BetaStability with rioja datasets

In betaStability: Quantify the Compositional Stability of Each Community Based on a Single Sampling Event

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
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BetaStability with rioja datasets

This vignette demonstrates the BetaStability package using linearPred with the Ponds dataset from the rioja package.

Installation

First, install the package from GitHub:

# Install from GitHub
# install.packages("devtools")
# devtools::install_github("gaoyu19920914/betaStability")

# OR install from BioConductor (in the future when it's available)
# if (!requireNamespace("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# BiocManager::install("betaStability")

Loading Required Packages

Load the BetaStability package and the rioja package for test data:

library(betaStability)
library(vegan)
library(ggplot2)
# Check if rioja is available and install it to load dataset
if (!requireNamespace("rioja", quietly = TRUE)) install.packages("rioja")
data("Ponds", package = "rioja")

rioja dataset with linearPred

comtable <- Ponds$spec
envmeta <- Ponds$env[, 6:19]

# Calculate stability with linearPred
stability_rioja_linear <- betaStability(
    comtable = comtable,
    envmeta = envmeta,
    method = "linearPred"
)

# Inspect the result
head(stability_rioja_linear)
p_rioja <- plotStability(stability_rioja_linear, sitenames = Ponds$env$Name)
p_rioja

print(sessionInfo())

betaStability documentation built on June 5, 2026, 5:08 p.m.