Merge pull request #13 from epiforecasts/11-first-data-fig

Issue 11: add first draft of first fig

Author: kaitejohnson

DESCRIPTION

@@ -29,6 +29,7 @@ Imports:
   roxyglobals,
   data.table,
   rlang,
+  cowplot,
   lubridate
 Suggests:
     bookdown,

NAMESPACE

@@ -31,6 +31,8 @@ importFrom(ggplot2,vars)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
 importFrom(lubridate,days)
+importFrom(lubridate,epiweek)
+importFrom(lubridate,epiyear)
 importFrom(lubridate,ymd)
 importFrom(rlang,arg_match)
 importFrom(rlang,sym)

R/daily_to_weekly.R

@@ -0,0 +1,40 @@
+#' Convert sequence data from daily to weekly
+#'
+#' @param daily_data Data.frame of sequence counts by location and clade
+#'
+#' @returns Data aggregated by epiweek.
+#' @importFrom lubridate epiweek epiyear
+daily_to_weekly <- function(daily_data) {
+  date_spine <- tibble(
+    date = seq(
+      from = min(daily_data$date),
+      to = max(daily_data$date), by = "day"
+    )
+  ) |>
+    mutate(
+      epi_week = epiweek(date),
+      epi_year = epiyear(date),
+      wday = wday(date, label = TRUE)
+    ) |>
+    filter(wday == "Sat")
+
+  metadata <- daily_data |>
+    select(location, location_name, location_code, population, type) |>
+    unique()
+  weekly_data <- daily_data |>
+    mutate(
+      epi_week = epiweek(date),
+      epi_year = epiyear(date)
+    ) |>
+    group_by(
+      epi_year, epi_week,
+      location, clades_modeled
+    ) |>
+    summarise(
+      sequences = sum(sequences),
+      .groups = "drop"
+    ) |>
+    left_join(date_spine, by = c("epi_week", "epi_year")) |>
+    left_join(metadata, by = "location")
+  return(weekly_data)
+}