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active_analyses.R
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# Create output directory ------------------------------------------------------
fs::dir_create(here::here("lib"))
# Create empty data frame ------------------------------------------------------
df <- data.frame(cohort = character(),
exposure = character(),
outcome = character(),
ipw = logical(),
strata = character(),
covariate_sex = character(),
covariate_age = character(),
covariate_other = character(),
cox_start = character(),
cox_stop = character(),
study_start = character(),
study_stop = character(),
cut_points = character(),
controls_per_case = numeric(),
total_event_threshold = numeric(),
episode_event_threshold = numeric(),
covariate_threshold = numeric(),
age_spline = logical(),
analysis = character(),
stringsAsFactors = FALSE)
# Set constant values ----------------------------------------------------------
age_spline <- TRUE
exposure <- "exp_date_covid19_confirmed"
strata <- "cov_cat_region"
covariate_sex <- "cov_cat_sex"
covariate_age <- "cov_num_age"
cox_start <- "index_date"
cox_stop <- "end_date_outcome"
study_stop <- "2021-12-14"
total_event_threshold <- 50L
episode_event_threshold <- 5L
covariate_threshold <- 5L
# Specify cohorts --------------------------------------------------------------
cohorts <- c("vax","unvax_extf","prevax_extf")
# Specify outcomes -------------------------------------------------------------
## Outcomes for which we will run ALL analyses
outcomes_runall <- c("out_date_depression",
"out_date_serious_mental_illness")
## Outcomes for which we will run MAIN analyses only
outcomes_runmain <- c(outcomes_runall,
"out_date_anxiety_general",
"out_date_self_harm",
"out_date_anxiety_ptsd",
"out_date_eating_disorders",
"out_date_suicide",
"out_date_addiction")
# Add active analyses ----------------------------------------------------------
for (c in cohorts) {
ipw <- ifelse(c=="unvax", FALSE, TRUE)
for (i in outcomes_runmain) {
## Reduce sampling for common outcomes due to memory issues ----------------
controls_per_case <- ifelse(i %in% outcomes_runall, 10L, 20L)
## analysis: main ----------------------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "main")
## analysis: sub_covid_hospitalised ----------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_covid_hospitalised")
## analysis: sub_covid_nonhospitalised -------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_covid_nonhospitalised")
}
for (i in outcomes_runall) {
controls_per_case <- 10L
## analysis: sub_covid_history ---------------------------------------------
if (c!="prevax_extf") {
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_covid_history")
}
## analysis: sub_sex_female ------------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = "NULL",
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_sex_female")
## analysis: sub_sex_male --------------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = "NULL",
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_sex_male")
## analysis: sub_age_18_39 ------------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = FALSE,
analysis = "sub_age_18_39")
## analysis: sub_age_40_59 ------------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = FALSE,
analysis = "sub_age_40_59")
## analysis: sub_age_60_79 ------------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = FALSE,
analysis = "sub_age_60_79")
## analysis: sub_age_80_110 ------------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = FALSE,
analysis = "sub_age_80_110")
## analysis: sub_ethnicity_white -------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_ethnicity_white")
## analysis: sub_ethnicity_black -------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_ethnicity_black")
## analysis: sub_ethnicity_mixed -------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_ethnicity_mixed")
## analysis: sub_ethnicity_asian -------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_ethnicity_asian")
## analysis: sub_ethnicity_other -------------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = "cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm",
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_ethnicity_other")
## analysis: sub_history_none -----------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = gsub(";;",";",gsub(gsub("out_date","cov_cat_history",i),"","cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm")),
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_history_none")
## analysis: sub_history_notrecent ------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = gsub(";;",";",gsub(gsub("out_date","cov_cat_history",i),"","cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm")),
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_history_notrecent")
## analysis: sub_history_recent ---------------------------------------
df[nrow(df)+1,] <- c(cohort = c,
exposure = exposure,
outcome = i,
ipw = ipw,
strata = strata,
covariate_sex = covariate_sex,
covariate_age = covariate_age,
covariate_other = gsub(";;",";",gsub(gsub("out_date","cov_cat_history",i),"","cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm")),
cox_start = cox_start,
cox_stop = cox_stop,
study_start = ifelse(c=="prevax_extf", "2020-01-01", "2021-06-01"),
study_stop = study_stop,
cut_points = ifelse(c=="prevax_extf", "28;197;365;714", "28;197"),
controls_per_case = controls_per_case,
total_event_threshold = total_event_threshold,
episode_event_threshold = episode_event_threshold,
covariate_threshold = covariate_threshold,
age_spline = TRUE,
analysis = "sub_history_recent")
}
}
# Add day 0 analyses -----------------------------------------------------------
df$analysis <- paste0("day0_",df$analysis)
df$cut_points <- gsub("28","1;28",df$cut_points)
# Assign unique name -----------------------------------------------------------
df$name <- paste0("cohort_",df$cohort, "-",
df$analysis, "-",
gsub("out_date_","",df$outcome))
# Check names are unique and save active analyses list -------------------------
if (length(unique(df$name))==nrow(df)) {
saveRDS(df, file = "lib/active_analyses.rds")
} else {
stop(paste0("ERROR: names must be unique in active analyses table"))
}