NEWS.md
split_data
function that now accepts Surv(start, stop, event)
type inputs, e.g., to construct left-truncated data.as_ped.ped
now also works for transformations with time-dependent covariatespamm
, which is a thin wrapper around mgcv::gam
with some arguments pre-set.predictSurvProb.pamm
pec
as_ped
changed. The vertical bar |
is no longer necessary to indicate concurrent or cumulative effectsFunctions get_hazard
and add_hazard
also gain reference
argument. Allows to calculate (log-)hazard ratios.
Introduces breaking changes to add_term
function. Argument relative
is replaced by reference
, makes calculation of relative (log-)hazards, i.e. hazard ratios, more flexible. Argument se.fit
is replaced by ci
.
make_newdata
loses arguments expand
and n
and gains ...
where arbitrary covariate specifications can be placed, i.e. e.g. age=seq_range(age, n=20)
. Multiple such expression can be provided and a data frame with one row for each combination of the evaluated expressions will be returned. All variables not specified in will be set to respective mean or modus values. For data of class ped
or fped
make_newdata
will try to specify time-dependent variables intelligently.
te_var
argument in concurrent
and cumulative
was renamed to tz_var
te
arguments have been replaced by tz
(time points at which z
was observed) in all functions to avoid confusion with mgcv::te
(e.g., gg_laglead
)
Overall better support for cumulative effects
Added convenience functions for work with cumulative effects, namely
gg_partial
andgg_slice
Added helper functions to calculate and visualize Lag-lead windows
get_laglead
gg_laglead
Added convenience geom
s for piece-wise constant hazards (see examples in ?geom_hazard
, cumulative hazards and survival probabilities (usually aes(x=time, y = surv_prob)
, but data set doesn’t contain extra row for time = 0
), thus
geom_stephazard
adds row (x=0, y = y[1]) to the data before plottinggeom_hazard
adds row (x = 0, y = 0) before plotting (can also be used for cumulative hazard)geom_surv
add row (x = 0, y = 1) before plottingAll data transformation is now handled using as_ped
(see data transformation vignette)
Data transformation now handles
Added functionality to flexibly simulate data from PEXP including cumulative effects, see ?sim_pexp
Added functionality to calculate Aalen-model style cumulative coefficients, see ?cumulative_coefficient
Breaking change in split_data
(as_ped
now main data trafo function):
max.end
argumentmax_time
argument to introduce administrative censoring at max_time
when no custom interval split points are provided