Type: Package
Package: raretrans
Title: Bayesian Priors for Matrix Population Models
Version: 1.0.4
Authors@R: 
    c(person(given = "Raymond",
             family = "Tremblay",
             role = c("aut","cre","cph"),
             email = "raymond.tremblay@upr.edu",
             comment = c(ORCID = "0000-0002-8588-4372")),
      person(given = "Andrew",
             family = "Tyre",
             role = c("aut","cph"),
             email = "atyre2@gmail.com",
             comment = c(ORCID = "0000-0001-9736-641X")),
      person(given = "Maria-Eglee",
             family = "Perez",
             role = "aut",
             email = "mariaeglee@gmail.com",
             comment = c(ORCID = "0000-0001-8641-8405")),
      person(given = "Sasha",
             family = "Tenhumberg",
             role = "ctb"))
Description: Provides functions to correct biased transition and fertility
    estimates in population projection matrices caused by small sample sizes.
    Small or short-term studies frequently produce structural zeros
    (biologically possible transitions never observed) and structural ones
    (transitions estimated at 100% survival, stasis, or mortality that are
    biologically implausible). Both distort matrix structure and bias
    estimates of population growth. Implements a multinomial-Dirichlet
    Bayesian prior for transition probabilities and a Gamma-Poisson prior
    for reproduction, allowing analysts to incorporate prior biological
    knowledge and regularise estimates from rare or unobserved events.
    Includes functions to compute marginal posterior credible intervals for
    all transition probabilities (transition_CrI()), visualise those
    intervals as point-range plots (plot_transition_CrI()), and display
    the full posterior beta density for each matrix entry
    (plot_transition_density()). Methods are described in Tremblay et al.
    (2021) <doi:10.1016/j.ecolmodel.2021.109526>.
URL: https://atiretoo.github.io/raretrans/,
        https://github.com/atiretoo/raretrans
BugReports: https://github.com/atiretoo/raretrans/issues
License: MIT + file LICENSE
Depends: R (>= 4.1.0)
Imports: ggplot2, rlang, stats
Suggests: bslib, covr, dplyr, formatR, gridExtra, huxtable, knitr,
        MultinomialCI, popdemo, popbio, purrr, rmarkdown, RColorBrewer,
        shiny, testthat, tibble, tidyr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-04-17 14:23:21 UTC; rlt
Author: Raymond Tremblay [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-8588-4372>),
  Andrew Tyre [aut, cph] (ORCID: <https://orcid.org/0000-0001-9736-641X>),
  Maria-Eglee Perez [aut] (ORCID:
    <https://orcid.org/0000-0001-8641-8405>),
  Sasha Tenhumberg [ctb]
Maintainer: Raymond Tremblay <raymond.tremblay@upr.edu>
Repository: CRAN
Date/Publication: 2026-04-21 19:32:17 UTC
Built: R 4.6.0; ; 2026-04-26 09:47:36 UTC; unix
