Convert a multi-state dataset with irreversible transitions containing 3 health states to a dataset with one row per patient and progression-free survival (PFS) and overall survival (OS) time-to-event outcomes.
as_pfs_os(
data,
patient_vars,
status = "status",
time_stop = "time_stop",
transition = "transition_id"
)A multi-state dataset.
Character vector of the names of patient specific variables.
Character string with the name of the status variable (1 = event, 0 = censored).
Character string with the name of the stopping time variable (i.e., time patient transitions from state \(r\) to state \(s\)).
Character string with the name of the variable identifying a transition. The transition variable should be integer valued with values 1, 2, and 3 for the Stable -> Progression, Stable -> Death, and Progression -> Death transitions, respectively.
A data.table with one row per patient containing each variable in
patient_vars as well as a time variable and status indicator for both
PFS (pfs_status, pfs_time) and OS (os_time, os_status).
as_pfs_os(onc3, patient_vars = c("patient_id", "strategy_name", "female", "age"))
#> Key: <patient_id, strategy_name, female, age>
#> patient_id strategy_name female age pfs_time pfs_status os_status
#> <int> <fctr> <int> <num> <num> <num> <int>
#> 1: 1 New 2 0 59.85813 2.4202260 1 1
#> 2: 2 New 2 0 62.57282 7.4974635 0 0
#> 3: 3 SOC 1 61.44379 2.3658666 1 1
#> 4: 4 New 2 0 62.90770 9.3422652 1 0
#> 5: 5 New 1 1 63.94785 4.4758108 0 0
#> ---
#> 2996: 2996 New 2 0 57.56747 8.1176909 1 0
#> 2997: 2997 SOC 0 59.78248 2.5573202 0 0
#> 2998: 2998 New 2 0 52.53633 9.1286646 1 1
#> 2999: 2999 New 1 0 60.39916 0.1838243 0 0
#> 3000: 3000 SOC 1 64.66686 4.2119803 1 1
#> os_time
#> <num>
#> 1: 14.6202585
#> 2: 7.4974635
#> 3: 2.3658666
#> 4: 11.3830946
#> 5: 4.4758108
#> ---
#> 2996: 15.0000000
#> 2997: 2.5573202
#> 2998: 9.1286646
#> 2999: 0.1838243
#> 3000: 11.3425810