Python import_popdata Examples

Example #1

File: chain_binomial_sim_pop_disease_model_v070815.py Project: ate510/metapopulation_model

### fraction children = alpha (a) = (#ch)/(#ch + #ad)
#### alt option - (find dif fraction for each metro area)

## data ##
# AGE SPLIT #
# POLYMOD contact study (Ref 22 in Apollini 2013)
## Children: (5 - 19) 
## Adults: (20 - 69) 
#popdata
#totalpop_age.csv

# import csv file of pop data
popdata = csv.reader(open('Dropbox/Anne_Bansal_lab/SDI_Data/totalpop_age.csv', 'r'),delimiter = ',')

# import data into dicts
d_pop_for_yr_age, ages, years = func.import_popdata(popdata, 0, 1, 2)

#group ages into children and adults

d_childpop, d_adultpop = func.pop_child_adult(d_pop_for_yr_age, years)

# set value of alpha from U.S. pop data
year = 2010 # decided to use pop from 2010 bc most recent
a = func.pop_child_frac(year, d_childpop, d_adultpop)
#print a # = 0.239 for 2010 with 60-69; was 0.27 without 60-69

metro, ages = func.assign_metro(a)

print metro

#totpop of metros = 10817

Example #2

File: R0_eigenvalue_from_beta_v073015.py Project: ate510/metapopulation_model

    # calc eigenvalues from R matrix
    # should return in descending order (largest will be first)
    evals, matrix_v = np.linalg.eig(R) # matrix_v --> normalized eigenvectors
    
    # largest eigenvalue is R0
    R0 = max(evals)
       
    return R0   
    
###################################################
if __name__ == "__main__":
    
    # READ POPULATION DATA FROM FILE
    popdata = csv.reader(open('Dropbox/Anne_Bansal_lab/SDI_Data/totalpop_age.csv', 'r'),delimiter = ',')
    dict_popdata, ages, years = func.import_popdata(popdata, 0, 1, 2)
    dict_childpop, dict_adultpop = func.pop_child_adult (dict_popdata, years)
    
    # READ GERMAN CONTACT DATA FROM FILE
    filename_germ_contact_data = 'Dropbox/Anne_Bansal_lab/Contact_Data/polymod_germany_contact_matrix_Mossong_2008.csv'
    filename_germ_pop_data = 'Dropbox/Anne_Bansal_lab/UNdata_Export_2008_Germany_Population.csv'

    # DEFINE DISEASE PARAMETERS
    beta = 0.0165
    gamma = 0.2
    
    # CALCULATE ALPHA
    year = 2010
    alpha = func.calc_alpha(year, dict_childpop, dict_adultpop)

    # CALCULATE R MATRIX

Example #3

File: unit_test_no_transmission.py Project: ate510/metapopulation_model

import population_parameters as pop_func
import chain_binomial as bin_func
    
### program ###
###################################################  
# import data #

# READ METRO NETWORK FROM FILE
filename_metropop = 'Dropbox/Anne_Bansal_lab/Python_Scripts/Modeling_Project/air_traffic_data/metedges.txt'
d_metropop, metro_ids = pop_func.import_metropop(filename_metropop, 2, 3)
filename_air_network = 'Dropbox/Anne_Bansal_lab/Python_Scripts/Modeling_Project/air_traffic_data/air_traffic_edgelist.txt'
air_network = bin_func.read_edgelist_anne(filename_air_network)

# READ US population data
us_popdata = csv.reader(open('Dropbox/Anne_Bansal_lab/SDI_Data/totalpop_age.csv', 'r'),delimiter = ',')
dict_popdata, ages, years = pop_func.import_popdata(us_popdata, 0, 1, 2)
dict_childpop, dict_adultpop = pop_func.pop_child_adult (dict_popdata, years)

# READ Germany contact data
#filename_germ_contact_data = 'Dropbox/Anne_Bansal_lab/Contact_Data/polymod_germany_contact_matrix_Mossong_2008.csv'
filename_germ_within_group_contact_data = 'Dropbox/Anne_Bansal_lab/Contact_Data/within_group_polymod_germany_contact_matrix_Mossong_2008.csv'
filename_germ_all_contact_data = 'Dropbox/Anne_Bansal_lab/Contact_Data/all_ages_polymod_germany_contact_matrix_Mossong_2008.csv'

# READ Germany population data
filename_germ_pop_data = 'Dropbox/Anne_Bansal_lab/UNdata_Export_2008_Germany_Population.csv'
   
     
# DEFINE POPULATION PARAMETERS
year = 2010
alpha = pop_func.calc_alpha(year, dict_childpop, dict_adultpop)
d_metro_age_pop = pop_func.calc_metro_age_pop(filename_metropop, alpha)