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

## ----echo=FALSE, out.width = '33%'--------------------------------------------
knitr::include_graphics("hex-hce.png")

## ----setup--------------------------------------------------------------------
library(hce)
packageVersion("hce")

## -----------------------------------------------------------------------------
table(COVID19)

## -----------------------------------------------------------------------------
COVID19HCE <- hce(GROUP = COVID19$GROUP, TRTP = COVID19$TRTP)
SUM0 <- summaryWO(COVID19HCE, ref = "Placebo")
SUM <- SUM0$summary
SUM$Ptie <- round(SUM$TIE/SUM$TOTAL, 2)
SUM

## -----------------------------------------------------------------------------
WO <- calcWO(COVID19HCE, ref = "Placebo")[, c("WO", "LCL", "UCL")]
round(WO, 2)

## -----------------------------------------------------------------------------
set.seed(1)
n <- 100
dat0 <- data.frame(TRTP = rep(c("A", "P"), each = n), 
                  DEATH = c(rbinom(n = n, size = 1, prob = 0.6), 
                            rbinom(n = n, size = 1, prob = 0.8)),
                  HOSP = c(rbinom(n = n, size = 1, prob = 0.5), 
                            rbinom(n = n, size = 1, prob = 0.8)))

## -----------------------------------------------------------------------------
dat1 <- dat0
dat1$AVAL <- ifelse(dat1$DEATH == 1, 1, ifelse(dat1$HOSP == 1, 2, 3))
dat1 <- as_hce(dat1)
summaryWO(dat1)$summary

## -----------------------------------------------------------------------------
dat2 <- dat0
dat2$ORD <- 2*dat2$DEATH + dat2$HOSP
unique(dat2[, c("DEATH", "HOSP", "ORD")])

## -----------------------------------------------------------------------------
dat2$AVAL <- max(dat2$ORD) - dat2$ORD 
dat2 <- as_hce(dat2)
unique(dat2[, c("DEATH", "HOSP", "ORD", "AVAL")])
summaryWO(dat2)$summary

## ----echo=FALSE---------------------------------------------------------------
HCE2 <- data.frame(Order = c("I", "II", "III", "IV", "V", "VI", "VII"), 
                  Category = c("Death", 
                               "Dialysis or kidney transplantation", 
                               "Sustained GFR < 15 ml/min per 1.73 m2", 
                               "Sustained GFR decline from baseline of >= 57%", 
                               "Sustained GFR decline from baseline of >= 50%",
                               "Sustained GFR decline from baseline of >= 40%",
                               "Individual GFR slope")
)
HCE2

## -----------------------------------------------------------------------------
dat <- KHCE
Order <- c("Death (adj)", "Chronic dialysis (adj) >=90 days", 
           "Sustained eGFR<15 (mL/min/1.73 m2)", "Sustained >=57% decline in eGFR", 
           "Sustained >=50% decline in eGFR", "Sustained >=40% decline in eGFR", "eGFR slope")   
dat$GROUP <- factor(dat$GROUP, levels = Order)
table(dat$GROUP, dat$TRTP)

## ----echo=FALSE---------------------------------------------------------------
HCE <- data.frame(Order = c("I", "II", "III", "IV", "V"), 
                  Category = c("Death", 
                               "More than one new or worsened organ dysfunction events", 
                               "One new or worsened organ dysfunction event", 
                               "Hospitalized at the end of follow-up (Day 30)", 
                               "Discharged from hospital before Day 30")
)
HCE

## ----echo=FALSE---------------------------------------------------------------
HCE3 <- data.frame(Order = c("I", "II", "III", "IV"), 
                  Category = c("Cardiovascular death", 
                               "Total (first and recurrent) HF hospitalizations", 
                               "Total urgent HF visits", 
                               "Improvement/deterioration in KCCQ-TSS"))
HCE3

## ----eval=FALSE---------------------------------------------------------------
# simKHCE(
#   n,
#   CM_A,
#   CM_P = -4,
#   n0 = n,
#   TTE_A = 1000,
#   TTE_P = TTE_A,
#   fixedfy = 2,
#   Emin = 20,
#   Emax = 100,
#   sigma = NULL,
#   Sigma = 3,
#   m = 10,
#   theta = -0.4605,
#   phi = 0,
#   two_meas = c("no", "base", "postbase", "both")
# )

## -----------------------------------------------------------------------------
Rates_A <- c(10, 20)
Rates_P <- c(20, 20)
dat1 <- simHCE(n = 2500, TTE_A = Rates_A, TTE_P = Rates_P, 
CM_A = -3, CM_P = -6, CSD_A = 15, fixedfy = 3, theta = 1, seed = 1)
dat2 <- simHCE(n = 2500, TTE_A = Rates_A, TTE_P = Rates_P, 
CM_A = -3, CM_P = -6, CSD_A = 15, fixedfy = 3, theta = 1.0001, seed = 1)
dat3 <- simHCE(n = 2500, TTE_A = Rates_A, TTE_P = Rates_P, 
CM_A = -3, CM_P = -6, CSD_A = 15, fixedfy = 3, theta = 10, seed = 1)
calcWO(dat1)
calcWO(dat2)
calcWO(dat3)