The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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, and purrr. 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/raretrans@v1.0.0")

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.