methods 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.
dplyr reverse dependency (see #101)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 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te arguments have been replaced by tz (time points at which z was observed) in all functions to avoid confusion with mgcv::te (e.g., gg_laglead)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