Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis

The Piece-wise exponential (Additive Mixed) Model (PAMM; Bender and Scheipl (2018) ) is a powerful model class for the analysis of survival (or time-to-event) data, based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender and others (2018) . pammtools provides tidy workflow for survival analysis with PAMMs, including data simulation, transformation and other functions for data preprocessing and model post-processing as well as visualization.


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Installation

Install from CRAN or GitHub using:

# CRAN
install.packages("pammtools")
# GitHub
devtools::install_github("adibender/pammtools")

Overview

pammtools offers various utilities and convenience functions that facilitate working with Piece-wise exponential Additive Mixed Models (PAMMs).

To get started, see the Articles section.

An overview over the packages functionality is given in

  • Andreas Bender and Fabian Scheipl, 2018: "pammtools: Piece-wise exponential Additive Mixed Modeling tools", arXiv eprint, 2018, https://arxiv.org/abs/1806.01042

For a tutorial-like introduction to PAMMs see:

A general framework for the representation and estimation of cumulative effects (or exposure-lag-response associations) is described in:

  • Andreas Bender, Fabian Scheipl, Wolfgang Hartl, Andrew G Day, Helmut Küchenhoff; "Penalized estimation of complex, non-linear exposure-lag-response associations", Biostatistics, , kxy003, https://doi.org/10.1093/biostatistics/kxy003

News

pammtools 0.1.11

bugs

  • fixes bug in dplyr reverse dependency (see #101)
  • fixes bug in tidiers for Aalen models (see #99)

documentation

  • Better documentation and functionality for make_newdata
  • Added new vignette linking to tutorial paper (online only)

pammtools 0.1.9

  • maintainance update: fixes CRAN issues due to new RNG

pammtools 0.1.8

documentation

  • Updates to cummulative effect vignette
  • Updates to time-dependent covariate vignette (+ data transformation)
  • Update citation information

Features

  • concurrent now has a lag = 0 argument, can be set to positive integer values
  • as_ped accepts multiple concurrent specials with different lag specifications

Bug/Issue fixes

  • Fixed bug caused by changes in checkmate #73
  • Bug Fixes #42, #76, #63, #77

pammtools 0.1.7

  • Further improved support for cumulative effects
  • Added vignette on estimation and visualization of cumulative effect
  • Updated vignette on convenience functions (now "Workflow and convenience functions")
  • Other (minor) upgrades/updates to documentation/vignettes
  • Updates homepage (via pkgdown)

pammtools 0.1.3

Minor changes

  • Update documentation
  • More tests/improved coverage
  • Lag-lead column is adjusted in make-newdata.fped

Bug fixes

  • visualization functions gg_laglead and gg_partial_ll did not calculate the lag-lead-window correctly when applied to ped data

pammtools 0.1.0

Features

  • Better support for cumulative effects
  • Lag-Lead matrix now contains quadrature weights
  • Better support for visualization of cumulative effects

pammtools 0.0.9

Breaking changes

  • make_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 \code{...} 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)

Updates and new features

  • Overall better support for cumulative effects

  • Added convenience functions for work with cumulative effects, namely

    • gg_partial and
    • gg_slice
  • Added helper functions to calculate and visualize Lag-lead windows

    • get_laglead
    • gg_laglead
  • Added 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 plotting
    • geom_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 plotting

pammtools 0.0.8

  • All data transformation is now handled using as_ped (see data transformation vignette)

  • Data transformation now handles

    • standard time-to-event data
    • time-to-event data with concurrent effects of time-dependent covariates
    • time-to-event data with cumulative effects of time-dependent covariates
  • Added functionality to flexibly simulate data from PEXP including cumulative effects, see ?sim_pexp

  • Added functionality to calculate Aaalen-model style cumulative coefficients, see ?cumulative_coefficient

  • Breaking change in split_data (as_ped now main data trafo function):

    • removed max.end argument
    • added max_time argument to introduce administrative censoring at max_time when no custom interval split points are provided

pammtools 0.0.3

pammtools 0.0.3.2

  • More tidyeval adaptations
  • consistent handling of "no visible global binding" NOTEs
  • Release used in
    A. Bender, Groll A., Scheipl F., "A generalized additive model approach to time-to-event analysis" (2017). Statistical Modelling (to appear)

pammtools 0.0.3.1

  • some adaptations to tidyeval
  • Minor bug fixes

pammtools 0.0.2

  • Ported pamm package to pammtools due to naming conflicts with PAMM package on CRAN

Reference manual

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install.packages("pammtools")

0.2.2 by Andreas Bender, 20 days ago


https://github.com/adibender/pammtools


Report a bug at https://github.com/adibender/pammtools/issues


Browse source code at https://github.com/cran/pammtools


Authors: Andreas Bender [aut, cre] , Fabian Scheipl [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports mgcv, survival, checkmate, magrittr, rlang, tidyr, ggplot2, dplyr, purrr, tibble, lazyeval, Formula, mvtnorm, pec

Suggests testthat


See at CRAN