as_ped | R Documentation |
This is the general data transformation function provided by the
pammtools
package. Two main applications must be distinguished:
Transformation of standard time-to-event data.
Transformation of left-truncated time-to-event data.
Transformation of time-to-event data with time-dependent covariates (TDC).
For the latter, the type of effect one wants to estimate is also
important for the data transformation step.
In any case, the data transformation is specified by a two sided formula.
In case of TDCs, the right-hand-side of the formula can contain formula specials
concurrent
and cumulative
.
See the data-transformation
vignette for details.
as_ped(data, ...)
## S3 method for class 'data.frame'
as_ped(
data,
formula,
cut = NULL,
max_time = NULL,
tdc_specials = c("concurrent", "cumulative"),
censor_code = 0L,
transition = character(),
timescale = c("gap", "calendar"),
min_events = 1L,
...
)
## S3 method for class 'nested_fdf'
as_ped(data, formula, ...)
## S3 method for class 'list'
as_ped(
data,
formula,
tdc_specials = c("concurrent", "cumulative"),
censor_code = 0L,
...
)
is.ped(x)
## S3 method for class 'ped'
as_ped(data, newdata, ...)
## S3 method for class 'pamm'
as_ped(data, newdata, ...)
as_ped_multistate(
data,
formula,
cut = NULL,
max_time = NULL,
tdc_specials = c("concurrent", "cumulative"),
censor_code = 0L,
transition = character(),
timescale = c("gap", "calendar"),
min_events = 1L,
...
)
data |
Either an object inheriting from data frame or in case of time-dependent covariates a list of data frames (of length 2), where the first data frame contains the time-to-event information and static covariates while the second (and potentially further data frames) contain information on time-dependent covariates and the times at which they have been observed. |
... |
Further arguments passed to the |
formula |
A two sided formula with a |
cut |
Split points, used to partition the follow up into intervals. If unspecified, all unique event times will be used. |
max_time |
If |
tdc_specials |
A character vector. Names of potential specials in
|
censor_code |
Specifies the value of the status variable that indicates censoring.
Often this will be |
x |
any R object. |
newdata |
A new data set ( |
A data frame class ped
in piece-wise exponential data format.
tumor[1:3, ]
tumor[1:3, ] %>% as_ped(Surv(days, status)~ age + sex, cut = c(0, 500, 1000))
tumor[1:3, ] %>% as_ped(Surv(days, status)~ age + sex)
## Not run:
data("cgd", package = "frailtyHL")
cgd2 <- cgd %>%
select(id, tstart, tstop, enum, status, age) %>%
filter(enum %in% c(1:2))
ped_re <- as_ped_multistate(
formula = Surv(tstart, tstop, status) ~ age + enum,
data = cgd2,
transition = "enum",
timescale = "calendar")
## End(Not run)
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