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02d_models_cox_vs_aft.R
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02d_models_cox_vs_aft.R
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######################################
# This script:
# - imports processed data
# - fits a number of stratified coxph and AFT models to several subsets of the data
######################################
# Preliminaries ----
## Import libraries
library('tidyverse')
library('lubridate')
library('survival')
library('gtsummary')
library('gt')
library("survminer")
## Create output directory
dir.create(here::here("output", "models", "cox_vs_aft"), showWarnings = FALSE, recursive=TRUE)
## Import processed data
data_tte <- read_rds(here::here("output", "data", "data_modelling.rds"))
## Converts logical to integer so that model coefficients print nicely in gtsummary methods
data_cox <- data_tte %>%
mutate(
across(
where(is.logical),
~.x*1L
)
)
# MODELS ----
## Stratified Cox model
mod.stratcoxph.adj <- coxph(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15 +
strata(practice_id_latest_active_registration),
data = data_cox)
write_rds(mod.stratcoxph.adj, here::here("output", "models", "cox_vs_aft", "mod_stratcoxph_adj.rds"), compress="gz")
## AFT models
### Weibull
mod.aft.adj.weibull <- survreg(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15,
dist = "weibull",
data = data_cox)
write_rds(mod.aft.adj.weibull, here::here("output", "models", "cox_vs_aft", "mod_aft_weibull_adj.rds"), compress="gz")
### Exponential
mod.aft.adj.exponential <- survreg(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15,
dist = "exponential",
data = data_cox)
write_rds(mod.aft.adj.exponential, here::here("output", "models", "cox_vs_aft", "mod_aft_exponential_adj.rds"), compress="gz")
### Loglogistic
mod.aft.adj.loglogistic <- survreg(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15,
dist = "loglogistic",
data = data_cox)
write_rds(mod.aft.adj.loglogistic, here::here("output", "models", "cox_vs_aft", "mod_aft_loglogistic_adj.rds"), compress="gz")
### Lognormal
mod.aft.adj.lognormal <- survreg(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15,
dist = "lognormal",
data = data_cox)
write_rds(mod.aft.adj.lognormal, here::here("output", "models", "cox_vs_aft", "mod_aft_lognormal_adj.rds"), compress="gz")
## AFT models with random effects
### Weibull
mod.aft.re.adj.weibull <- survreg(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15 +
frailty(practice_id_latest_active_registration),
dist = "weibull",
data = data_cox)
write_rds(mod.aft.re.adj.weibull, here::here("output", "models", "cox_vs_aft", "mod_aft_re_weibull_adj.rds"), compress="gz")
### Exponential
mod.aft.re.adj.exponential <- survreg(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15 +
frailty(practice_id_latest_active_registration),
dist = "exponential",
data = data_cox)
write_rds(mod.aft.re.adj.exponential, here::here("output", "models", "cox_vs_aft", "mod_aft_re_exponential_adj.rds"), compress="gz")
### Loglogistic
mod.aft.re.adj.loglogistic <- survreg(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15 +
frailty(practice_id_latest_active_registration),
dist = "loglogistic",
data = data_cox)
write_rds(mod.aft.re.adj.loglogistic, here::here("output", "models", "cox_vs_aft", "mod_aft_re_loglogistic_adj.rds"), compress="gz")
### Lognormal
mod.aft.re.adj.lognormal <- survreg(Surv(follow_up_time, covid_vax) ~
ageband + sex + ethnicity + morbid_obesity + chronic_heart_disease +
diabetes + chronic_kidney_disease_diagnostic + chronic_kidney_disease_all_stages +
chronic_kidney_disease_all_stages_3_5 + sev_mental_ill + learning_disability +
chronic_neuro_dis_inc_sig_learn_dis + asplenia + chronic_liver_disease +
chronis_respiratory_disease + immunosuppression_diagnosis +
immunosuppression_medication + imd + rural_urban + prior_covid +
flu_vaccine + shielded + shielded_since_feb_15 +
frailty(practice_id_latest_active_registration),
dist = "lognormal",
data = data_cox)
write_rds(mod.aft.re.adj.lognormal, here::here("output", "models", "cox_vs_aft", "mod_aft_re_lognormal_adj.rds"), compress="gz")