---
title: "BetaStability with rioja datasets"
author: "Yu Gao(gaoyu19920914@gmail.com)"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
    %\VignetteIndexEntry{BetaStability with rioja datasets}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)
```

# 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:

```{r installation, eval = FALSE}
# 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:

```{r load-packages}
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

```{r data preparation}
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
```

```{r}
print(sessionInfo())
```