Bayesian Priors for Matrix Population Models.
raretrans
Functions to create matrix population models from a combination of data on stage/age transitions and Bayesian prior information. This compensates for structural problems caused by missing observations of rare transitions (“holey matrices”).
Based on methods described in:
Tremblay, R. L., Tyre, A. J., Pérez, M.-E., & Ackerman, J. D. (2021). Population projections from holey matrices: Using prior information to estimate rare transition events. Ecological Modelling, 447, 109526. https://doi.org/10.1016/j.ecolmodel.2021.109526
Requirements
- R >= 4.1.0
- Core package dependencies:
ggplot2,rlang - Vignette dependencies:
tidyverse,popbio,huxtable,popdemo,googledrive
Note: The core functions work on any R >= 4.1.0. Vignettes require R >= 4.1.0 due to dependencies in
popdemo,dplyr, andpurrr. If you are on an older version of R, install without vignettes (see below) and read them online at https://atiretoo.github.io/raretrans/.
Installation
Install the stable release from CRAN:
install.packages("raretrans")
Or install the development version from GitHub:
# install.packages("remotes") # if needed
remotes::install_github("atiretoo/raretrans")
The code and data used to produce the published paper are tagged v1.0.0:
remotes::install_github("atiretoo/[email protected]")
Overview
The main functions in this package are:
| Function | Purpose |
|---|---|
fill_transitions() | Fill a transition matrix using a Dirichlet-multinomial prior |
fill_fertility() | Fill a fertility matrix using a Gamma prior |
sim_transitions() | Simulate posterior transition matrices |
transition_CrI() | Compute credible intervals for all transition probabilities |
plot_transition_CrI() | Visualise posterior means and credible intervals |
plot_transition_density() | Visualise full posterior beta densities as a matrix plot |
All functions take a TF list of two matrices as their first argument: a transition matrix T and a fertility matrix F. These can be constructed by hand or created with popbio::projection.matrix(..., TF = TRUE) from individual-level transition data.
Interactive Application
raretrans includes an interactive Shiny application to explore the effects of different Bayesian priors on transition matrices dynamically.
raretrans::run_app()
Quick Start
library(raretrans)
# Example with *Lepanthes eltoroensis* data included in the package
data(L_elto)
# Build a TF list from individual transition data
TF <- popbio::projection.matrix(L_elto, TF = TRUE)
# Fill structural zeros and perfect (1.0) survival,
# transitions, stasis and fertilities using uninformative priors
fill_transitions(TF)
fill_fertility(TF)
Vignettes
| # | Vignette | Topic |
|---|---|---|
| 01 | Quick start | Minimal worked example with Lepanthes eltoroensis |
| 02 | Introduction | Full workflow walkthrough |
| 03 | Single population | Working with one population and transition period |
| 04 | Credible intervals | transition_CrI() and plotting with Cypripedium calceolus |
| 05 | Prior information | Effect of priors on transitions and fertility |
| 06 | Animal matrices | Examples with animal population data |
Browse all vignettes at https://atiretoo.github.io/raretrans/.
Getting Help
- Report bugs or request features at https://github.com/atiretoo/raretrans/issues
- Read the full function reference at https://atiretoo.github.io/raretrans/reference/
Reference
Caswell, H. (2001). Matrix Population Models: Construction, Analysis, and Interpretation (2nd ed.). Sinauer Associates.
Code of Conduct
Please note that the raretrans project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.