--- a
+++ b/overview/cohort-tables.R
@@ -0,0 +1,51 @@
+data.filename <- '../../data/cohort-sanitised.csv'
+
+source('../lib/shared.R')
+
+# Load the data and convert to data frame to make column-selecting code in
+# prepData simpler
+COHORT.full <- fread(data.filename)
+
+print(nrow(COHORT.full))
+
+# Remove the patients we shouldn't include
+COHORT.full <-
+  COHORT.full[
+    # remove negative times to death
+    COHORT.full$time_death > 0 &
+    # remove patients who should be excluded
+    !COHORT.full$exclude
+    ,
+    ]
+
+# Total study population
+print(nrow(COHORT.full))
+
+# Age, 5, 50, 95, %missing
+print(quantile(COHORT.full$age, c(0.5, 0.05, 0.95)))
+
+# Gender
+print(table(COHORT.full$gender))
+print(table(COHORT.full$gender))/nrow(COHORT.full)*100
+
+# Deprivation, 5, 50, 95, %missing
+print(quantile(COHORT.full$imd_score, c(0.5, 0.05, 0.95), na.rm = TRUE))
+print(percentMissing(COHORT.full$imd_score))
+
+# Smoking, by category, %missing
+print(table(COHORT.full$smokstatus))/nrow(COHORT.full)*100
+print(percentMissing(COHORT.full$smokstatus))
+
+# Diabetes, yes/no
+print(
+  ( sum(COHORT.full$diabetes == 'Diabetes unspecified type') +
+    sum(COHORT.full$diabetes == 'Type 1 diabetes') +
+    sum(COHORT.full$diabetes == 'Type 2 diabetes')) /nrow(COHORT.full)*100
+)
+
+# Follow-up, 5, 50, 95
+print(quantile(COHORT.full$endpoint_death_date, c(0.5, 0.05, 0.95)))/365.25
+
+# Death vs censored, %
+print(table(COHORT.full$endpoint_death))
+print(table(COHORT.full$endpoint_death)) /nrow(COHORT.full)*100