latest_date_outcomes.R

################################################################
# This script performs data cleaning and preparation
################################################################


# For running locally only #
# setwd("C:/Users/aschaffer/OneDrive - Nexus365/Documents/GitHub/vax-fourth-dose-RD")
# getwd()

# Import libraries #
library('tidyverse')
library('lubridate')
library('arrow')
library('here')
library('reshape2')
library('dplyr')
library('fs')
library('ggplot2')
library('RColorBrewer')
library('lubridate')
library('purrr')


dir_create(here::here("output", "cohort"), showWarnings = FALSE, recurse = TRUE)
dir_create(here::here("output", "descriptive"), showWarnings = FALSE, recurse = TRUE)


anyadmitted <- read.csv(here::here("output", "cohort", "outcomes_nov_anyadmitted.csv")) %>%
  mutate(date = as.Date(date, format = "%Y-%m-%d")) %>%
  subset(!is.na(date) & date >= as.Date("2022-11-01") & date < as.Date("2023-03-01"))

anydeath <- read.csv(here::here("output", "cohort", "outcomes_nov_anydeath.csv")) %>%
  mutate(date = as.Date(date, format = "%Y-%m-%d")) %>%
  subset(!is.na(date) & date >= as.Date("2022-11-01") & date < as.Date("2023-03-01"))

anyadmit_bydate <- anyadmitted %>%
  group_by(date) %>%
  summarise(n = n())

anydeath_bydate <- anydeath %>%
  group_by(date) %>%
  summarise(n = n())


# Check latest admission date
ggplot(anyadmit_bydate) +
  geom_bar(aes(x = date, y = n), stat = "identity") +
  theme_bw()

ggsave(here::here("output", "descriptive", "over_time_admit.png"),
       dpi = 300, units = "in", width = 3, height = 3)


# Check latest admission date
ggplot(anydeath_bydate) +
  geom_bar(aes(x = date, y = n), stat = "identity") +
  theme_bw()

ggsave(here::here("output", "descriptive", "over_time_death.png"),
       dpi = 300, units = "in", width = 3, height = 3)