More diversity indices-Potential pull request

[jibarozzo]

Hi! Thank you for this package and great paper.

I needed to calculate more diversity indices and opted to modify alphadivDF to wrap vegan::specnumber and "simpson" and "invsimpson". I was aided by AI cuz time is crunching. Maybe it can be a pull request to add.

alphadivDF <- <- function(x, diversity = c("shannon", "simpson", "invsimpson")) {
    md <- sample_data(x[[1]])

    # Calculate observed richness
    t_otu_table <- t(rep_otu_df(x))
    observed <- specnumber(t_otu_table)
    observed_richness_df <- rownames_to_column(as.data.frame(observed), var = "Unique_ID")

    div_df_list <- lapply(diversity, function(index) {
        div_values <- vegan::diversity(t(repotu_df(x)), index = index)
        if (!is.matrix(div_values)) {
            div_values <- as.matrix(div_values, ncol = 1, dimnames = list(rownames(div_values), NULL))
        }
        colnames(div_values) <- paste0(index, "_", colnames(div_values))
        return(data.frame(Unique_ID = rownames(div_values), div_values, stringsAsFactors = FALSE))
    })

    final <- reduce(div_df_list, function(df1, df2) inner_join(df1, df2, by = "Unique_ID"))

    # Merge observed richness with the final dataframe
    final <- merge(final, observed_richness_df, by = "Unique_ID", all.x = TRUE)

    final <- cbind(md, final)

    return(final)
}