R/beta_diversity.R

In Chang-Yu-Chang/MigrationCommunity: Microbial Consumer-Resource Model

#' Calculate mean beta diversity
#' @description Mean beta diversity
#' @name beta_diversity
#' @param x community matrix whose columns represent species and rows indicate sites
#' @return ...

beta_diversity <- function(x, method = "bray") {
  x_dist <- x %>%
    select(-function_group) %>%
    group_by(treatment, replicate) %>%
    spread(variable, value, fill = 0) %>%
    `[`(., -c(1, 2)) %>%
    as.matrix() %>%
    vegdist(method = method)
<<<<<<< HEAD

  return(list(
    mean = mean(x_dist),
    sd = sd(x_dist)
  ))
}
=======
  
  return(data.frame(mean = mean(x_dist),
              sd = sd(x_dist)))
}
>>>>>>> 381875eedd7472bfbaf2cfd62d780ca03ff9b601