NEWS.md

In pammtools: Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis

pammtools 0.5.92

• 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 0.5.8

• 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 0.5.7

• added staph data with recurrent events

pammtools 0.5.6

• maintenance fix
• fixes to URLs and DOIs

pammtools 0.5.4

• 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 0.2.4

• CRAN fix. Discrepancy between man page and code.

pammtools 0.2.3

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

pammtools 0.2.2

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

pammtools 0.2.1

• 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 0.1.14

• 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 0.1.11

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

• maintenance update: fixes CRAN issues due to new RNG

pammtools 0.1.8

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

• 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 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

pammtools documentation built on July 26, 2023, 6:07 p.m.