High-Performance Open-Source Archive
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.MultinomialCI from Suggests (no
longer used in the vignette).covr from Suggests: no CI step
uploaded coverage, so the dependency was unused.sim_transitions()
tests to reflect the corrected fertility posterior.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).fill_transitions() and
sim_transitions(): replaced missing(P) with
is.null(P) so that passing P = NULL correctly
triggers the uniform prior default.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().onepopperiod vignette: removed
devtools::load_all() call that would fail during CRAN’s
vignette build.L_elto dataset,
including accurate descriptions of all 13 variables, stage code
definitions, and references.@examples to all exported functions.URL and BugReports
fields.atiretoo).tidyverse in Suggests with the
specific packages used (dplyr, purrr,
tibble).ggplot2 and rlang to
Imports.NEWS.md file to track changes to the
package.
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