# Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis

## Documentation for package ‘pammtools’ version 0.7.4

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

add_cif | Add cumulative incidence function to data
add_cif.default | Add cumulative incidence function to data
add_counterfactual_transitions | Add counterfactual observations for possible transitions
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
add_trans_prob | Add transition probabilities
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
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