Skip to contents

Changelog

Source: NEWS.md

primarycensoreddist 0.5.0.1000

This is the development version of primarycensoreddist and is not yet ready for release.

Package

  • Split “Why it works” vignette into two separate vignettes, “Why it works” and “Analytic solutions for censored delay distributions”.

primarycensoreddist 0.5.0

This release adds a new {touchstone} based benchmark suite to the package. It also adds a new “How it works” vignette which aims to give the reader more details into how the primary censored distributions work.

As part of the “How it works” we (@SamuelBrand1) found analytical solutions for the gamma, lognormal, and weibull distributions with uniform primary censoring. These are now implemented for the lognormal and gamma distributions in the R and stan code providing significant speedups to the fitting process (~10-20 times faster). The Weibull will be added in the next release.

Package

  • Add {touchstone} based benchmarks for benchmarking R utility functions, and fitting the stan and fitdistplus models.
  • Added a “How it works” vignette.
  • Added R infrastructure for analytical solutions via the primary_censored_dist S3 class.
  • Added Weibull analytical solution to “How it works” vignette.
  • Added analytical solutions for the gamma and lognormal distributions with uniform primary censoring to both the R and stan code.
  • Added numerical protection to ensure that CDFs for delays greater than the maximum truncation are exactly 1.

primarycensoreddist 0.4.0

In this release, we have added a new package stan model for fitting distributions using the cmdstanr package. We have also added a new function fitdistdoublecens() to allow for fitting of double censored and truncated data using the fitdistrplus package. As well as these functionality improvements this release focuses on improving the stability of the stan model and improving the speed of the primary_censored_ode function.

Package

  • Added a new function fitdistdoublecens() to allow for fitting of double censored and truncated data using the fitdistrplus package.
  • Added low level tests for the Stan primary_censored_ode function.
  • Rephrased the stan code to use a ODE solver rather than a numerical integration method. This allows for much faster and more stable computation of the likelihood
  • Added a CmdStan model for fitting distributions using the cmdstanr package.
  • Added helpers functions for working with the new CmdStan model and added an example to the vignette.
  • Added parameter recovery tests for the new CmdStan model which tests the primary_censored_dist_lpmf function when used with NUTS based fitting.

primarycensoreddist 0.3.0

This release fixes and improves truncation handling across the code base. It also adds a new vignette showcasing how to use the primarycensoreddist and fitdistrplus packages together to fit distributions.

Package

  • Updated the approach to truncation to be outside the primary censored distribution integral.
  • Improved tests that compare random sampling and probability mass/density functions between R and Stan.
  • Improved cross-testing between R and Stan implementations of the primary censored distributions.
  • Worked on improving the stability of the primary_censored_dist_lpmf when used for NUTS based fitting (i.e. in Stan).

Documentation

  • @athowes improved the getting started vignette by catching a few grammar errors and simplifying language.
  • Added a new vignette showcasing how to use the primarycensoreddist and fitdistrplus packages together to fit distributions.

primarycensoreddist 0.2.0

This release puts in place initial documentation and vignettes. It also includes a new primary censored distribution interface to allow for non-secondary event censored distributions. Development of this release as identified some numerical issues in the gradient evaluations for the primary censored distributions which may lead to breaking interface changes in 0.3.0 for the Stan code.

Package

  • Added support for swindow = 0 to rprimarycensoreddist to allow for non-secondary event censored distributions.
  • Adapted rprimarycensoreddist so that truncation is based on the primary censored distribution before secondary events are censored. This better matches the generative process.
  • Added a new Stan interface tool to enable finding which files functions are implemented in the Stan code.

Documentation

  • Added a getting started vignette.
  • Added a vignette showcasing how to use the package Stan code with cmdstanr.
  • Added a vignette showcasing how to fit distributions using the cmdstanr package.

primarycensoreddist 0.1.0

This is the initial primarycensoreddist release and includes R and stan tools for dealing with potentially truncated primary event censored delay distributions. We expect all current features to work but the UI may change as the package matures over the next few versions.

Package

  • Added package skeleton.
  • Added checking input functions.
  • Added stan functions for primary censored and truncated distributions.
  • Added R functions for primary censored and truncated distributions.
  • Add R function to facilitate working with the Stan code.
  • Added tests for primary censored and truncated distributions.
  • Added tests to compare R and Stan implementations.
  • Added tests for the R functions that facilitate working with the Stan code.
  • Resolved R CMD check errors, warnings and notes.
  • Added a hexsticker.
  • Added vignette skeletons in preparation for 0.2.0 release.