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)