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data_process_baseline.R
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data_process_baseline.R
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################################################################
# This script defines exclusion criteria and extracts
# final study population
################################################################
# 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')
## 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", "descriptive"), showWarnings = FALSE, recurse = TRUE)
# Load functions
source(here::here("analysis", "custom_functions.R"))
end_date = as.Date("2023-02-04")
#######################################
# Prepare data
#######################################
# Read in and clean data
baseline <- read_feather(here::here("output", "input_baseline.feather")) %>%
mutate_at(c(vars(c(contains("_date")))), as.Date, format = "%Y-%m-%d") %>%
mutate(dob = as.Date(as.character(as.POSIXct(dob)), format = "%Y-%m-%d"),
# Set DOB to mid-month
dob = dob + 14,
# Flag for clinically vulnerable people
cv = immunosuppressed | chronic_kidney_disease | chronic_resp_disease |
diabetes | chronic_liver_disease | chronic_neuro_disease | asplenia |
chronic_heart_disease | sev_mental | sev_obesity | asthma,
# Determine earliest recorded date of flu vaccination
flu_vax_date = pmin(flu_vax_med_date, flu_vax_tpp_date,
flu_vax_clinical_date, na.rm = TRUE),
# Booster date (if received)
boost_date = case_when(
(!is.na(covid_vax_4_date) &
covid_vax_4_date >= as.Date("2022-09-05") &
covid_vax_4_date < end_date) ~ covid_vax_4_date,
(!is.na(covid_vax_3_date) & is.na(covid_vax_4_date) &
covid_vax_3_date >= as.Date("2022-09-05") &
covid_vax_3_date < end_date) ~ covid_vax_3_date,
TRUE ~ as.Date(NA)),
# Received booster anytime in 2022/23
booster = if_else(!is.na(boost_date), 1, 0, 0),
# If received fourth dose prior to second booster campaign
covid_vax4_early = if_else(covid_vax_4_date < as.Date("2022-09-05"), 1, 0, missing = 0),
# If received third dose prior to first booster campaign
covid_vax3_early = if_else(covid_vax_3_date < as.Date("2021-09-16"), 1, 0, missing = 0),
# Received another COVID vaccine in 3 months prior to start of campaign
covid_vax_recent = if_else((
(covid_vax_3_date >= as.Date("2022-07-15") &
covid_vax_3_date <= as.Date("2022-10-15")) |
(covid_vax_2_date >= as.Date("2022-07-15") &
covid_vax_2_date <= as.Date("2022-10-15")) |
(covid_vax_1_date >= as.Date("2022-07-15") &
covid_vax_1_date <= as.Date("2022-10-15"))
), 1, 0, 0),
# Received 2nd dose at least 3 months prior to start of campaign
covid_vax2 = if_else(!is.na(covid_vax_2_date) &
covid_vax_2_date < as.Date("2022-07-15"), 1, 0, missing = 0),
# Received 3rd dose at least 3 months prior to start of campaign
covid_vax3 = if_else(!is.na(covid_vax_3_date) &
covid_vax_3_date < as.Date("2022-07-15"), 1, 0, missing = 0),
any_exclusion = (carehome == 1 | cv == 1 | hscworker == 1 |
endoflife == 1 | housebound == 1 | covid_vax4_early == 1 |
covid_vax3_early == 1 | covid_vax2 != 1 | covid_vax_recent == 1)
)
####################################################
# Overview of study population prior to exclusions
####################################################
pop_before_exclusions_byage <- baseline %>%
subset(age >= 45 & age < 55) %>%
group_by(age) %>%
mutate(total = n()) %>%
ungroup() %>%
group_by(age, total) %>%
summarise(
carehome = sum(carehome == 1),
immunosuppressed = sum(immunosuppressed == 1),
ckd = sum(chronic_kidney_disease == 1),
chronic_resp_disease = sum(chronic_resp_disease == 1),
asthma = sum(asthma == 1),
diabetes = sum(diabetes == 1),
asplenia = sum(asplenia == 1),
chronic_liver_disease = sum(chronic_liver_disease == 1),
chronic_neuro_disease = sum(chronic_neuro_disease == 1),
chronic_heart_disease = sum(chronic_heart_disease == 1),
sev_mental = sum(sev_mental == 1),
sev_obesity = sum(sev_obesity == 1),
cv = sum(cv == 1),
hscworker = sum(hscworker == 1),
endoflife = sum(endoflife == 1),
housebound = sum(housebound == 1),
covid_vax4_early = sum(covid_vax4_early == 1),
covid_vax3_early = sum(covid_vax3_early == 1),
covid_vax3 = sum(covid_vax3 == 1),
covid_vax2 = sum(covid_vax2 == 1),
covid_vax_recent = sum(covid_vax_recent == 1),
any_exclusion = sum(any_exclusion)
) %>%
ungroup() %>%
# Redaction and rounding
mutate(across(-age, redact), across(-age, rounding))
pop_before_exclusions_total <- baseline %>%
subset(age >= 45 & age < 55) %>%
mutate(total = n(), age = "All") %>%
group_by(total, age) %>%
summarise(
carehome = sum(carehome == 1),
immunosuppressed = sum(immunosuppressed == 1),
ckd = sum(chronic_kidney_disease == 1),
chronic_resp_disease = sum(chronic_resp_disease == 1),
asthma = sum(asthma == 1),
diabetes = sum(diabetes == 1),
asplenia = sum(asplenia == 1),
chronic_liver_disease = sum(chronic_liver_disease == 1),
chronic_neuro_disease = sum(chronic_neuro_disease == 1),
chronic_heart_disease = sum(chronic_heart_disease == 1),
sev_mental = sum(sev_mental == 1),
sev_obesity = sum(sev_obesity == 1),
cv = sum(cv == 1),
hscworker = sum(hscworker == 1),
endoflife = sum(endoflife == 1),
housebound = sum(housebound == 1),
covid_vax4_early = sum(covid_vax4_early == 1),
covid_vax3_early = sum(covid_vax3_early == 1),
covid_vax3 = sum(covid_vax3 == 1),
covid_vax2 = sum(covid_vax2 == 1),
covid_vax_recent = sum(covid_vax_recent == 1),
any_exclusion = sum(any_exclusion)
) %>%
ungroup() %>%
# Redaction and rounding
mutate(across(-age, redact), across(-age, rounding))
# Combine
pop_before_exclusions <- rbind(pop_before_exclusions_byage,
pop_before_exclusions_total)
# Save
write.csv(pop_before_exclusions,
here::here("output", "descriptive", "total_pop_before_exclusions.csv"),
row.names = FALSE)
#################################################
# Save final population after exclusions
#################################################
final <- baseline %>%
subset(any_exclusion == 0) %>%
dplyr::select(!c(covid_vax_recent, endoflife,
cv, hscworker, carehome, housebound,
immunosuppressed, chronic_kidney_disease,
chronic_resp_disease, asthma, diabetes,
chronic_liver_disease, chronic_neuro_disease,
asplenia, chronic_heart_disease, sev_mental,
sev_obesity, flu_vax_tpp_date, flu_vax_med_date,
flu_vax_clinical_date)
)
# Number of obs
print(paste0("Final population (n): ", nrow(final)))
#Save
write.csv(final,
here::here("output", "cohort", "cohort_final_sep.csv"),
row.names = FALSE)