raretrans 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.

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.

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

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

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

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).

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

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.

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”).

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.

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