Retrieves the daily prevalence of a PANGO lineage(s) by location
getPrevalence(
pangolin_lineage = NULL,
location = NULL,
mutations = NULL,
cumulative = FALSE,
logInfo = TRUE
)(optional) PANGO lineage name or vector of PANGO lineage names. Either `pangolin_lineage` or `mutations` needs to be specified. A list of lineages will return a long dataframe with `lineage` as a variable; if you want to calculate the prevalence of lineage1 or lineage2 together, enter the lineages separated by " OR ". For instance, to calculate the prevalence of Delta, you'll need to supply `"B.1.617.2 OR AY.1 OR AY.2 OR ..."` **Be sure to include the space around "OR" and it must be capitalized.**
(optional) a location name
(optional) a `vector` of mutation(s). Either `pangolin_lineage` or `mutations` needs to be specified. Mutations should be specified in the format `gene:mutation`, like "S:E484K"
(optional) `Boolean` (T/F), T returns cumulative prevalence since first day of detection
(optional) `Boolean` (T/F), T logs helper messages during API calls.
dataframe
# lineage: P.1 in Brazil
p1_brazil = getPrevalence(pangolin_lineage = "P.1", location = "Brazil")
#> Retrieving data...
# AY.4, AY.34, and B.1.617.2 in Brazil (AY.4, AY.34, and B.1.617.2 separately)
delta_and_brazil = getPrevalence(pangolin_lineage = c("AY.4", "AY.34", "B.1.617.2"), location = "Brazil")
#> Retrieving data...
#> Retrieving data...
#> Retrieving data...
delta_and_brazil[delta_and_brazil$date == "2021-09-01",]
#> date total_count lineage_count total_count_rolling
#> 48 2021-09-01 591 0 442.5714
#> 454 2021-09-01 591 0 442.5714
#> 965 2021-09-01 591 2 442.5714
#> lineage_count_rolling proportion proportion_ci_lower proportion_ci_upper
#> 48 0.0000000 0.000000000 1.107804e-06 0.005651072
#> 454 0.0000000 0.000000000 1.107804e-06 0.005651072
#> 965 0.8571429 0.001936733 2.436692e-04 0.010501680
#> lineage location
#> 48 AY.4 Brazil
#> 454 AY.34 Brazil
#> 965 B.1.617.2 Brazil
# AY.4 OR B.1.617.2 in Brazil (AY.4, AY.34 and B.1.617.2 combined)
delta_or_brazil = getPrevalence(pangolin_lineage = "AY.4 OR AY.34 OR B.1.617.2", location = "Brazil")
#> Retrieving data...
delta_or_brazil[delta_and_brazil$date == "2021-09-01",]
#> date total_count lineage_count total_count_rolling
#> 48 2021-06-01 636 0 390.4286
#> 454 2022-07-12 370 0 333.8571
#> NA <NA> NA NA NA
#> lineage_count_rolling proportion proportion_ci_lower proportion_ci_upper
#> 48 0 0 1.258255e-06 0.006416079
#> 454 0 0 1.469062e-06 0.007486989
#> NA NA NA NA NA
#> lineage location
#> 48 AY.4 OR AY.34 OR B.1.617.2 Brazil
#> 454 AY.4 OR AY.34 OR B.1.617.2 Brazil
#> NA <NA> <NA>
# S:E484K mutation prevalence worldwide
se484k = getPrevalence(mutations = c("S:E484K"))
#> Retrieving data...
# B.1.1.7 + S:E484K mutation worldwide
b117_se484k = getPrevalence(pangolin_lineage = "B.1.1.7", mutations = c("S:E484K"))
#> Retrieving data...