Solution 6: Functional code and packages

# Pseudocode to generate a cohort from Vandelay data based on demographic
#   diagnosis, biomarker, and follow-up time inclusion criteria

library(vandelay)

# Create a connection to the data
connect_vandelay(path = "path/to/vandelay/data") |>

# Start a breast cancer cohort
cohort_start(type = "breast") |>

# Define index date to be the date of metastatic diagnosis
define_index(index_date = "metastatic_diagnosis_date") |>

# Add patient's biomarker status for the biomarker "x" at index
add_biomarker_status_at_index(bm_name = "x") |>

# Add followup time to last visit
add_followup_time(censor = "last_visit") |>

# Define inclusion criteria
add_inclusion(sex = "female"
              age_at_index >= 18,
              x_status = "Positive",
              followup_time >= months(6)) |>

# Create a table 1
add_table_one(vars = c("sex", "age_at_index", "x_status", "followup_time")