geom_stepribbonmethods from pamm. Can be specified via .... Fixes #200warn_about_new_time_points when original data not stored in model object. Fixes #203split_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.pammpecas_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_newdataconcurrent now has a lag = 0 argument, can be set to positive integer valuesas_ped accepts multiple concurrent specials with different lag specificationsmake-newdata.fpedgg_laglead and gg_partial_ll did not
calculate the lag-lead-window correctly when applied to ped datamake_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 \code{...} 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te arguments have been replaced by tz (time points at which z was observed) in all functions to avoid confusion with mgcv::te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_sliceAdded helper functions to calculate and visualize Lag-lead windows
get_lagleadgg_lagleadAdded convenience geoms 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 providedtidyeval adaptationstidyevalpamm package to pammtools due to naming conflicts with PAMM
package on CRAN