This minor release improves the documentation and the internal system used to automatically discover analytical solutions. It also adds lookups for supported supported distributions and tooling for working with these lookups. This makes it easier for package developers using primarycensored and also makes it easier to work with the Stan likelihood functions by improving the discoverability of the distribution functions. Minor bugs were also fixed.
epidist.pdist_name and dprimary_name arguments throughout. Users wishing to pass distribution names (i.e. to potentially leverage analytical solutions) are advised to use the newly introduced add_name_attribute() function. Adds transient dependency on lifecycle and rlang packages. See #188 by @pearsonca.pcd_stan_dist_id() to allow for discovery of distribution IDs for Stan models.pcd_dist_name() to allow for discovery of distribution names for R functions as needed for add_name_attribute().methods(pcens_cdf) to find analytical solutions.pcd_distributions and pcd_primary_distributions to document the distributions supported by primarycensored.primarycensored_lcdf().@family tag to the pcens functions. This omission resulted in the Weibull analytical solution not being visible in the package documentation.primarycensored_cdf() stan function, avoiding errors on some platforms due to narrowing conversions in aggregate initialisation.D to be of type real in pcens_model.stan in order to support infinite relative_obs_time.num_elements() over size() in all stan code to resolve compilation issues on some platforms as reported by @sbfnk.This is the first major release of primarycensored and has been submitted to CRAN.
primary_lpdf.rhub checks to the Github Actions workflow.dependencies: "hard" to the R-CMD-check workflow to ensure checks pass without optional dependencies.This release renames the package to primarycensored from primarycensoredist and also renames many of the functions to remove the dist in their name. This was done to make the package name and the functions more consistent and to remove the need to use the dist suffix. It also aligns it with the new PrimaryCensored.jl package in our Julia ecosystem.
Aside from name changes, this release also adds an analytical solution for the weibull distribution with uniform primary censoring, removes the need to assign functions to the global environment for fitdistdoublecens() by using withr, and adds a check_truncation() function to check if the truncation time is larger than the maximum observed delay. This is used in fitdistdoublecens() and pcd_as_stan_data() to ensure that the truncation time is appropriate to maximise computational efficiency.
fitdistdoublecens() by using withr.check_truncation() function to check if the truncation time is larger than the maximum observed delay. This is used in fitdistdoublecens() and pcd_as_stan_data() to ensure that the truncation time is appropriate to maximise computational efficiency.pcd_as_cmdstan_data() has been renamed to pcd_as_stan_data() to better reflect that it is used for Stan models in general rather than just the CmdStan models.stan folder and the stan model has been moved into the stan folder. All paths to the stan code have been updated to reflect this.primarycensored as have all functions that use "dist" in their name.pdist, dprimary, rdist, and rprimary arguments in the getting started vignette to make it easier to link to mathematical details.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.
{touchstone} based benchmarks for benchmarking R utility functions, and fitting the stan and fitdistplus models.primarycensored S3 class.R and stan code.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 primarycensored_ode function.
fitdistdoublecens() to allow for fitting of double censored and truncated data using the fitdistrplus package.primarycensored_ode function.CmdStan model for fitting distributions using the cmdstanr package.CmdStan model and added an example to the vignette.CmdStan model which tests the primarycensored_lpmf function when used with NUTS based fitting.This release fixes and improves truncation handling across the code base. It also adds a new vignette showcasing how to use the primarycensored and fitdistrplus packages together to fit distributions.
primarycensored_lpmf when used for NUTS based fitting (i.e. in Stan).primarycensored and fitdistrplus packages together to fit distributions.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.
swindow = 0 to rprimarycensored to allow for non-secondary event censored distributions.rprimarycensored so that truncation is based on the primary censored distribution before secondary events are censored. This better matches the generative process.cmdstanr.cmdstanr package.This is the initial primarycensored 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.
0.2.0 release.