hce (version 0.8.8)

KHCE: Kidney Hierarchical Composite Endpoint dataset.

Description

A dataset with kidney ordinal scale outcomes of 1500 patients in the ADSL dataset.

Usage

KHCE

Format

a data frame with 1500 rows and 11 variables:

ID

patient identifiers, numeric

TRTPN

treatment values, 1 Active or 2 Placebo, numeric

AVAL0

original values for each type of the event, time for TTE outcomes 1-6, numeric values for Continuous outcome 7, numeric

AVAL

AVAL = AVAL0 + GROUPN, ordinal analysis values for the HCE analysis, numeric, but caution NOT to apply numeric operations; will give meaningless results

GROUP

name of the event, character

GROUPN

ordinal outcomes corresponding to PARAMN values, numeric

PARAMCD

coded name of the event, character

PARAMN

severity of the event, outcomes 1-7, where a higher value means a better outcome, character

STRATAN

strata 1-4, higher value means more severe kidney disease, numeric

EGFRBL

Baseline GFR values of patients, numeric

TRTP

treatment values, A Active or P Placebo, character

PADY

primary analysis day (in years), length of the fixed follow-up, numeric

Examples

# Adjusted win odds
res <- regWO(x = KHCE, AVAL = "AVAL", TRTP = "TRTP", COVAR = "STRATAN", ref = "P")
res
# Convert the dataset to an adhce object.
## First check that `GROUP` is a factor with the correct ordering of outcomes.
class(KHCE$GROUP) # "factor"
levels(KHCE$GROUP)
dat1 <- as_hce(KHCE)
class(dat1)
calcWO(dat1)
## Re-derive individual patient eGFR slopes using a linear regression model, 
## based on the eGFR measurements in the `ADLB` dataset
dat2 <- KHCE
l <- lapply(
split(ADLB, ADLB$ID), 
function(x) coef(lm(AVAL ~ ADAY, data = x))[2])
new_slopes <- do.call(rbind, l)
new_slopes <- as.data.frame(new_slopes)
names(new_slopes) <- "LINEAR"
new_slopes$ID <- as.numeric(row.names(new_slopes))
dat2 <- merge(KHCE, new_slopes, by = "ID", all.x = TRUE)
dat2$AVAL0[dat2$PARAMCD == "eGFR"] <- dat2$LINEAR[dat2$PARAMCD == "eGFR"]
dat2$AVAL0[is.na(dat2$AVAL0)] <- 0 
dat2 <- as_hce(dat2)
calcWO(dat2)