Piece-Wise Exponential Additive Mixed Modeling Tools

The Piece-wise exponential (Additive Mixed) Model (PAMM; Bender and Scheipl (2018) ) is a powerful model class for survival analysis, 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 et. al. (2018) . pammtools provides tidy workflow for survival analysis with PAMMs, including data transformation and other pre- and post-processing functions 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")

0.1.11 by Andreas Bender, 3 months 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, msm, lazyeval, Formula, mvtnorm

Suggests RColorBrewer, scam, coxme, testthat, timereg, knitr, rmarkdown, grid, gridExtra, covr, pkgdown


See at CRAN