R/sp_richg.R

In PaulESantos/diversity.tool: Tools for biodiversity data manipulation

#' Richness and frequency by treatment.
#' @description The function returns a tibble: "n_plot" the frequency of grouped variable. "n_species" species richness of the grouped variable.
#'
#' @param comm community data matrix.
#' @param char characteristic from the community.
#' @param factor name of the variable used for build a grouped community data.
#'
#' @return a tibble
#'
#' @export
#'
#' @importFrom dplyr as_tibble left_join rename group_by filter n_distinct summarise
#' @importFrom tibble has_rownames
#' @importFrom tidyr gather
#' @importFrom tibble rownames_to_column as_tibble
#' @examples
#' library(vegan)
#' data("dune")
#' data("dune.env")
#' sp_richg(dune, dune.env, factor = "Management")
sp_richg <- function(comm,char, factor = "" ) {
y <- factor

if(inherits(comm, "matrix") & tibble::has_rownames(comm) == FALSE){
  comm <- comm |>
    dplyr::as_tibble(rownames = "plot") |>
    tidyr::gather(species, abundance, -1)
}
else if(inherits(comm, "data.frame") & tibble::has_rownames(comm) == TRUE)
{
  comm <- comm |>
    dplyr::as_tibble(rownames = "plot") |>
    tidyr::gather(species, abundance, -1)
}
else if(inherits(comm, "data.frame") & tibble::has_rownames(comm) == FALSE)
{
  comm <- comm |>
    tidyr::gather(species, abundance, -1)
  colnames(comm)[1] <- "plot"
}



x <- comm
xx <- char |>
  tibble::rownames_to_column("plot") |>
  tibble::as_tibble()

x1 <- xx |>
  dplyr::left_join(x, by = "plot") |>
  dplyr::rename(group = factor) |>
  tidyr::gather(species, richness, -c(1:6)) |>
  dplyr::filter(richness != 0) |>
  dplyr::group_by(group) |>
  dplyr::summarise(n_plot = dplyr::n_distinct(plot),
              n_species = dplyr::n_distinct(species))
colnames(x1) <- c(paste0(factor), "n_plot", "n_species")
return(x1)
}