Changelog

Source: NEWS.md

pammtools 0.5.922023-07-12

• Fixed competing risks data trafo in case of more than 2 causes

pammtools 0.5.9

• Fixes issue 154: direction argument to geom_stepribbon

pammtools 0.5.82022-01-09

• removed argument methods from pamm. Can be specified via .... Fixes #200
• adapted warn_about_new_time_points when original data not stored in model object. Fixes #203
• Fixed issue where not all ped attributes were retained when applying dplyr functions #202

pammtools 0.5.72021-06-21

• added staph data with recurrent events

pammtools 0.5.62021-03-29

• maintenance fix
• fixes to URLs and DOIs

pammtools 0.5.42020-12-18

• updates to the split_data function that now accepts Surv(start, stop, event) type inputs, e.g., to construct left-truncated data.
• Support and vignette for left truncated data
• Support and vignette for competing risks data
• Support and vignette for recurrent events data

pammtools 0.2.42020-06-06

• CRAN fix. Discrepancy between man page and code.

pammtools 0.2.32020-05-27

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

pammtools 0.2.22020-03-12

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

pammtools 0.2.12020-02-09

• 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

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

pammtools 0.1.142019-09-08

• Support for new interface to tidyr

pammtools 0.1.13

• 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 0.1.112019-04-18

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 0.1.92019-03-14

• maintenance update: fixes CRAN issues due to new RNG

pammtools 0.1.82019-01-02

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 0.1.72018-11-16

• 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

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 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 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

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