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)
#> stability_Linear
#> 4 -0.03592404
#> 7 0.11670026
#> 31 0.06042562
#> 34 0.04890066
#> 37 0.03335611
#> 42 -0.08761045
p_rioja <- plotStability(stability_rioja_linear, sitenames = Ponds$env$Name)
p_rioja
print(sessionInfo())
#> R version 4.5.3 (2026-03-11 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 26200)
#>
#> Matrix products: default
#> LAPACK version 3.12.1
#>
#> locale:
#> [1] LC_COLLATE=C
#> [2] LC_CTYPE=English_United States.utf8
#> [3] LC_MONETARY=English_United States.utf8
#> [4] LC_NUMERIC=C
#> [5] LC_TIME=English_United States.utf8
#>
#> time zone: Asia/Shanghai
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] ggplot2_4.0.2 vegan_2.7-3 permute_0.9-10
#> [4] betaStability_0.0.4
#>
#> loaded via a namespace (and not attached):
#> [1] sass_0.4.10 generics_0.1.4 shape_1.4.6.1
#> [4] stringi_1.8.7 lattice_0.22-9 usedist_0.4.0
#> [7] digest_0.6.39 magrittr_2.0.4 rioja_1.0-7
#> [10] evaluate_1.0.5 grid_4.5.3 RColorBrewer_1.1-3
#> [13] BBmisc_1.13.1 iterators_1.0.14 fastmap_1.2.0
#> [16] xgboost_3.2.1.1 glmnet_4.1-10 Matrix_1.7-5
#> [19] foreach_1.5.2 doParallel_1.0.17 plyr_1.8.9
#> [22] jsonlite_2.0.0 backports_1.5.0 survival_3.8-6
#> [25] mgcv_1.9-4 scales_1.4.0 pbapply_1.7-4
#> [28] codetools_0.2-20 jquerylib_0.1.4 cli_3.6.5
#> [31] rlang_1.1.7 splines_4.5.3 withr_3.0.2
#> [34] cachem_1.1.0 yaml_2.3.12 otel_0.2.0
#> [37] tools_4.5.3 parallel_4.5.3 reshape2_1.4.5
#> [40] checkmate_2.3.4 dplyr_1.2.0 gdm_1.6.0-7
#> [43] vctrs_0.7.2 R6_2.6.1 lifecycle_1.0.5
#> [46] randomForest_4.7-1.2 stringr_1.6.0 MASS_7.3-65
#> [49] cluster_2.1.8.2 pkgconfig_2.0.3 pillar_1.11.1
#> [52] bslib_0.10.0 gtable_0.3.6 data.table_1.18.2.1
#> [55] glue_1.8.0 Rcpp_1.1.1 xfun_0.57
#> [58] tibble_3.3.1 tidyselect_1.2.1 rstudioapi_0.18.0
#> [61] knitr_1.51 farver_2.1.2 nlme_3.1-169
#> [64] htmltools_0.5.9 labeling_0.4.3 rmarkdown_2.31
#> [67] compiler_4.5.3 S7_0.2.1