In hrbrmstr/cdcfluview: Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal

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:mask: cdcfluview

Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal

Description

The U.S. Centers for Disease Control (CDC) maintains a portal https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html for accessing state, regional and national influenza statistics as well as Mortality Surveillance Data. The Flash interface makes it difficult and time-consuming to select and retrieve influenza data. This package provides functions to access the data provided by the portal's underlying API.

What's Inside The Tin

The following functions are implemented:

• age_group_distribution: Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories
• cdc_basemap: Retrieve CDC U.S. base maps
• geographic_spread: State and Territorial Epidemiologists Reports of Geographic Spread of Influenza
• get_weekly_flu_report: Retrieves (high-level) weekly (XML) influenza surveillance report from the CDC
• hospitalizations: Laboratory-Confirmed Influenza Hospitalizations
• ilinet: Retrieve ILINet Surveillance Data
• ili_weekly_activity_indicators: Retrieve weekly state-level ILI indicators per-state for a given season
• pi_mortality: Pneumonia and Influenza Mortality Surveillance
• state_data_providers: Retrieve metadata about U.S. State CDC Provider Data
• surveillance_areas: Retrieve a list of valid sub-regions for each surveillance area.
• who_nrevss: Retrieve WHO/NREVSS Surveillance Data

MMWR ID Utilities:

• mmwrid_map: MMWR ID to Calendar Mappings
• mmwr_week: Convert a Date to an MMWR day+week+year
• mmwr_weekday: Convert a Date to an MMWR weekday
• mmwr_week_to_date: Convert an MMWR year+week or year+week+day to a Date object

Deprecated functions:

• get_flu_data: Retrieves state, regional or national influenza statistics from the CDC (deprecated)
• get_hosp_data: Retrieves influenza hospitalization statistics from the CDC (deprecated)
• get_state_data: Retrieves state/territory-level influenza statistics from the CDC (deprecated)

The following data sets are included:

• hhs_regions: HHS Region Table (a data frame with 59 rows and 4 variables)
• census_regions: Census Region Table (a data frame with 51 rows and 2 variables)
• mmwrid_map: MMWR ID to Calendar Mappings (it is exported & available, no need to use data())

Installation

# CRAN
install.packages("cdcfluview")

# main branch
remotes::install_git("https://git.rud.is/hrbrmstr/cdcfluview.git")
remotes::install_git("https://sr.ht/~hrbrmstr/cdcfluview")
remotes::install_git("https://gitlab.com/hrbrmstr/cdcfluview")
remotes::install_github("hrbrmstr/cdcfluview")

Usage

library(cdcfluview)
library(hrbrthemes)
library(tidyverse)

# current version
packageVersion("cdcfluview")

Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories

glimpse(age_group_distribution(years=2015))

Retrieve CDC U.S. Coverage Map

plot(cdc_basemap("national"))
plot(cdc_basemap("hhs"))
plot(cdc_basemap("census"))
plot(cdc_basemap("states"))
plot(cdc_basemap("spread"))
plot(cdc_basemap("surv"))

State and Territorial Epidemiologists Reports of Geographic Spread of Influenza

glimpse(geographic_spread())

Laboratory-Confirmed Influenza Hospitalizations

surveillance_areas()

glimpse(fs_nat <- hospitalizations("flusurv"))

ggplot(fs_nat, aes(wk_end, rate)) + 
  geom_line(aes(color=age_label, group=age_label)) +
  facet_wrap(~sea_description, scales="free_x") +
  scale_color_viridis_d(name=NULL) +
  labs(x=NULL, y="Rates per 100,000 population",
       title="FluSurv-NET :: Entire Network :: All Seasons :: Cumulative Rate") +
  theme_ipsum_rc()

glimpse(hospitalizations("eip", years=2015))

glimpse(hospitalizations("eip", "Colorado", years=2015))

glimpse(hospitalizations("ihsp", years=2015))

glimpse(hospitalizations("ihsp", "Oklahoma", years=2010))

Retrieve ILINet Surveillance Data

walk(c("national", "hhs", "census", "state"), ~{

  ili_df <- ilinet(region = .x)

  print(glimpse(ili_df))

  ggplot(ili_df, aes(week_start, unweighted_ili, group=region, color=region)) +
    geom_line() +
    viridis::scale_color_viridis(discrete=TRUE) +
    labs(x=NULL, y="Unweighted ILI", title=ili_df$region_type[1]) +
    theme_ipsum_rc(grid="XY") +
    theme(legend.position = "none") -> gg

  print(gg)

})

Retrieve weekly state-level ILI indicators per-state for a given season

ili_weekly_activity_indicators(2017)

xdf <- map_df(2008:2017, ili_weekly_activity_indicators)

count(xdf, weekend, activity_level_label) %>% 
  complete(weekend, activity_level_label) %>% 
  ggplot(aes(weekend, activity_level_label, fill=n)) + 
  geom_tile(color="#c2c2c2", size=0.1) +
  scale_x_date(expand=c(0,0)) +
  viridis::scale_fill_viridis(name="# States", na.value="White") +
  labs(x=NULL, y=NULL, title="Weekly ILI Indicators (all states)") +
  coord_fixed(100/1) +
  theme_ipsum_rc(grid="") +
  theme(legend.position="bottom")

Pneumonia and Influenza Mortality Surveillance

(nat_pi <- pi_mortality("national"))

select(nat_pi, week_end, percent_pni, baseline, threshold) %>% 
  gather(measure, value, -week_end) %>% 
  ggplot(aes(week_end, value)) + 
  geom_line(aes(group=measure, color=measure)) + 
  scale_y_percent() +
  scale_color_ipsum(name = NULL, labels=c("Baseline", "Percent P&I", "Threshold")) +
  labs(x=NULL, y="% of all deaths due to P&I",
       title="Percentage of all deaths due to pneumonia and influenza, National Summary") +
  theme_ipsum_rc(grid="XY") +
  theme(legend.position="bottom")

(st_pi <- pi_mortality("state", years=2015))

(reg_pi <- pi_mortality("region", years=2015))

Retrieve metadata about U.S. State CDC Provider Data

state_data_providers()

Retrieve WHO/NREVSS Surveillance Data

glimpse(xdat <- who_nrevss("national"))

mutate(xdat$combined_prior_to_2015_16, 
       percent_positive = percent_positive / 100) %>% 
  ggplot(aes(wk_date, percent_positive)) +
  geom_line() +
  scale_y_percent(name="% Positive") +
  labs(x=NULL, title="WHO/NREVSS Surveillance Data (National)") +
  theme_ipsum_rc(grid="XY")

who_nrevss("hhs", years=2016)

who_nrevss("census", years=2016)

who_nrevss("state", years=2016)

cdcfluview Metrics

cloc::cloc_pkg_md()

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

hrbrmstr/cdcfluview documentation built on Nov. 25, 2022, 7:55 p.m.