Man pages for pammtools
Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis
| add_cif | Add cumulative incidence function to data |
| add_counterfactual_transitions | Add counterfactual observations for possible transitions |
| add_hazard | 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... |
| add_trans_ci | Add transition probabilities confidence intervals |
| add_trans_prob | Add transition probabilities |
| as.data.frame.crps | Transform crps object to data.frame |
| as_ped | Transform data to Piece-wise Exponential Data (PED) |
| as_ped_cr | Competing risks trafo |
| calc_ci | Calculate confidence intervals |
| combine_df | Create a data frame from all combinations of data frames |
| compute_cumu_diff | Calculate difference in cumulative hazards and respective... |
| cumulative_coefficient | Extract cumulative coefficients (cumulative hazard... |
| daily | Time-dependent covariates of the 'patient' data set. |
| dplyr_verbs | 'dplyr' Verbs for 'ped'-Objects |
| elra_matrix | Create matrix components for cumulative effects |
| fcumu | A formula special used to handle cumulative effect... |
| formula_helpers | Extract variables from the left-hand-side of a formula |
| from_to_pairs | Extract transition information from different objects |
| geom_hazard | (Cumulative) (Step-) Hazard Plots. |
| geom_stepribbon | Step ribbon plots. |
| get_cif | Calculate CIF for one cause |
| get_cumu_eff | Calculate (or plot) cumulative effect for all time-points of... |
| get_cumu_hazard | Calculate cumulative hazard |
| get_cumulative | Expand time-dependent covariates to functionals |
| get_cut | Obtain interval break points |
| get_event_types | Exctract event types |
| get_hazard | Calculate predicted hazard |
| get_intervals | Information on intervals in which times fall |
| get_laglead | Construct or extract data that represents a lag-lead window |
| get_ped_form | Extract variables from the left-hand-side of a formula |
| get_plotinfo | Extract plot information for all special model terms |
| get_sim_ci | Calculate simulation based confidence intervals |
| get_sim_cumu | helper function for add_trans_ci |
| get_surv_prob | Calculate survival probabilities |
| get_tdc_form | Extract variables from the left-hand-side of a formula |
| get_tdc_vars | Extract variables from the left-hand-side of a formula |
| get_term | Extract partial effects for specified model terms |
| get_terms | Extract the partial effects of non-linear model terms |
| gg_fixed | Forrest plot of fixed coefficients |
| gg_laglead | Plot Lag-Lead windows |
| gg_partial | Visualize effect estimates for specific covariate... |
| 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_tensor | Plot tensor product effects |
| has_tdc | Checks if data contains timd-dependent covariates |
| int_info | Create start/end times and interval information |
| make_X | Create design matrix from a suitable object |
| make_X.scam | Create design matrix from a suitable object |
| modus | Calculate the modus |
| nest_tdc | Create nested data frame from data with time-dependent... |
| newdata | Construct a data frame suitable for prediction |
| pamm | Fit a piece-wise exponential additive model |
| pammtools | pammtools: Piece-wise exponential Additive Mixed Modeling... |
| patient | Survival data of critically ill ICU patients |
| ped_info | Extract interval information and median/modus values for... |
| pipe | Pipe operator |
| predictSurvProb.pamm | S3 method for pamm objects for compatibility with package pec |
| prep_concurrent | Extract information on concurrent effects |
| rpexp | Draw random numbers from piece-wise exponential distribution. |
| sample_info | Extract information of the sample contained in a data set |
| 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... |
| sim_pexp_cr | Simulate data for competing risks scenario |
| smooth.construct.fdl.smooth.spec | New basis for penalized lag selection |
| specials | Formula specials for defining time-dependent covariates |
| split_data | Function to transform data without time-dependent covariates... |
| split_data_multistate | Split data to obtain recurrent event data in PED format |
| staph | Time until staphylococcus aureaus infection in children, with... |
| tidiers | Extract 1d smooth objects in tidy data format. |
| tidy_fixed | Extract fixed coefficient table from model object |
| tidy_smooth | Extract random effects in tidy data format. |
| tidy_smooth2d | Extract 2d smooth objects in tidy format. |
| tumor | Stomach area tumor data |
| warn_about_new_time_points | Warn if new t_j are used |
| warn_about_new_time_points.glm | Warn if new t_j are used |
