## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## ----load-api, eval = FALSE---------------------------------------------------
# library(ofhsyn)

## ----basic-run, eval = FALSE--------------------------------------------------
# out <- generate_ofh_cohort(
#   n = 1000,
#   seed = 123
# )
# 
# names(out)

## ----objects-only, eval = FALSE-----------------------------------------------
# out_objects_only <- generate_ofh_cohort(
#   n = 1000,
#   seed = 123,
#   save_csv = FALSE,
#   return_objects = TRUE
# )

## ----code-lists, eval = FALSE-------------------------------------------------
# out <- generate_ofh_cohort(
#   n = 1000,
#   seed = 123,
#   icd10 = c(
#     I210 = "STEMI of anterolateral wall",
#     I500 = "Congestive heart failure"
#   ),
#   opcs4 = c(
#     K401 = "Percutaneous transluminal balloon angioplasty of coronary artery"
#   ),
#   bnf_codes = data.frame(
#     BNFCode = c("0212000B0", "0601023A0"),
#     BNFName = c("Atorvastatin 20 mg tablets", "Metformin 500 mg tablets"),
#     Formulation = c("tablets", "tablets"),
#     Strength = c("20 mg", "500 mg"),
#     stringsAsFactors = FALSE
#   )
# )

## ----code-files, eval = FALSE-------------------------------------------------
# out <- generate_ofh_cohort(
#   n = 1000,
#   seed = 123,
#   icd10_file = "icd10_codes.txt",
#   opcs4_file = "opcs4_codes.txt",
#   bnf_codes_file = "bnf_medications.csv"
# )

## ----probabilities, eval = FALSE----------------------------------------------
# out_custom <- generate_ofh_cohort(
#   n = 1000,
#   seed = 123,
#   proportions = list(
#     nhse_outpat = 0.25,
#     nhse_inpat = 0.20,
#     nhse_ed = 0.30,
#     nhse_primcare_meds = 0.75
#   ),
#   record_multipliers = list(
#     nhse_outpat = 1.2,
#     nhse_inpat = 1.1,
#     nhse_ed = 1.3
#   ),
#   code_config = list(
#     nhse_outpat_data = list(diag_4_02_missing_prob = 0.70),
#     nhse_inpat_data = list(single_diag_prob = 0.85)
#   )
# )

## ----oop-run, eval = FALSE----------------------------------------------------
# syn <- OFHCohortSynthesizer$new(project_root = ".", seed = 123)
# 
# syn$set_code_pools(
#   icd10 = c(I210 = "STEMI of anterolateral wall"),
#   opcs4 = c(K401 = "Percutaneous transluminal balloon angioplasty of coronary artery"),
#   bnf_meds = data.frame(
#     BNFCode = c("0212000B0", "0601023A0"),
#     BNFName = c("Atorvastatin 20 mg tablets", "Metformin 500 mg tablets"),
#     Formulation = c("tablets", "tablets"),
#     Strength = c("20 mg", "500 mg"),
#     stringsAsFactors = FALSE
#   )
# )
# 
# out <- syn$run_all(n = 800)