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.