Retrieves up-to-date COVID-19 genomic data from outbreak.info according to user specifications.
getGenomicData(
query_url,
location = NULL,
cumulative = NULL,
pangolin_lineage = NULL,
mutations = NULL,
ndays = NULL,
frequency = NULL,
subadmin = NULL,
other_threshold = NULL,
nday_threshold = NULL,
other_exclude = NULL,
logInfo = TRUE
)dataframe
uk_b117 = getGenomicData(query_url="prevalence-by-location", location="United Kingdom", pangolin_lineage = "B.1.1.7")
#> Retrieving data...
head(uk_b117)
#> date total_count lineage_count total_count_rolling
#> 1 2020-03-20 411 1 276.7143
#> 2 2020-03-21 434 0 315.0000
#> 3 2020-03-22 390 0 347.2857
#> 4 2020-03-23 794 0 433.1429
#> 5 2020-03-24 735 0 496.5714
#> 6 2020-03-25 685 0 542.2857
#> lineage_count_rolling proportion proportion_ci_lower proportion_ci_upper
#> 1 0.1428571 0.0005162623 1.771087e-06 0.009019280
#> 2 0.1428571 0.0004535147 1.557602e-06 0.007936431
#> 3 0.1428571 0.0004113534 1.414065e-06 0.007207711
#> 4 0.1428571 0.0003298153 1.133374e-06 0.005781129
#> 5 0.1428571 0.0002876870 9.874998e-07 0.005038930
#> 6 0.1428571 0.0002634352 9.055496e-07 0.004621730
#> query_key
#> 1 B.1.1.7
#> 2 B.1.1.7
#> 3 B.1.1.7
#> 4 B.1.1.7
#> 5 B.1.1.7
#> 6 B.1.1.7