prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, lineage_crumbs=False)

outbreak_data.prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, server='api.outbreak.info')

Returns the daily prevalence of a PANGO lineage by location.

Arguments:
pango_lin:

(Required). List of lineages separated by ,

location_id:

(Optional). Default location: USA

mutations:

(Optional). List of mutations separated by AND

cumulative:

(Optional). If true returns the cumulative global prevalence since the first day of detection.

datemin:

(Optional). A string representing the first cutoff date for returned date. Must be in YYYY-MM-DD format and be before ‘datemax’

datemax:

(Optional). A string representing the second cutoff date. Must be in YYY-MM-DD format and be after ‘datemin’

return:

A pandas dataframe.

Example usage:

  1. Get the daily prevalence of lineage ‘BA.2’ in India since first detection:

    df1 = od.daily_prev('ba.2', "IND")
print(df1)
Output
             date  total_count  lineage_count  total_count_rolling  \
 0     2020-08-01           39              1            29.000000
 1     2020-08-02          100              0            41.285714
 2     2020-08-03           38              0            42.000000
 3     2020-08-04           20              0            42.285714
 4     2020-08-05           26              0            36.000000
 ...          ...          ...            ...                  ...
 1017  2023-05-15            2              0             5.857143
 1018  2023-05-16            3              0             5.142857
 1019  2023-05-17            3              0             3.285714
 1020  2023-05-18            2              0             3.142857
 1021  2023-05-20            1              0             2.000000

       lineage_count_rolling  proportion  proportion_ci_lower  \
 0                  0.142857    0.004926             0.000017
 1                  0.142857    0.003460             0.000012
 2                  0.142857    0.003401             0.000012
 3                  0.142857    0.003378             0.000012
 4                  0.142857    0.003968             0.000014
 ...                     ...         ...                  ...
 1017               0.000000    0.000000             0.000078
 1018               0.000000    0.000000             0.000093
 1019               0.000000    0.000000             0.000151
 1020               0.000000    0.000000             0.000151
 1021               0.000000    0.000000             0.000217

       proportion_ci_upper
 0                0.082286
 1                0.059076
 2                0.057719
 3                0.057719
 4                0.066944
 ...                   ...
 1017             0.330389
 1018             0.379377
 1019             0.535583
 1020             0.535583
 1021             0.666822

  1. Get a cumulative summary of information regarding ‘BA.2’ in India:

    df2 = od.daily_prev('ba.2', "IND", cumulative = True)
print(df2)
Output
                        Values
 first_detected     2020-08-01
 global_prevalence    0.109641
 last_detected      2023-04-26
 lineage_count           25561
 total_count            233134