Type: Package
Package: raretrans
Title: Bayesian Priors for Matrix Population Models
Version: 1.0.5
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, dplyr, formatR, gridExtra, huxtable, knitr, popdemo,
        popbio, purrr, rmarkdown, RColorBrewer, shiny, testthat,
        tibble, tidyr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
Config/roxygen2/version: 8.0.0
Repository: https://atiretoo.r-universe.dev
Date/Publication: 2026-05-15 21:24:34 UTC
RemoteUrl: https://github.com/atiretoo/raretrans
RemoteRef: HEAD
RemoteSha: b1f2e5c4265ab96c495986ab7c63fb0e2acd161b
NeedsCompilation: no
Packaged: 2026-07-14 05:46:37 UTC; root
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>