            else:
+                new_df.loc[(slice(None),region),:] = df[df['sub_region_2']==region][list(variable_mapping.values())].values
+        df = new_df
+    else:
+
+        # Extract national values
+        df=df[df['sub_region_1'].isnull().values]
+        df = df.set_index("date")
+        df.index.freq = 'D'
+        df = df[list(variable_mapping.values())]
 
     if filename_plot and not plot:
         print("Filename plot has no effect, plot is not activated. Set `plot=True` to create plot.")
 
     if plot:
-        fig, ax = google_mobility(data)
+        if provincial:
+            print("\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+            print("Plotting of provincial-level google community mobility data is not implemented (yet).")
+            print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n")
+
+        fig, ax = google_mobility(df)
 
         if filename_plot:
             plt.savefig(filename_plot, dpi=600, bbox_inches='tight',
                         orientation='portrait', papertype='a4')
         else:
             plt.show()
 
-    return data
+    return df
 
 
 

src/covid19model/models/models.py

@@ -1020,7 +1020,7 @@ class COVID19_SEIRD_spatial_vacc(BaseModel):
     # En verder moet je aan de start van je code Nc = real_Nc plaatsen
 
     state_names = ['S', 'E', 'I', 'A', 'M', 'C', 'C_icurec', 'ICU', 'R', 'D', 'H_in', 'H_out', 'H_tot', 'R_C', 'R_ICU', 'S_v', 'E_v', 'I_v', 'A_v', 'M_v', 'C_v', 'C_icurec_v', 'ICU_v', 'R_v']
-    parameter_names = ['beta_R', 'beta_U', 'beta_M', 'alpha', 'K_inf1', 'K_inf2', 'K_hosp', 'sigma', 'omega', 'zeta', 'da', 'dm', 'dc_R', 'dc_D', 'dICU_R', 'dICU_D', 'dICUrec', 'dhospital', 'e_i', 'e_s', 'e_h', 'e_a', 'd_vacc', 'xi', 'season_factor']
+    parameter_names = ['beta_R', 'beta_U', 'beta_M', 'alpha', 'K_inf1', 'K_inf2', 'K_hosp', 'sigma', 'omega', 'zeta', 'da', 'dm', 'dc_R', 'dc_D', 'dICU_R', 'dICU_D', 'dICUrec', 'dhospital', 'e_i', 'e_s', 'e_h', 'e_a', 'd_vacc', 'xi']
     parameters_stratified_names = [['area', 'sg', 'p'], ['s','a','h', 'c', 'm_C','m_ICU', 'N_vacc']]
     stratification = ['place','Nc'] # mobility and social interaction: name of the dimension (better names: ['nis', 'age'])
     coordinates = ['place'] # 'place' is interpreted as a list of NIS-codes appropriate to the geography
@@ -1030,7 +1030,7 @@ class COVID19_SEIRD_spatial_vacc(BaseModel):
     @staticmethod
 
     def integrate(t, S, E, I, A, M, C, C_icurec, ICU, R, D, H_in, H_out, H_tot, R_C, R_ICU, S_v, E_v, I_v, A_v, M_v, C_v, C_icurec_v, ICU_v, R_v, # time + SEIRD classes
-                  beta_R, beta_U, beta_M, alpha, K_inf1, K_inf2, K_hosp, sigma, omega, zeta, da, dm, dc_R, dc_D, dICU_R, dICU_D, dICUrec, dhospital, e_i, e_s, e_h, e_a, d_vacc, xi, season_factor, # SEIRD parameters
+                  beta_R, beta_U, beta_M, alpha, K_inf1, K_inf2, K_hosp, sigma, omega, zeta, da, dm, dc_R, dc_D, dICU_R, dICU_D, dICUrec, dhospital, e_i, e_s, e_h, e_a, d_vacc, xi, # SEIRD parameters
                   area, sg, p,  # spatially stratified parameters. Might delete sg later.
                   s, a, h, c, m_C, m_ICU, N_vacc, # age-stratified parameters
                   place, Nc): # stratified parameters that determine stratification dimensions
@@ -1126,7 +1126,7 @@ def integrate(t, S, E, I, A, M, C, C_icurec, ICU, R, D, H_in, H_out, H_tot, R_C,
 
         # Define spatially stratified infectivity beta with three degrees of freedom beta_R, beta_U, beta_M, based on stratification
         # Default values for RU_threshold and UM_threshold are taken. beta[patch]
-        beta = season_factor*stratify_beta(beta_R, beta_U, beta_M, agg, area, T.sum(axis=1))
+        beta = stratify_beta(beta_R, beta_U, beta_M, agg, area, T.sum(axis=1))
 
         # Define the number of contacts multiplier per patch and age, multip[patch,age]
         # Note how part of the vaccinated people still contribute to infection pressure, but ...

src/covid19model/visualization/data.py

@@ -4,7 +4,7 @@
 import matplotlib.dates as mdates
 
 def google_mobility(data):
-    """Create plot of google mobility data
+    """Create plot of national-level google mobility data
 
     Parameters
     ----------