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03_model_final.R
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03_model_final.R
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######################################
# This script:
# - imports processed data
# - fit univariate and multivariable stratified cox model(s) using the coxph package
# - saves models
######################################
# Preliminaries ----
## Import libraries
library('tidyverse')
library('lubridate')
library('survival')
library('gtsummary')
library('gt')
library('survminer')
#library('ehahelper')
## Create output directory
dir.create(here::here("output", "models", "final"), showWarnings = FALSE, recursive=TRUE)
## Import processed data
data_tte <- read_rds(here::here("output", "data", "data_modelling.rds"))
# MODELS ----
## Stratified Cox PH model - adjusted; baseline demographics + comorbs,
mod.strat.coxph.adj <- coxph(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + imd + immunosuppression + ckd +
chronic_respiratory_disease + diabetes + chronic_liver_disease +
chronic_neuro_dis_inc_sig_learn_dis + chronic_heart_disease + asplenia +
sev_mental_ill + morbid_obesity + strata(practice_id_latest_active_registration),
data = data_tte)
write_rds(mod.strat.coxph.adj, here::here("output", "models", "final", "mod_strat_coxph_adj.rds"), compress="gz")