all_lineage_prevalences(location, startswith)

outbreak_data.all_lineage_prevalences(location, ndays=180, nday_threshold=10, other_threshold=0.05, other_exclude=None, cumulative=None, server='api.outbreak.info', auth=None, startswith=None)

Loads prevalence data from a location

Arguments:
location:

A string

other_threshold (Default:

  1. Minimum prevalence threshold below which lineages must be accumulated under “Other”.

nday_threshold (Default:

  1. Minimum number of days in which the prevalence of a lineage must be below other_threshold to be accumulated under “Other”.

ndays (Default:

  1. The number of days before the current date to be used as a window to accumulate lineages under “Other”.

other_exclude:

Comma separated lineages that are NOT to be included under “Other” even if the conditions specified by the three thresholds above are met.

cumulative:

(Default: false) If true return the cumulative prevalence.:startswith: A string; loads data for all lineages beginning with first letter(s) of name

return:

A pandas dataframe

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]