Package primarycensored updated to version 1.4.0 with previous version 1.3.0 dated 2025-12-01

Fri, 06 Mar 2026 08:02:00 CDT

Title: Primary Event Censored Distributions
Description: Provides functions for working with primary event censored distributions and 'Stan' implementations for use in Bayesian modeling. Primary event censored distributions are useful for modeling delayed reporting scenarios in epidemiology and other fields (Charniga et al. (2024) <doi:10.48550/arXiv.2405.08841>). It also provides support for arbitrary delay distributions, a range of common primary distributions, and allows for truncation and secondary event censoring to be accounted for (Park et al. (2024) <doi:10.1101/2024.01.12.24301247>). A subset of common distributions also have analytical solutions implemented, allowing for faster computation. In addition, it provides multiple methods for fitting primary event censored distributions to data via optional dependencies.
Author: Sam Abbott [aut, cre, cph] , Sam Brand [aut] , Adam Howes [ctb] , James Mba Azam [aut] , Carl Pearson [aut] , Sebastian Funk [aut] , Kelly Charniga [aut]
Maintainer: Sam Abbott <contact@samabbott.co.uk>

Diff between primarycensored versions 1.3.0 dated 2025-12-01 and 1.4.0 dated 2026-03-06

 primarycensored-1.3.0/primarycensored/man/dot-name_deprecation.Rd                               |only
 primarycensored-1.4.0/primarycensored/DESCRIPTION                                               |   10
 primarycensored-1.4.0/primarycensored/MD5                                                       |  133 ++--
 primarycensored-1.4.0/primarycensored/NAMESPACE                                                 |    2
 primarycensored-1.4.0/primarycensored/NEWS.md                                                   |   29
 primarycensored-1.4.0/primarycensored/R/check.R                                                 |   49 +
 primarycensored-1.4.0/primarycensored/R/dprimarycensored.R                                      |  104 ++-
 primarycensored-1.4.0/primarycensored/R/fitdistdoublecens.R                                     |  106 +--
 primarycensored-1.4.0/primarycensored/R/pcd-stan-tools.R                                        |  169 +++++
 primarycensored-1.4.0/primarycensored/R/pcd_cmdstan_model.R                                     |   19
 primarycensored-1.4.0/primarycensored/R/pcens.R                                                 |   10
 primarycensored-1.4.0/primarycensored/R/pcens_quantile.R                                        |   17
 primarycensored-1.4.0/primarycensored/R/pprimarycensored.R                                      |  103 ++-
 primarycensored-1.4.0/primarycensored/R/primarycensored-package.R                               |    5
 primarycensored-1.4.0/primarycensored/R/qprimarycensored.R                                      |   18
 primarycensored-1.4.0/primarycensored/R/rprimarycensored.R                                      |   55 +
 primarycensored-1.4.0/primarycensored/R/utils.R                                                 |   41 -
 primarycensored-1.4.0/primarycensored/README.md                                                 |    6
 primarycensored-1.4.0/primarycensored/build/vignette.rds                                        |binary
 primarycensored-1.4.0/primarycensored/data/pcd_distributions.rda                                |binary
 primarycensored-1.4.0/primarycensored/inst/WORDLIST                                             |    7
 primarycensored-1.4.0/primarycensored/inst/doc/analytic-solutions.Rmd                           |    2
 primarycensored-1.4.0/primarycensored/inst/doc/analytic-solutions.html                          |    8
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 primarycensored-1.4.0/primarycensored/inst/doc/why-it-works.Rmd                                 |    2
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 primarycensored-1.4.0/primarycensored/inst/stan/functions/expgrowth.stan                        |   61 +-
 primarycensored-1.4.0/primarycensored/inst/stan/functions/primarycensored.stan                  |  293 +++++++---
 primarycensored-1.4.0/primarycensored/inst/stan/functions/primarycensored_analytical_cdf.stan   |   82 +-
 primarycensored-1.4.0/primarycensored/inst/stan/functions/primarycensored_ode.stan              |   63 +-
 primarycensored-1.4.0/primarycensored/inst/stan/pcens_model.stan                                |   14
 primarycensored-1.4.0/primarycensored/man/check_pdist.Rd                                        |    7
 primarycensored-1.4.0/primarycensored/man/dot-check_truncation_bounds.Rd                        |only
 primarycensored-1.4.0/primarycensored/man/dot-check_truncation_bounds_df.Rd                     |only
 primarycensored-1.4.0/primarycensored/man/dot-dpcens.Rd                                         |    6
 primarycensored-1.4.0/primarycensored/man/dot-normalise_cdf.Rd                                  |   10
 primarycensored-1.4.0/primarycensored/man/dprimarycensored.Rd                                   |   53 -
 primarycensored-1.4.0/primarycensored/man/fitdistdoublecens.Rd                                  |   22
 primarycensored-1.4.0/primarycensored/man/new_pcens.Rd                                          |   17
 primarycensored-1.4.0/primarycensored/man/pcd_as_stan_data.Rd                                   |   10
 primarycensored-1.4.0/primarycensored/man/pcd_load_stan_functions.Rd                            |    9
 primarycensored-1.4.0/primarycensored/man/pcd_stan_dist_id.Rd                                   |    1
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 primarycensored-1.4.0/primarycensored/man/pcd_stan_path.Rd                                      |    1
 primarycensored-1.4.0/primarycensored/man/pcens_quantile.Rd                                     |   12
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 primarycensored-1.4.0/primarycensored/tests/testthat/Rplots.pdf                                 |binary
 primarycensored-1.4.0/primarycensored/tests/testthat/test-dprimarycensored.R                    |  175 +++++
 primarycensored-1.4.0/primarycensored/tests/testthat/test-expgrowth.R                           |   68 ++
 primarycensored-1.4.0/primarycensored/tests/testthat/test-fitdistdoublecens.R                   |  178 ++----
 primarycensored-1.4.0/primarycensored/tests/testthat/test-pcd-stan-tools.R                      |   92 +++
 primarycensored-1.4.0/primarycensored/tests/testthat/test-pcens_cdf.R                           |   56 -
 primarycensored-1.4.0/primarycensored/tests/testthat/test-pprimarycensored.R                    |  110 +++
 primarycensored-1.4.0/primarycensored/tests/testthat/test-qprimarycensored.R                    |   60 ++
 primarycensored-1.4.0/primarycensored/tests/testthat/test-rpd-primarycensored.R                 |  100 +++
 primarycensored-1.4.0/primarycensored/tests/testthat/test-rprimarycensored.R                    |   66 ++
 primarycensored-1.4.0/primarycensored/tests/testthat/test-stan-dist_lcdf.R                      |only
 primarycensored-1.4.0/primarycensored/tests/testthat/test-stan-expgrowth.R                      |   48 +
 primarycensored-1.4.0/primarycensored/tests/testthat/test-stan-primarycensored_analytical_cdf.R |    6
 primarycensored-1.4.0/primarycensored/tests/testthat/test-stan-primarycensored_ode.R            |    6
 primarycensored-1.4.0/primarycensored/tests/testthat/test-stan-rpd-primarycensored.R            |  162 +++++
 primarycensored-1.4.0/primarycensored/vignettes/analytic-solutions.Rmd                          |    2
 primarycensored-1.4.0/primarycensored/vignettes/primarycensored.Rmd                             |   14
 primarycensored-1.4.0/primarycensored/vignettes/why-it-works.Rmd                                |    2
 70 files changed, 2093 insertions(+), 789 deletions(-)

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