data-raw/testdata-drug_tx_by_visit.R

In JayAchar/hisreportr: hisreportr: Automating MSF OCA EMR reporting

# test data for drug_tx_by_visit()

hcv_treatment_decisions <- c("Waiting List",
                            "Initiation/ Re-initiation",
                            "Continuation same dose",
                            "Modification due to adverse event",
                            "Modification due to other reasons",
                            "Discontinuation due to adverse event",
                            "Discontinuation (Stop) for other reasons",
                            "Treatment finished",
                            "Not specified")

hiv_treatment_decisions <- c("Initiation/ Re-initiation",
                             "Continuation same dose",
                             "Modification of regimen",
                             "Stop all ARVs",
                             "Not specified")

hcv_treatment <- data.frame(
  patient_id = c(1, 1, 1, 
                 2, 2, 
                 3, 3,
                 4, 
                 5, 5, 5),
  visit_date = lubridate::dmy(c("1/1/2010", "5/1/2010", NA_character_,
                                "12/12/2009", "1/1/2010",
                                "20/3/2011", "20/3/2011",
                                "12/6/2013",
                                "1/1/2017", "1/1/2017", "1/1/2017")),
  tx_status = c("Eligible / Already under treatment", "Eligible / Already under treatment",
                "Not eligible",
                "Not eligible", "Not eligible",
                "Follow up after treatment", "Follow up after treatment",
                "Not eligible", 
                "Eligible / Already under treatment", "Eligible / Already under treatment", "Eligible / Already under treatment"),
  tx_decision = c("Initiation/ Re-initiation", "Initiation/ Re-initiation", "Initiation/ Re-initiation",
                  "Modification due to adverse event", "Initiation/ Re-initiation",
                  "Initiation/ Re-initiation", "Initiation/ Re-initiation",
                  NA_character_,
                  "Initiation/ Re-initiation", "Initiation/ Re-initiation", "Initiation/ Re-initiation"),
  tx_prescribed = c("SOF/DCV (FDC)", "GLE/PIB (FDC)", "SOF/DCV (FDC)",
                    "GLE/PIB (FDC)", "SOF/DCV (FDC)",
                    "Sofosbuvir (SOF)","Daclatasvir (DCV)",
                    "SOF/DCV (FDC)", 
                    "Sofosbuvir (SOF)", "Ribavirin (RBV)", "Daclatasvir (DCV)"),
  stringsAsFactors = FALSE
)

hiv_treatment <- data.frame(
  patient_id = c(1, 2, 3, 3, 4, 5, 5),
  visit_date = lubridate::dmy(c("1/1/2010", "12/12/2018", "6/3/2019", "6/3/2019", "7/1/2018",
                                "1/12/2013", "1/12/2013")),
  tx_decision = c(hiv_treatment_decisions[1], hiv_treatment_decisions[2], 
                  hiv_treatment_decisions[3], hiv_treatment_decisions[3],
                  hiv_treatment_decisions[1], hiv_treatment_decisions[1], hiv_treatment_decisions[1]),
  tx_prescribed = c("ABC/3TC (FDC)", "Efavirenz (EFV)", "TDF/3TC/DTG (FDC)", "TDF/3TC/DTG (FDC)",
                    "ATV/r (FDC)", "Lamivudine (3TC)", "Tenofovir (TDF)"),
  stringsAsFactors = FALSE
)

drug_tx_testdata <- list(hcv = hcv_treatment, hiv = hiv_treatment)

# save tb_month raw data for SQL testing db
saveRDS(drug_tx_testdata, "inst/testdata/testdata-drug_tx_by_visit.rds", version = 2)