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adjustedCurves 0.11.5 (developmental version)

Bug Fixes

  • Fixed a small bug that occurred in adjustedsurv() with method="iptw_km", when one or more rows of the supplied data contained an event exactly at time 0.

adjustedCurves 0.11.4

Enhancements

  • Numbers at risk and number of events are now included in the output of as_ggsurvplot_df(), even when method = "km" was used. Additionally, with multiple imputation, the correctly pooled values are now included, instead of nothing.
  • Updated all ggplot2 based functions, so that the weird messages about unused labels no longer appear with newer versions of ggplot2.

Bug Fixes

  • Fixed a bug that occurred when using plot.adjustedsurv() with the times argument in case a dataset with multiple imputation was supplied.
  • Fixed a bug in which the estimates of the cumulative incidence function were incorrectly extracted from the cuminc() function when using adjustedcif() with method="aalen_johansen". Essentially, the step functions were evaluated at the time before the actual step, so that any results obtained by using the previous versions were off by one time step. With many points in time the changes should be small, but with only a few events there might be substantial differences.
  • Fixed a bug where survival estimates were returned if adjustedcif() was used with non-competing risks data and method="iptw_pseudo", method="aiptw_pseudo" or method="direct_pseudo".

adjustedCurves 0.11.3

New features

  • Added the extend_to_last argument to method="iptw_km" in adjustedsurv(), which allows users to draw the IPTW survival curves up to the last observed point in time per group whether that time was censored or not. Unpublished simulation studies have shown that estimates beyond the last event time are very unstable, which is why in previous versions of this package (<= 0.11.2), this argument did not exist, but was essentially set to FALSE. To get the same results as with old versions, set this argument to FALSE.

Refactor:

  • Now uses README.Rmd instead of the regular README.md
  • Removed the already deprecated difference and ratio argument from adjusted_rmst() and adjusted_rmtl()

Bug Fixes

  • The correct way to pool standard errors when using multiple imputation is now also used when using bootstrapping + multiple imputation
  • Corrected a typo that lead to the censoring_model argument being ignored when using method="aiptw" in adjustedcif().
  • When using risk_table=TRUE with risk_table_type="n_events" or risk_table_type="n_cens", events or censored observations at the same point in time were mistakenly excluded (a < was used internally instead of <=). This has been fixed, potentially leading to different results than earlier with discrete values of time.

adjustedCurves 0.11.2

Bug Fixes

  • Fixed a bug that resulted in additional arguments passed by the user through the three-dot (...) syntax not being correctly evaluated. For example, supplying estimand="ATT" to adjustedsurv() with method="iptw_km" and a formula in the treatment_model argument would result in the estimand argument not being passed to weightit().
  • Fixed issues that ocurred with plot.adjustedsurv() when the adjustedsurv object was created in a function or loop
  • In previous versions the formula to pool standard errors when using multiple imputation was not implemented correctly. Fixed now, might lead to slightly different results when using multiply imputed data in the new and earlier versions. Many thanks to Dr. Jack M Wolf for finding and fixing this issue.

adjustedCurves 0.11.1

Enhancements

  • Re-factored internal code to vastly increase speed of bootstrapping related computations

New features

  • Added risk table functionality for plot.adjustedsurv() (all arguments starting with risk_table)
  • Allow estimation of difference and ratios in plot_rmst_curve() function
  • Allow estimation of difference and ratios in plot_rmtl_curve() function
  • Allow estimation of difference and ratios in adjusted_surv_quantile() function

Refactored

  • Re-factored examples to only be executed if suggested packages are installed
  • Renamed adjsurv and adjcif output objects of adjustedsurv() and adjsutedcif() respectively to adj
  • Put functionality of difference and ratio arguments into one contrast argument in adjusted_rmst(), adjusted_rmtl(), adjusted_surv_quantile(), plot_rmst_curve() and plot_rmtl_curve() functions
  • Temporarily removed support for tmle in adjustedsurv() and adjustedcif() due to concrete being removed from CRAN

Documentation

  • Re-worked introduction vignette
  • Added FAQ vignette
  • Added Group Comparison vignette

adjustedCurves 0.11.0

Enhancements

  • Added arguments iso_reg and force_bounds to adjustedsurv() and adjustedcif() functions to allow applying correction techniques outside plotting as well
  • Added better support for multiple imputation when variable, ev_time or event contain missings, includes the new mi_extrapolation argument in adjustedsurv() and adjustedcif()
  • Added the ratio argument to adjusted_rmst() and adjusted_rmtl() functions
  • Added support for multiple to values in adjusted_rmst() and adjusted_rmtl(), which speeds up plot_rmst_curve() and plot_rmtl_curve() considerably

Bug Fixes

  • There was a small bug in internal functions used to calculate integrals, which lead to slightly incorrect results whenever a survival curve reached 0 (or a CIF reached 1) and the "to" value was greater than the last observed time point. This may have impacted standard error estimates in adjusted_rmst(), adjusted_rmtl() and output of adjusted_curve_test() and functions that rely on those functions. This is fixed now, but may lead to slightly different estimates than in previous versions.

New Features

  • Added the new methods surv_tmle and cif_tmle, based on the concrete package
  • Added new instrumental variable based method surv_iv_2SRIF
  • Added new methods surv_prox_iptw, surv_prox_aiptw based on code from Andrew Ying
  • Added the adjusted_curve_ratio() function
  • Added the plot_curve_ratio() function

Documentation

  • Changed examples for the usage of WeightIt as suggested by Noah Greifer
  • Added a new vignette with an overview of implemented features of each method
  • Small changes to formulations

adjustedCurves 0.10.1

  • Fixed small issues in unit tests caused by changes in the WeightIt package
  • Made some small documentation updates

adjustedCurves 0.10.0

  • Removed support for tmle, ostmle methods
  • Changed citation information because manuscript was published
  • Changed print method to be equal to summary method
  • Fixed issues with unit-tests that require packages under "Suggests" only

adjustedCurves 0.9.1

  • Include CRAN in installation instructions
  • Updated code and tests to run with updated versions of the mice and ggplot2 packages
  • Updated documentation of package man page to include features not supported at the moment

adjustedCurves 0.9.0

  • This is the first release of this package