# 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.

## 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.

# raretrans 1.0.4

# raretrans 1.0.3

# raretrans 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.

# raretrans 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.

# raretrans 1.0.0

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