raretrans: Bayesian Priors for Matrix Population Models

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>.

Version: 1.0.4
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
Published: 2026-04-21
DOI: 10.32614/CRAN.package.raretrans (may not be active yet)
Author: Raymond Tremblay ORCID iD [aut, cre, cph], Andrew Tyre ORCID iD [aut, cph], Maria-Eglee Perez ORCID iD [aut], Sasha Tenhumberg [ctb]
Maintainer: Raymond Tremblay <raymond.tremblay at upr.edu>
BugReports: https://github.com/atiretoo/raretrans/issues
License: MIT + file LICENSE
URL: https://atiretoo.github.io/raretrans/, https://github.com/atiretoo/raretrans
NeedsCompilation: no
Language: en-US
Materials: README, NEWS
CRAN checks: raretrans results

Documentation:

Reference manual: raretrans.html , raretrans.pdf
Vignettes: 06 Matrices of animal populations (source, R code)
04 Credible intervals for transition probabilities: Cypripedium calceolus (source, R code)
02 Introduction to raretrans (source, R code)
03 Working with a single population and transition (source, R code)
01 Quick start: credible intervals for transition probabilities (source, R code)
05 Effect of prior information on transition probabilities and fertility (source, R code)

Downloads:

Package source: raretrans_1.0.4.tar.gz
Windows binaries: r-devel: not available, r-release: raretrans_1.0.4.zip, r-oldrel: raretrans_1.0.4.zip
macOS binaries: r-release (arm64): raretrans_1.0.4.tgz, r-oldrel (arm64): not available, r-release (x86_64): raretrans_1.0.4.tgz, r-oldrel (x86_64): raretrans_1.0.4.tgz

Linking:

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