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data_process_outcomes_1.R
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data_process_outcomes_1.R
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################################################################
# 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')
## Create directories
dir_create(here::here("output"), showWarnings = FALSE, recurse = TRUE)
dir_create(here::here("output", "cohort"), showWarnings = FALSE, recurse = TRUE)
dir_create(here::here("output", "index"), showWarnings = FALSE, recurse = TRUE)
dir_create(here::here("output", "descriptive"), showWarnings = FALSE, recurse = TRUE)
## Load functions
source(here::here("analysis", "custom_functions.R"))
####################################################
# Function extracting outcomes in follow-up period
####################################################
out <- function(start_date){
start_date = as.Date(start_date)
end_date = start_date + 42
read_feather(here::here("output", "index", paste0("input_outcomes_1_",start_date,".feather"))) %>%
mutate_at(c(vars(c(contains("_date")))), as.Date, format = "%Y-%m-%d") %>%
# Exclude if died before start date
subset(is.na(any_death_date) | any_death_date >= as.Date(start_date)) %>%
mutate(dob = as.Date(dob, format = "%Y-%m-%d"),
dod = as.Date(dod, format = "%Y-%m-%d"),
# Age in months
age_mos = (dob %--% start_date) %/% months(1),
age_yrs = (dob %--% start_date) %/% years(1),
# Calendar birth month
birth_month = as.factor(month(dob)),
# Flag for having received flu vax before start date
flu_vax = if_else(!is.na(flu_vax_date) & flu_vax_date < as.Date(start_date), 1, 0, 0),
# Flag for bosster before start date
boost = if_else(!is.na(boost_date) & boost_date < as.Date(start_date), 1, 0, 0),
# Create flag for each outcomes
anydeath = if_else(!is.na(any_death_date) & (any_death_date >= start_date) &
(any_death_date <= end_date), 1, 0, 0),
respdeath = if_else(!is.na(respdeath_date) & (respdeath_date >= start_date) &
(respdeath_date <= end_date), 1, 0, 0),
coviddeath = if_else(!is.na(coviddeath_date) & (coviddeath_date >= start_date) &
(coviddeath_date <= end_date), 1, 0, 0),
covidadmitted = if_else(!is.na(covidadmitted_date), 1, 0, 0),
covidemerg = if_else(!is.na(covidemergency_date), 1, 0, 0),
covidcomposite = if_else(covidadmitted == 1 | coviddeath == 1 |
covidemerg == 1, 1, 0, 0),
anyadmitted = if_else(!is.na(admitted_unplanned_date), 1, 0, 0),
respadmitted = if_else(!is.na(respadmitted_date), 1, 0, 0),
respcomposite = if_else(respadmitted == 1 | respdeath == 1, 1, 0, 0),
) %>%
select(!c(contains("_date")))
}
#################################################
# Outcomes by start date
#################################################
### Outcomes starting in September (control)
outcomes_sep <- out("2022-09-03")
print(paste0("September cohort (no. rows): ", nrow(outcomes_sep)))
print(paste0("September cohort (no. people): ", n_distinct(outcomes_sep$patient_id)))
write.csv(outcomes_sep, here::here("output", "cohort", "outcomes_2022-09-03.csv"), row.names = FALSE)
### Outcomes starting in October (control)
outcomes_oct <- out("2022-10-15")
print(paste0("October cohort (no. rows): ", nrow(outcomes_oct)))
print(paste0("October cohort (no. people): ", n_distinct(outcomes_oct$patient_id)))
write.csv(outcomes_oct, here::here("output", "cohort", "outcomes_2022-10-15.csv"), row.names = FALSE)