Changes in version 1.0.5                        

Bug fixes

  - fill_fertility(): fixed a vector-recycling bug where the beta_post
    computation used + N instead of sweep(..., 2, N, FUN = "+") when
    priorweight > 0. The bug caused the [seedling, parent] β posterior
    to pick up N[seedling] instead of N[parent], inflating Gamma
    posterior means (and hence λ) when N[seedling] was small or zero
    (#5, #6). Thanks to Drew Tyre for the fix.

Vignettes

  - transition_priors: removed the multinomial confidence interval
    overlay on the credible-intervals figure. The MultinomialCI package
    is no longer accessible via CRAN's mainstream repositories, so the
    comparison layer has been dropped. The beta-density panels (the main
    point of the figure) are unchanged.

DESCRIPTION

  - Removed MultinomialCI from Suggests (no longer used in the
    vignette).
  - Removed covr from Suggests: no CI step uploaded coverage, so the
    dependency was unused.

Internal

  - Regenerated reference objects for sim_transitions() tests to reflect
    the corrected fertility posterior.

                 Changes in version 1.0.4 (2026-04-21)                  

                        Changes in version 1.0.3                        

                        Changes in version 1.0.2                        

Maintainer

  - Raymond Tremblay (University of Puerto Rico at Humacao) is now the
    package maintainer. Andrew Tyre remains as author.

New functions

  - transition_CrI(): computes marginal posterior beta credible
    intervals for all entries of the transition matrix, returning a tidy
    data frame.
  - plot_transition_CrI(): visualises posterior mean transition
    probabilities and credible intervals as a point-range plot, with
    optional exclusion of the dead fate (include_dead).
  - plot_transition_density(): visualises the full posterior beta
    density for each matrix entry, arranged as an n x n matrix plot
    mirroring the structure of the population projection matrix, with
    optional exclusion of the dead fate (include_dead).

Bug fixes

  - Fixed fill_transitions() and sim_transitions(): replaced missing(P)
    with is.null(P) so that passing P = NULL correctly triggers the
    uniform prior default.

Vignettes

  - Added introduction vignette: a beginner-friendly walkthrough of the
    full raretrans workflow using a published Chamaedorea elegans matrix
    (Burns et al. 2013 / COMPADRE). Covers entering matrices directly,
    uniform and informative priors, fill_transitions(),
    fill_fertility(), sim_transitions(), transition_CrI(),
    plot_transition_CrI(), and plot_transition_density().
  - Fixed onepopperiod vignette: removed devtools::load_all() call that
    would fail during CRAN's vignette build.

Documentation

  - Completed full documentation for the L_elto dataset, including
    accurate descriptions of all 13 variables, stage code definitions,
    and references.
  - Added @examples to all exported functions.
  - Fixed typo in package-level documentation ("observatons" ->
    "observations").

DESCRIPTION

  - Fixed duplicate URL and BugReports fields.
  - Updated URLs to point to the current repository (atiretoo).
  - Replaced tidyverse in Suggests with the specific packages used
    (dplyr, purrr, tibble).
  - Added ggplot2 and rlang to Imports.
  - Version bumped from 1.0.1.9000 to 1.0.2.

                     Changes in version 1.0.1.9000                      

Breaking changes

  - Fixed Issue #2, which means code that worked with v1.0.0 will not
    work without warnings, and will likely produce incorrect results.

Additions

  - Added tests for all major functions

Minor fixes

  - Added a NEWS.md file to track changes to the package.
  - Used tidy styling, added issue template, contribution guidelines
    etc.

                        Changes in version 1.0.0                        

  - First version of package, used to create figures in Tremblay et al.
    (submitted)