Skip to content

Latest commit

 

History

History
109 lines (91 loc) · 6.67 KB

graph_info.md

File metadata and controls

109 lines (91 loc) · 6.67 KB
Raw

Constructing the Graph

The Bucky model does not do any data manipulation, smoothing, or correcting to the data it receives from the graph (by design). If data needs to be manipulated or corrected, it should be done before it is placed on the graph.

The graph is created using admin2-level data. If data can not be found at the admin2-level, admin2-level information can be extrapolated using admin2 population and national or state level data (this is expanded upon in the Population Data section).

The following data sources are used to create the graph:

  • admin2-level shapefile
  • admin2-level population data stratified by age
  • Historical admin2-level case and death data
  • Contact matrix information for the country
  • Mobility data (or a proxy)

All data is placed into a single dataframe, joined by the admin2-level key (e.g., FIPS for United States), with the exception of mobility data (which is used to create edges, not nodes).

NOTE: This graph should be able to be constructed on the province or state level, but may require model changes. If this is the case, talk to Matt Kinsey.

Graph-Level Attributes

Administrative information is placed on the top graph-level. For example:

'adm1_key' : 'adm1',
'adm2_key' : 'adm2',
'adm1_to_str' : {1 : 'Alabama'}, ...,
'adm0_name': 'US',
'start_date' : '2020-09-25'

NOTE: adm1_to_str is a dict with key-value pairs indicating the adm1 names for each adm1 value appearing in the graph.

Contact matrices are also on this level under the key 'contact_mats'.

Sample Node

The following is an example node on the graph for the United States. The rest of the documentation will describe what data is necessary to construct this node.

(0,
 {'adm1': 1,
  'Confirmed': 1757.0,
  'Deaths': 25.0,
  'adm2_name': 'Autauga County',
  'N_age_init': array([3364., 3423., 3882., 3755., 3173., 3705., 3461., 3628., 3616.,
         3966., 3811., 3927., 3237., 2589., 2311., 3753.]),
  'Population': 55601.0,
  'IFR': array([6.75414158e-06, 1.24643105e-05, 2.26550214e-05, 4.05345945e-05,
         7.68277004e-05, 1.38382882e-04, 2.54273120e-04, 4.63844627e-04,
         8.51898589e-04, 1.55448599e-03, 2.87077658e-03, 5.20528393e-03,
         9.47735996e-03, 1.73603179e-02, 3.14646839e-02, 9.38331984e-02]),
  'case_hist': array([1207.64227528, 1234.9656055 , 1243.85366911, 1244.13444753,
         1255.27521116, 1268.95333353, 1270.38458817, 1288.05778954,
         1295.55174933, 1297.29129258, 1312.35308192, 1321.2898892 ,
         1323.10534634, 1354.97350342, 1358.88036484, 1362.43488575,
         1377.67551466, 1392.4338964 , 1406.70605635, 1446.3924143 ,
         1450.47616771, 1462.67851762, 1458.98710032, 1470.52271903,
         1481.12998684, 1501.75698721, 1508.06090303, 1513.9178672 ,
         1518.26245703, 1532.99858052, 1553.97101414, 1564.24619451,
         1579.10859377, 1590.56170754, 1597.77332362, 1616.97996262,
         1619.        , 1624.        , 1664.        , 1673.        ,
         1690.        , 1691.        , 1714.        , 1715.        ,
         1738.        , 1757.        ]),
  'death_hist': array([22.76748794, 22.80142062, 22.81307638, 22.79580414, 22.79344408,
         22.79578013, 22.81581338, 22.80532061, 22.7902682 , 22.79603286,
         22.79689139, 22.79601336, 22.79344923, 22.85912123, 22.90405033,
         22.91397178, 22.97898824, 23.02565004, 23.05597481, 23.09719551,
         23.13913548, 24.12323294, 24.17184064, 24.2852927 , 24.38579416,
         24.41284998, 24.41330133, 24.41175889, 24.40910247, 24.41419481,
         24.43286524, 24.47610337, 24.52580854, 24.5245916 , 24.53522989,
         24.54591406, 24.        , 24.        , 24.        , 24.        ,
         24.        , 24.        , 25.        , 25.        , 25.        ,
         25.        ]),
  'adm2': 1001.0})

Population Data

Population data should be at a admin2 level and stratified in 16 5-year age bins (if using Prem et al contact matrices):

  • 0-4 years
  • 5-9 years
  • 10-14 years
  • 15-19 years
  • 20-24 years
  • 25-29 years
  • 30-34 years
  • 35-39 years
  • 40-44 years
  • 45-49 years
  • 50-54 years
  • 55-59 years
  • 60-64 years
  • 65-69 years
  • 70-74 years
  • 75+ years

If population data for an admin2 area is known (i.e. number of total people per admin2), but it is not age-stratified, this data can be extrapolated assuming age-stratified population data exists at some level. For example, assume a country has age-stratified data provided at the national-level. To get the admin2-level age data, the data is separated into the 16 bins (as a 1-dimensional array of length 16). These bins are then normalized by dividing by the sum. Then, the fraction of people living in the admin2 is calculated by dividing admin2 population by the total national population. For each district, this fraction is multiplied by the age vector to produce a admin2-level age vector. This vector is placed on the node under the key N_age_init.

The total population for an admin2 is placed on the node under the key Population.

Case Data

Case data should be at the admin2-level and include cumulative data as of the start date of the simulation and historical data for the 45-day period preceding the start date:

  • case_hist: Cumulative historical case data
  • death_hist : Cumulative historical death data

Historical data is structured as numerical vectors on the node with the keys case_hist, death_hist. Historical data for every node must have data points for the 45 days preceding the simulation. If there are known errors in the historical data, they must be corrected before being placed on the graph.

Contact Matrices

Currently, contact matrix data is downloaded from here, which has contact matrices for 152 countries. If a country does not appear in this dataset, a country culturally close can be substituted (for example, Pakistan's contact rates were used for Afghanistan), or another dataset can be used. If another dataset is used, the contact matrix must be formatted such that it has the same shape as the number of age demographic bins (i.e. if there are 16 bins, the matrix must be of size 16 x 16).

Mobility Data

Mobility data is used to construct the edges of the graph. Mobility data, or a proxy for it, is used to describe the contact rates between counties.

The baseline mobility data shows up as an edge attributed called weight. R0_frac is a factor that is multiplied with the baseline mobility value to model the effect of NPIs, etc., on mobility. For example, given baseline mobility data from February 2020, R0_frac would be computed by dividing recent mobility data values with the February 2020 baseline. R0_frac exists to provide a knob to tune during the simulation to model NPIs.