lineage_by_sub_admin¶
- outbreak_data.lineage_by_sub_admin(pango_lin, mutations=None, location=None, ndays=180, detected=False, **req_args)¶
Get clinical data from the most recent date with more than zero sequences for each sublocation.
- Parameters
pangolin_lineage -- A list or string of lineage names to query for. Results for each lineage are returned on separate rows.
mutations -- A list or string of mutations to query for; only sequences with all of these mutations will match against pangolin_lineage.
location_id -- A string containing a location ID. If not specified, returns global data at the country level.
ndays -- A positive integer number of days back from the current date to calculative cumuative counts within.
detected -- If true return a list of locations where at least one matching sequence has been detected.
- Returns
A pandas dataframe containing sequence count data.
- Parameter example
{ 'pango_lin': ['BA.1', 'BA.2'], 'location': 'USA' }
Example Usage
Get the number of lineages sequenced and recorded in each province in France:
>>> df = od.lineage_by_sub_admin('xbb.1.15', location='FRA')
>>> df
date id total_count \
name query
xbb.1.15 2024-05-13 FRA_FR-None 1
Bretagne xbb.1.15 2024-04-25 FRA_FR-BT 1
Corse xbb.1.15 2024-04-29 FRA_FR-CE 1
Grand Est xbb.1.15 2024-04-15 FRA_FR-AO 2
Normandie xbb.1.15 2024-04-08 FRA_FR-ND 2
Occitanie xbb.1.15 2024-05-06 FRA_FR-LP 3
Pays de la Loire xbb.1.15 2024-04-02 FRA_FR-PL 5
lineage_count cum_total_count cum_lineage_count \
name query
xbb.1.15 0 4504 0
Bretagne xbb.1.15 0 398 0
Corse xbb.1.15 0 51 0
Grand Est xbb.1.15 0 784 0
Normandie xbb.1.15 0 195 0
Occitanie xbb.1.15 0 618 0
Pays de la Loire xbb.1.15 0 229 0
proportion proportion_ci_lower \
name query
xbb.1.15 0.0 1.090158e-07
Bretagne xbb.1.15 0.0 1.232980e-06
Corse xbb.1.15 0.0 9.581002e-06
Grand Est xbb.1.15 0.0 6.261197e-07
Normandie xbb.1.15 0.0 2.514896e-06
Occitanie xbb.1.15 0.0 7.942326e-07
Pays de la Loire xbb.1.15 0.0 2.141914e-06
proportion_ci_upper
name query
xbb.1.15 0.000558
Bretagne xbb.1.15 0.006288
Corse xbb.1.15 0.047830
Grand Est xbb.1.15 0.003198
Normandie xbb.1.15 0.012783
Occitanie xbb.1.15 0.004055
Pays de la Loire xbb.1.15 0.010897