Changelog

Source: NEWS.md

pammtools 0.5.6 2021-03-29

  • maintenance fix
  • fixes to URLs and DOIs

pammtools 0.5.4 2020-12-18

pammtools 0.2.4 2020-06-06

  • CRAN fix. Discrepancy between man page and code.

pammtools 0.2.3 2020-05-27

  • CRAN fix. Compliance with new dplyr version (1.0.0)

pammtools 0.2.2 2020-03-12

  • CRAN fix, removed plyr dependency (see issue #141)
  • as_ped.ped now also works for transformations with time-dependent covariates

pammtools 0.2.1 2020-02-09

  • Adds a new interface for model estimation called pamm, which is a thin wrapper around mgcv::gam with some arguments pre-set.
  • Adds S3 method predictSurvProb.pamm
  • Adds support and vignette for model evaluation using package pec
  • Fixed bug when CIs were calculated simulation based and model contained factor variables
  • Removed unnecessary dependencies in Imports/Suggests

pammtools 0.1.15 Unreleased

  • Interface for specification of data transformation in as_ped changed. The vertical bar | is no longer necessary to indicate concurrent or cumulative effects

pammtools 0.1.14 2019-09-08

  • Support for new interface to tidyr

pammtools 0.1.13 Unreleased

  • Functions get_hazard and add_hazard also gain reference argument. Allows to calculate (log-)hazard ratios.

  • Introduces breaking changes to add_term function. Argument relative is replaced by reference, makes calculation of relative (log-)hazards, i.e. hazard ratios, more flexible. Argument se.fit is replaced by ci.

pammtools 0.1.11 2019-04-18

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 2019-03-14

  • maintenance update: fixes CRAN issues due to new RNG

pammtools 0.1.8 2019-01-02

documentation

  • Updates to cumulative 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 2018-11-16

  • 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 Unreleased

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 Unreleased

Features

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

pammtools 0.0.9 Unreleased

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 Unreleased

  • 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 Aalen-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 Unreleased

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 Unreleased

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