## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = TRUE,
  echo = TRUE,
  include = TRUE,
  fig.show = "asis",
  fig.keep = "high",
  warning = FALSE,
  message = FALSE
)

## -----------------------------------------------------------------------------
library(PDRobust)
data("ImperfectConSample", package = "PDRobust")
data("BiSample", package = "PDRobust")

## -----------------------------------------------------------------------------
data("BiSample", package = "PDRobust")
head(BiSample)

## -----------------------------------------------------------------------------
head(ImperfectConSample)

## -----------------------------------------------------------------------------
map <- Mapping(
  id = "patient_id",
  time = "visit_month",
  treatment = "treatment",
  survival = "alive_status",
  outcome = "clinical_outcome",
  baseline_time = 0,
  cutoff_time = 12,
  covariates = paste0("X", 1:6),
  interest_vars = c("X1", "X2"),
  y_type = "C" # "B"
)


## -----------------------------------------------------------------------------
print(map)

## -----------------------------------------------------------------------------
attributes(map)

## -----------------------------------------------------------------------------
check <- DataCheck(ImperfectConSample, map, strict = FALSE)

attributes(check)

## -----------------------------------------------------------------------------
check$valid
check$ready_for_analysis
check$manual_resolution_required
check$can_standardize

## -----------------------------------------------------------------------------
head(check$diagnostics)

## -----------------------------------------------------------------------------
pd_data <- DataStandard(ImperfectConSample, map, drop = TRUE)
class(pd_data)
head(pd_data)

## -----------------------------------------------------------------------------
names(attributes(pd_data))

## -----------------------------------------------------------------------------
attr(pd_data, "pd_original_mapping")
attr(pd_data, "pd_mapping")

## -----------------------------------------------------------------------------
standardization <- attr(pd_data, "pd_standardization")
names(standardization)

## -----------------------------------------------------------------------------
standardization$time_map

## -----------------------------------------------------------------------------
head(standardization$id_map)

## -----------------------------------------------------------------------------
standardization$attrition

## -----------------------------------------------------------------------------
attr(pd_data, "pd_check")$ready_for_analysis