all_lineage_prevalences

outbreak_data.all_lineage_prevalences(location=None, ndays=180, nday_threshold=10, other_threshold=0.05, other_exclude=None, cumulative=False, **req_args)

Get prevalences of lineages circulating in a location according to clinical sequencing data.

Parameters

  • location -- A string containing a location ID. If not specified, global data is returned.

  • other_threshold -- Minimum prevalence threshold below which lineages will be aggregated under "other".

  • nday_threshold -- Minimum number of days in which a lineage's prevalence must be above other_threshold in order to not be aggregated.

  • ndays -- The number of days before the current date to be used as a window to accumulate lineages under "other".

  • other_exclude -- List of lineages that are not to be included under "other".

  • cumulative -- If true return the cumulative prevalence; otherwise return daily data.

Returns

A pandas dataframe containing lineage prevalences.

Parameter example

{ 'location': 'USA_US-HI' }

Parameter example

{ 'cumulative': True }

Example usage:

#Find the prevalence all lineages in Argentina that begin with 'xbb.1'
df = od.prevalence_by_location("ARG", startswith = 'xbb.1')
print(df)
Output
             date  total_count  lineage_count  lineage  prevalence  \
 1454  2022-10-12            3              1    xbb.1    0.333333
 1455  2022-10-13            0              0    xbb.1    0.000000
 1456  2022-10-14            0              0    xbb.1    0.000000
 1457  2022-10-15            0              0    xbb.1    0.000000
 1458  2022-10-16            0              0    xbb.1    0.000000
 ...          ...          ...            ...      ...         ...
 1673  2023-03-17            0              0  xbb.1.5    0.000000
 1674  2023-03-18            0              0  xbb.1.5    0.000000
 1675  2023-03-19            0              0  xbb.1.5    0.000000
 1676  2023-03-20            0              0  xbb.1.5    0.000000
 1677  2023-03-21            1              1  xbb.1.5    1.000000

       prevalence_rolling
 1454            0.350000
 1455            0.179487
 1456            0.109375
 1457            0.065421
 1458            0.058577
 ...                  ...
 1673            1.000000
 1674            1.000000
 1675            1.000000
 1676            1.000000
 1677            1.000000

[224 rows x 6 columns]