get_survival_case_weights_and_data | R Documentation |
Function used to get data.frame
with weights for a static fit for survivals.
get_survival_case_weights_and_data( formula, data, by, max_T, id, init_weights, risk_obj, use_weights = TRUE, is_for_discrete_model = TRUE, c_outcome = "Y", c_weights = "weights", c_end_t = "t" )
formula |
|
data |
|
by |
interval length of the bins in which parameters are fixed. |
max_T |
end of the last interval interval. |
id |
vector of ids for each row of the in the design matrix. |
init_weights |
weights for the rows in |
risk_obj |
a pre-computed result from a |
use_weights |
|
is_for_discrete_model |
|
c_outcome, c_weights, c_end_t |
alternative names to use for the added columns described in the return section. Useful if you already have a column named |
This function is used to get the data.frame
for e.g. a glm
fit that is comparable to a ddhazard
fit in the sense that it is a static version. For example, say that we bin our time periods into (0,1]
, (1,2]
and (2,3]
. Next, consider an individual who dies at time 2.5. He should be a control in the the first two bins and should be a case in the last bin. Thus the rows in the final data frame for this individual is c(Y = 1, ..., weights = 1)
and c(Y = 0, ..., weights = 2)
where Y
is the outcome, ...
is the covariates and weights
is the weights for the regression. Consider another individual who does not die and we observe him for all three periods. Thus, he will yield one row with c(Y = 0, ..., weights = 3)
.
This function use similar logic as the ddhazard
for individuals with time varying covariates (see the vignette vignette("ddhazard", "dynamichazard")
for details).
If use_weights = FALSE
then the two previously mentioned individuals will yield three rows each. The first individual will have c(Y = 0, t = 1, ..., weights = 1)
, c(Y = 0, t = 2, ..., weights = 1)
, c(Y = 1, t = 3, ..., weights = 1)
while the latter will have three rows c(Y = 0, t = 1, ..., weights = 1)
, c(Y = 0, t = 2, ..., weights = 1)
, c(Y = 0, t = 3, ..., weights = 1)
. This kind of data frame is useful if you want to make a fit with e.g. gam
function in the mgcv
package as described en Tutz et. al (2016).
Returns a data.frame
where the following is added (column names will differ if you specified them): column Y
for the binary outcome, column weights
for weights of each row and additional rows if applicable. A column t
is added for the stop time of the bin if use_weights = FALSE
. An element Y
with the used Surv
object is added if is_for_discrete_model = FALSE
.
Tutz, Gerhard, and Matthias Schmid. Nonparametric Modeling and Smooth Effects. Modeling Discrete Time-to-Event Data. Springer International Publishing, 2016. 105-127.
ddhazard
, static_glm
library(dynamichazard) # small toy example with time-varying covariates dat <- data.frame( id = c( 1, 1, 2, 2), tstart = c( 0, 4, 0, 2), tstop = c( 4, 6, 2, 6), event = c( 0, 1, 0, 0), x1 = c(1.09, 1.29, 0, -1.16)) get_survival_case_weights_and_data( Surv(tstart, tstop, event) ~ x1, dat, by = 1, id = dat$id)$X get_survival_case_weights_and_data( Surv(tstart, tstop, event) ~ x1, dat, by = 1, id = dat$id, use_weights = FALSE)$X
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