hhs_hosp— title: “Hospitalization Vetting, age groups” output: html_document author: “Jacob Fenton” fig_width: 6 fig_height: 4 —
Data Source
The raw HHS file “provides state-aggregated data for hospital utilization in a timeseries format dating back to January 1, 2020. These are derived from reports with facility-level granularity across three main sources: (1) HHS TeleTracking, (2) reporting provided directly to HHS Protect by state/territorial health departments on behalf of their healthcare facilities” (and a third collection method used prior to July 2020). The file can be downloaded here.
Introduction
How has the vaccination rollout changed the age distribution of COVID patients? Most states began by vaccinating medical workers and older adults, who are most likely to suffer a severe case of COVID or die.
# Libraries
library(ggplot2)
library(tidyverse)
# setwd("/Users/jacob/github-whitelabel/covid-kids/juvenile_covid_analysis/hhs/")
#library(rmarkdown)
#file = "0508_Timeseries.csv"
file = "0515_Timeseries.csv"
hospdf <- read.csv(file, header=TRUE, sep=",")
hospdf$dateob = as.Date(hospdf$date)
# Sum total adult COVID: confirmed + suspected
hospdf$total_adult = hospdf$previous_day_admission_adult_covid_confirmed + hospdf$previous_day_admission_adult_covid_suspected
# Sum total pediatric COVID: confirmed + suspected
hospdf$total_ped = hospdf$previous_day_admission_pediatric_covid_confirmed + hospdf$previous_day_admission_pediatric_covid_suspected
hospdf$total_admissions <- hospdf$total_ped + hospdf$total_adult
hospdf$total_unk <- hospdf$previous_day_admission_adult_covid_suspected_unknown + hospdf$previous_day_admission_adult_covid_suspected_unknown
hospdf$total_80 <- hospdf$previous_day_admission_adult_covid_confirmed_80. + hospdf$previous_day_admission_adult_covid_suspected_80.
hospdf$total_70 <- hospdf$previous_day_admission_adult_covid_confirmed_70.79 + hospdf$previous_day_admission_adult_covid_suspected_70.79
hospdf$total_60 <- hospdf$previous_day_admission_adult_covid_confirmed_60.69 + hospdf$previous_day_admission_adult_covid_suspected_60.69
hospdf$total_50 <- hospdf$previous_day_admission_adult_covid_confirmed_50.59 + hospdf$previous_day_admission_adult_covid_suspected_50.59
hospdf$total_40 <- hospdf$previous_day_admission_adult_covid_confirmed_40.49 + hospdf$previous_day_admission_adult_covid_suspected_40.49
hospdf$total_30 <- hospdf$previous_day_admission_adult_covid_confirmed_30.39 + hospdf$previous_day_admission_adult_covid_suspected_30.39
hospdf$total_20 <- hospdf$previous_day_admission_adult_covid_confirmed_20.29 + hospdf$previous_day_admission_adult_covid_suspected_20.29
hospdf$total_1819 <- hospdf$previous_day_admission_adult_covid_confirmed_18.19 + hospdf$previous_day_admission_adult_covid_suspected_18.19
hospdf$total_adult_by_sum <- hospdf$total_80 + hospdf$total_70 + hospdf$total_60 + hospdf$total_50 + hospdf$total_40 + hospdf$total_30 + hospdf$total_20 + hospdf$total_1819 + + hospdf$total_unk80+ hospital admissions
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_80._coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_80._coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_80._coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - diffrence suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_80._coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_80.)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_80.)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
70-79
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_70.79_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_70.79_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_70.79_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - diffrence suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_70.79_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_70.79)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_70.79)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
60-69
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_60.69_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_60.69_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_60.69_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_60.69_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_60.69)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_60.69)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
50-59
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_50.59_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_50.59_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_50.59_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_50.59_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_50.59)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_50.59)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
40-49
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_40.49_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_40.49_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_40.49_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_40.49_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_40.49)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_40.49)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
30-39
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_30.39_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_30.39_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_30.39_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_30.39_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_30.39)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_30.39)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
20-29
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_20.29_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_20.29_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_20.29_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_20.29_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_20.29)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_20.29)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
18-19
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_18.19_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_18.19_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_18.19_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_18.19_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_18.19)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_18.19)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Age Unknown
Coverage - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_unknown_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference confirmed
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_confirmed_unknown_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - difference suspected
hospdf %>% ggplot(aes(x=dateob,y=staffed_adult_icu_bed_occupancy_coverage-previous_day_admission_adult_covid_suspected_unknown_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Coverage - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_unknown_coverage)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - suspected
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_suspected_unknown)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).
Raw counts - confirmed
hospdf %>% ggplot(aes(x=dateob,y=previous_day_admission_adult_covid_confirmed_unknown)) + geom_line() + facet_wrap( ~ state , scales = "free") + xlab("") + xlim(as.Date('2021-01-01'), as.Date('2021-05-19'))## Warning: Removed 306 row(s) containing missing values (geom_path).