lineage_by_sub_admin(pango_lin, mutations, location, ndays=0, detected)
- outbreak_data.lineage_by_sub_admin(pango_lin, mutations=None, location=None, ndays=0, detected=None, server='api.outbreak.info')
Cumulative prevalence of a PANGO lineage by the immediate admin level of a location
Arguments: :pangolin_lineage: (Required). A list or string. List of lineages separated by , :mutations: (Optional). A string or list of strings. Uses AND logic. :location_id: (Optional). A string. If not specified, returns cumulative prevalence at the country level globally. :ndays: (Optional). An integer. Specify number of days from current date to calculative cumuative counts. If not specified, there is no limit on the window. :detected: (Optional). If true returns only if at least found in location :return: A pandas dataframe.
Example usage:
df = od.lineage_by_sub_admin('xbb.1.15', location='FRA')
print(df)
Output:
date name id total_count lineage_count \
0 2023-06-04 FRA_FR-none 3 0
1 2023-05-31 Bretagne FRA_FR-BT 2 0
2 2023-05-22 Corse FRA_FR-CE 1 0
3 2023-05-30 Grand Est FRA_FR-AO 68 0
4 2023-06-04 Normandie FRA_FR-ND 2 0
5 2023-06-01 Occitanie FRA_FR-LP 2 0
6 2023-05-30 Pays de la Loire FRA_FR-PL 22 0
cum_total_count cum_lineage_count proportion proportion_ci_lower \
0 406320 10 0.000025 1.265376e-05
1 22070 1 0.000045 4.888926e-06
2 2007 0 0.000000 2.446305e-07
3 43954 1 0.000023 2.454796e-06
4 19479 0 0.000000 2.520808e-08
5 57933 0 0.000000 8.475868e-09
6 24556 0 0.000000 1.999632e-08
proportion_ci_upper
0 0.000044
1 0.000212
2 0.001251
3 0.000106
4 0.000129
5 0.000043
6 0.000102