In hrbrmstr/cdccovidview: Weekly Surveillance Summary of U.S. COVID-19 Activity

hrbrpkghelpr::global_opts()

hrbrpkghelpr::stinking_badges()

hrbrpkghelpr::yank_title_and_description()

What's Inside The Tin

The following functions are implemented:

hrbrpkghelpr::describe_ingredients()

Installation

hrbrpkghelpr::install_block()

Usage

library(cdccovidview)

# current version
packageVersion("cdccovidview")

library(cdccovidview)
library(hrbrthemes)
library(tidyverse)

hosp <- laboratory_confirmed_hospitalizations()

hosp

c(
  "0-4 yr", "5-17 yr", "18-49 yr", "50-64 yr", "65+ yr", "65-74 yr", "75-84 yr", "85+"
) -> age_f

mutate(hosp, start = mmwr_week_to_date(mmwr_year, mmwr_week)) %>% 
  filter(!is.na(weekly_rate)) %>% 
  filter(catchment == "Entire Network") %>% 
  select(start, network, age_category, weekly_rate) %>%  
  filter(age_category != "Overall") %>% 
  mutate(age_category = factor(age_category, levels = age_f)) %>% 
  ggplot() +
  geom_line(
    aes(start, weekly_rate)
  ) +
  scale_x_date(
    date_breaks = "2 weeks", date_labels = "%b\n%d"
  ) +
  facet_grid(network~age_category) +
  labs(
    x = NULL, y = "Rates per 100,000 pop",
    title = "COVID-NET Weekly Rates by Network and Age Group",
    caption = sprintf("Source: COVID-NET: COVID-19-Associated Hospitalization Surveillance Network, Centers for Disease Control and Prevention.\n<https://gis.cdc.gov/grasp/COVIDNet/COVID19_3.html>; Accessed on %s", Sys.Date())
  ) +
  theme_ipsum_es(grid="XY")

Clinical Labs

head(clinical_labs())

Public Health Labs

head(public_health_labs_national())

head(public_health_labs_regional())

Emergency Department Visits

head(nssp_er_visits_national())

head(nssp_er_visits_regional())

Mortality

head(mortality_surveillance_data())

pd <- provisional_death_counts()

head(pd$by_week)

head(pd$by_age)

head(pd$by_state)

head(pd$by_sex)

cdccovidview 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/cdccovidview documentation built on April 23, 2020, 11:40 a.m.