betaStability: Beta Stability Calculation with Multiple Prediction Methods

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

Beta Stability Calculation with Multiple Prediction Methods

Description

This function integrates various prediction methods (linear, multiple linear, generalized linear model, generalized additive model, generalized dissimilarity model, random forest, and xgboost) to calculate the stability of each site.

Usage

betaStability(
  comtable = NULL,
  envmeta = NULL,
  comdist = NULL,
  envdist = NULL,
  sitenames = NULL,
  method = "linearPred",
  X = NULL,
  Y = NULL,
  geo_enabled = TRUE,
  GAM.dist.method = "manhattan",
  vegdist.method = "bray",
  xgboost.params = NULL,
  seed = 42
)

Arguments

comtable	The community table (required).
envmeta	The environmental metadata table/matrix (required).
comdist	The community dissimilarity matrix (optional). If not provided, computed from comtable using vegdist().
envdist	The environmental dissimilarity matrix (optional). If not provided, computed from envmeta using euclidean distance on range-normalized envmeta.
sitenames	The names of the site (optional, default: NULL)
method	A character string or vector specifying the prediction method(s) to use. Available options: "linearPred", "mlPred", "glmPred", "gamPred", "gdmPred", "rfPred", "xgboostPred". Use "all" to run all methods. Default is "linearPred".
X	The X coordinates of the sites for gdmPred (optional, default: NULL)
Y	The Y coordinates of the sites for gdmPred (optional, default: NULL)
geo_enabled	Whether to include geographic info for gdmPred (default: TRUE)
GAM.dist.method	The method for calculating dist for gamPred (default: "manhattan")
vegdist.method	The method for calculating comdist from comtable (default: "bray")
xgboost.params	A list of parameters for the xgboost model (default: NULL). If NULL, default parameters will be used.
seed	The random seed for reproducibility of rfPred and xgboostPred (default: 42)

Value

If method = "all", returns a data frame with 7 columns, each representing results from each selected method. If method length is 1, returns a column vector of predicted stability values. If method length > 1, returns a data frame with each column representing results from each selected method.

Examples

library(vegan)
data(varespec)
data(varechem)

# Single method (linearPred)
result_linear <- betaStability(
    comtable = varespec,
    envmeta = varechem,
    method = "linearPred"
)

# Multiple methods
results_multi <- betaStability(
    comtable = varespec,
    envmeta = varechem,
    method = c("linearPred", "mlPred")
)

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