data-raw/testdata-prepare_hcv_report_data.R

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

# test data for prepare_hcv_report_data()


# initiate  list
d <- list()


d$hcv_start <- data.frame(
  patient_id = c(1, 2, 3, 3),
  starttre = lubridate::dmy(rep("1/1/2010", 3), "20/3/2011"),
  stringsAsFactors = FALSE
)


d$hcv_characteristics <- data.frame(
  patient_id = c(1, 2, 3),
  adm_date = c("2007-01-05T12:10:01.000+0200",
               NA_character_,
               "2001-05-18T12:10:01.000+0200"),
  gender = c(NA_character_, "F", "M"),
  age = c(1, 25, 7),
  stringsAsFactors = FALSE
)

assertthat::assert_that(all(unique(d$hcv_start$patient_id) ==
                          unique(d$hcv_characteristics$patient_id)))

d$hcv_perf_status <-
  data.frame(
    patient_id = c(1, 1, 2, 2, 3),
    assessment_date = lubridate::dmy(c("1/12/2009",
                                       "4/1/2010",
                                       "1/1/2010",
                                       NA_character_,
                                       "5/1/2010")),
    performance_status_ecog = c("3=Limited self care",
                                "2=Capable of self care",
                                NA_character_,
                                "0=Fully active",
                                "1=Ambulatory"),
    stringsAsFactors = FALSE
  )

d$hcv_weight_height <- data.frame(
  patient_id = c(1, 2, 3),
  assessment_date = lubridate::dmy(c("1/12/2009",
                                     "1/10/2009",
                                     "5/1/2010")),
  weight = c(58, 103, 24),
  height = c(162, 181, 136),
  stringsAsFactors = FALSE
)


d$hcv_genotype <- data.frame(
  patient_id = c(1, 1, 
                 2, 2, 
                 3),
  samp_date = lubridate::dmy(c("5/1/2010", "12/12/2009",
                               "5/1/2010", "1/1/2010",
                               NA_character_)),
  hcv_genotype_done = c("Yes", "Yes", 
                        "No", "Yes", 
                        NA_character_),
  hcv_genotype = c("Genotype 1", "Genotype 2",
                   "Genotype 3", "Genotype 4",
                   NA_character_),
  hcv_genotype_sub_type = c("Subtype a",
                            "Subtype b",
                            "Subtype c",
                            "Subtype d",
                            "Subtype e"),
  fib_score = c("F0 no fibrosis",
                "F1 mild fibrosis",
                "F2 moderate fibrosis",
                NA_character_,
                "F4 cirrhosis"),
  child_pugh = c(5, 10, NA_integer_, 16, 12),
  stringsAsFactors = FALSE
)


d$hcv_treatment <- data.frame(
  patient_id = c(1, 1, 1, 
                 2, 2, 
                 3, 3),
  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")),
  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"),
  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"),
  tx_prescribed = c("SOF/DCV (FDC)", "GLE/PIB (FDC)", "SOF/DCV (FDC)",
                    "GLE/PIB (FDC)", "SOF/DCV (FDC)",
                    "Sofosbuvir (SOF)","Daclatasvir (DCV)"),
  stringsAsFactors = FALSE
)


d$hcv_end <- data.frame(
  patient_id = c(1, 2, 3, 3),
  end_date = lubridate::dmy("12/12/2009",
                            "1/9/2010",
                            NA_character_,
                            "1/12/2011"),
  outcome = c("Died",
              "Cured", 
              "LTFU during treatment",
              "Failed"),
  end_fu = c("Yes", "Unknown", NA_character_, "No"),
  end_fu_reason = c("Death", "Cured", "Loss to Follow up", NA_character_),
  stringsAsFactors = FALSE
)


# save 
saveRDS(d, "inst/testdata/testdata-prepare_hcv_report_data.rds", version = 2)