Epi (version 2.66)

adtte2Lexis {Epi}: Create a Lexis Object Given an ADAM ADTTE Dataset.

Description

Takes (a subset of) an ADTTE ADaM-format dataset along with choices about recurrent events and outputs a corresponding Lexis-object. Time since first entry to each state is included as a time scale in the Lexis-object.

Usage

adtte2Lexis(dat,
            start.state,
            Tr.ev,
            Term.st)

Value

A Lexis-object with possible lex.Cst and lex.Xst states specified in Tr.ev and Tr.st, and with time-scales for calender period, per, age, age, time since entry, t.sE and additional time-scales for time since first entry into the states given in Tr.ev. Baseline information is not retained.

Arguments

dat

A data.frame with data on a format complying with CDISC ADaM BDS standards, see https://www.cdisc.org/standards/foundational/adam/adam-basic-data-structure-bds-time-event-tte-analyses-v1-0. See details for necessary columns, and Examples for an example.

start.state

A character string, used as the name of the common starting state of all individuals.

Tr.ev

A vector containing a subset of the values taken by the EVNTDSC variable in ADTTE indicating possible states.

Term.st

A user-specified text string containing the name of the unique censoring state.

Author

Lars Diaz,

Details

The ADTTE data.frame, dat, should contain the columns USUBJID, STARTDT, ADT, AGE, EVNTDESC and CNSR. All other columns, including baseline values and FL-variables, will be discarded. If they are necessary in later analyses, they will need to be added back to the resulting Lexis-object manually.

References

https://www.cdisc.org/standards/foundational/adam/adam-basic-data-structure-bds-time-event-tte-analyses-v1-0

Examples

## Creating columns in ADTTE dataset:
STUDYID <- c("ABC123", "ABC123", "ABC123", "ABC123",
             "ABC123", "ABC123", "ABC123", "ABC123", "ABC123", "ABC123",
             "ABC123") 

USUBJID <- c("SUBJ001", "SUBJ001", "SUBJ001", "SUBJ002",
             "SUBJ002", "SUBJ002", "SUBJ002", "SUBJ002", "SUBJ002",
             "SUBJ002", "SUBJ002") 

AGE <- c(65L, 65L, 65L, 67L, 67L, 67L, 67L, 67L, 67L, 67L,
         67L) 

SEX <- c("M", "M", "M", "F", "F", "F", "F", "F", "F", "F", "F") 

ARM <- c("Treatment A", "Treatment A", "Treatment A",
         "Treatment A", "Treatment A", "Treatment A", "Treatment A",
         "Treatment A", "Treatment A", "Treatment A", "Treatment A") 

PARAMCD <- c("HOSP", "RELAPSE", "RELAPSE", "HOSP", "HOSP",
             "HOSP", "HOSP", "RELAPSE", "RELAPSE", "RELAPSE", "RELAPSE") 

PARAM <- c("Time to Hospitl (days)",
           "Time to Relapse (days)",
           "Time to Relapse (days)",
           "Time to Hospitl (days)",
           "Time to Hospitl (days)",
           "Time to Hospitl (days)",
           "Time to Hospitl (days)",
           "Time to Relapse (days)",
           "Time to Relapse (days)",
           "Time to Relapse (days)",
           "Time to Relapse (days)") 

EVNTSEQ <- c(1, 1, 2, 1, 2, 3, 4, 1, 2, 3, 4) 

STARTDT <- c("2023-01-01", "2023-01-01", "2023-01-31",
             "2023-01-03", "2023-02-13", "2023-05-10", "2023-06-29",
             "2023-01-03", "2023-03-18", "2023-04-26", "2023-06-18") 

ADT <- c("2023-07-20", "2023-01-31", "2023-07-20",
         "2023-02-13", "2023-05-10", "2023-06-29", "2023-07-22",
         "2023-03-18", "2023-04-26", "2023-06-18", "2023-07-22") 

ADTF <- c(NA_character_, NA_character_, NA_character_,
          NA_character_, NA_character_, NA_character_, NA_character_,
          NA_character_, NA_character_, NA_character_, NA_character_) 

AVAL <- c(200, 30, 170, 41, 86, 50, 23, 74, 39, 53, 34) 

CNSR <- c(1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1) 

EVNTDESC <- c("Censored", "Relapse", "Censored",
              "Hospitl", "Hospitl", "Hospitl",
              "Censored", "Relapse", "Relapse", "Relapse", "Censored") 

ANL01FL <- c("Y", "Y", "Y", "Y", "Y", "Y", "Y", "Y", "Y",
             "Y", "Y") 

##collecting into example adtte dataset:
adtte <- data.frame(STUDYID, USUBJID, AGE, SEX, ARM, PARAMCD, PARAM, EVNTSEQ,
                    STARTDT, ADT, ADTF, AVAL, CNSR, EVNTDESC, ANL01FL)
head(adtte)

## transform to Lexis format
adtte2Lexis(adtte, 
            start.state = "Rand", 
            Tr.ev = c("Relapse", "Hospitl"),
            Term.st = "Censored") -> Lx
Lx
summary(Lx, timeScales = TRUE)