Piece-Wise Exponential Additive Mixed Modeling Tools for
Survival Analysis
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Documentation for package ‘pammtools’ version 0.5.93
Help Pages
| add_cif | Add cumulative incidence function to data |
| add_cif.default | Add cumulative incidence function to data |
| add_cumu_hazard | Add predicted (cumulative) hazard to data set |
| add_hazard | Add predicted (cumulative) hazard to data set |
| add_hazard.default | Add predicted (cumulative) hazard to data set |
| add_surv_prob | Add survival probability estimates |
| add_tdc | Add time-dependent covariate to a data set |
| add_term | Embeds the data set with the specified (relative) term contribution |
| as.data.frame.crps | Transform crps object to data.frame |
| daily | Time-dependent covariates of the 'patient' data set. |
| GeomHazard | (Cumulative) (Step-) Hazard Plots. |
| GeomStepHazard | (Cumulative) (Step-) Hazard Plots. |
| GeomStepribbon | Step ribbon plots. |
| GeomSurv | (Cumulative) (Step-) Hazard Plots. |
| geom_hazard | (Cumulative) (Step-) Hazard Plots. |
| geom_stephazard | (Cumulative) (Step-) Hazard Plots. |
| geom_stepribbon | Step ribbon plots. |
| geom_surv | (Cumulative) (Step-) Hazard Plots. |
| get_cumu_coef | Extract cumulative coefficients (cumulative hazard differences) |
| get_cumu_coef.aalen | Extract cumulative coefficients (cumulative hazard differences) |
| get_cumu_coef.cox.aalen | Extract cumulative coefficients (cumulative hazard differences) |
| get_cumu_coef.gam | Extract cumulative coefficients (cumulative hazard differences) |
| get_cumu_eff | Calculate (or plot) cumulative effect for all time-points of the follow-up |
| get_intervals | Information on intervals in which times fall |
| get_intervals.default | Information on intervals in which times fall |
| get_laglead | Construct or extract data that represents a lag-lead window |
| get_laglead.data.frame | Construct or extract data that represents a lag-lead window |
| get_laglead.default | Construct or extract data that represents a lag-lead window |
| get_partial_ll | Visualize effect estimates for specific covariate combinations |
| get_plotinfo | Extract plot information for all special model terms |
| get_terms | Extract the partial effects of non-linear model terms |
| gg_cumu_eff | Calculate (or plot) cumulative effect for all time-points of the follow-up |
| gg_fixed | Forrest plot of fixed coefficients |
| gg_laglead | Plot Lag-Lead windows |
| gg_laglead.default | Plot Lag-Lead windows |
| gg_laglead.LL_df | Plot Lag-Lead windows |
| gg_laglead.nested_fdf | Plot Lag-Lead windows |
| gg_partial | Visualize effect estimates for specific covariate combinations |
| gg_partial_ll | Visualize effect estimates for specific covariate combinations |
| gg_re | Plot Normal QQ plots for random effects |
| gg_slice | Plot 1D (smooth) effects |
| gg_smooth | Plot smooth 1d terms of gam objects |
| gg_smooth.default | Plot smooth 1d terms of gam objects |
| gg_tensor | Plot tensor product effects |
| make_newdata | Construct a data frame suitable for prediction |
| make_newdata.default | Construct a data frame suitable for prediction |
| make_newdata.fped | Construct a data frame suitable for prediction |
| make_newdata.ped | Construct a data frame suitable for prediction |
| pammtools | pammtools: Piece-wise exponential Additive Mixed Modeling tools. |
| patient | Survival data of critically ill ICU patients |
| ped_info | Extract interval information and median/modus values for covariates |
| ped_info.ped | Extract interval information and median/modus values for covariates |
| predictSurvProb.pamm | S3 method for pamm objects for compatibility with package pec |
| seq_range | Generate a sequence over the range of a vector |
| simdf_elra | Simulated data with cumulative effects |
| sim_pexp | Simulate survival times from the piece-wise exponential distribution |
| staph | Time until staphylococcus aureaus infection in children, with possible recurrence |
| tidy_re | Extract random effects in tidy data format. |
| tidy_smooth | Extract 1d smooth objects in tidy data format. |
| tidy_smooth2d | Extract 2d smooth objects in tidy format. |
| tumor | Stomach area tumor data |