├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── add-functions.R ├── as-ped.R ├── convenience-plots.R ├── cumulative-coefficient.R ├── cumulative-effect.R ├── data.R ├── formula-specials.R ├── formula-utils.R ├── geom-hazard.R ├── get-cut-points.R ├── get-terms.R ├── ggplot-extensions.R ├── helpers.R ├── interval-information.R ├── lag-lead-utils.R ├── make-newdata.R ├── model-evaluation.R ├── multi-state-helpers.R ├── nest-utils.R ├── pammfit.R ├── pammtools.R ├── penalized-lag-lead.R ├── predict.R ├── rpexp.R ├── sim-pexp.R ├── split-data.R ├── sysdata.rda ├── tdc-utils.R ├── tidiers.R ├── tidyverse-methods.R ├── utils-pipe.R ├── viz-elra.R ├── warnings.R └── zzz.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── cran-comments.md ├── data-raw ├── data-for-tests.R ├── hex-sticker.R ├── icu-patients.R ├── sim_elra.R ├── sofa-extubation.R ├── staph-recurrence.R └── veteran-ped.R ├── data ├── daily.rda ├── nuclear.rda ├── patient.rda ├── simdf_elra.rda ├── staph.rda └── tumor.rda ├── inst └── CITATION ├── man ├── add_cif.Rd ├── add_counterfactual_transitions.Rd ├── add_hazard.Rd ├── add_surv_prob.Rd ├── add_tdc.Rd ├── add_term.Rd ├── add_trans_ci.Rd ├── add_trans_prob.Rd ├── as.data.frame.crps.Rd ├── as_ped.Rd ├── as_ped_cr.Rd ├── calc_ci.Rd ├── combine_df.Rd ├── compute_cumu_diff.Rd ├── cumulative_coefficient.Rd ├── daily.Rd ├── dplyr_verbs.Rd ├── elra_matrix.Rd ├── fcumu.Rd ├── figures │ └── logo.png ├── formula_helpers.Rd ├── from_to_pairs.Rd ├── geom_hazard.Rd ├── geom_stepribbon.Rd ├── get_cif.Rd ├── get_cumu_eff.Rd ├── get_cumu_hazard.Rd ├── get_cumulative.Rd ├── get_cut.Rd ├── get_event_types.Rd ├── get_hazard.Rd ├── get_intervals.Rd ├── get_laglead.Rd ├── get_ped_form.Rd ├── get_plotinfo.Rd ├── get_sim_ci.Rd ├── get_sim_cumu.Rd ├── get_surv_prob.Rd ├── get_tdc_form.Rd ├── get_tdc_vars.Rd ├── get_term.Rd ├── get_terms.Rd ├── gg_fixed.Rd ├── gg_laglead.Rd ├── gg_partial.Rd ├── gg_re.Rd ├── gg_slice.Rd ├── gg_smooth.Rd ├── gg_tensor.Rd ├── has_tdc.Rd ├── int_info.Rd ├── make_X.Rd ├── make_X.scam.Rd ├── modus.Rd ├── nest_tdc.Rd ├── newdata.Rd ├── nuclear.Rd ├── pamm.Rd ├── pammtools.Rd ├── patient.Rd ├── ped_info.Rd ├── pipe.Rd ├── predictSurvProb.pamm.Rd ├── prep_concurrent.Rd ├── rpexp.Rd ├── sample_info.Rd ├── seq_range.Rd ├── sim_pexp.Rd ├── sim_pexp_cr.Rd ├── simdf_elra.Rd ├── smooth.construct.fdl.smooth.spec.Rd ├── specials.Rd ├── split_data.Rd ├── split_data_multistate.Rd ├── staph.Rd ├── tidiers.Rd ├── tidy_fixed.Rd ├── tidy_smooth.Rd ├── tidy_smooth2d.Rd ├── tumor.Rd ├── warn_about_new_time_points.Rd └── warn_about_new_time_points.glm.Rd ├── tests ├── testthat.R └── testthat │ ├── test-add-functions.R │ ├── test-as-ped-cr.R │ ├── test-as-ped.R │ ├── test-cumulative-coefficients.R │ ├── test-cumulative-effect.R │ ├── 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