8 Diversity Metrics

Diversity metric in general combine the measure of taxonomic evenness and taxonomic richness. A number of diversity metrics can be calculated using taxa_div():

1. Shannon-Wiener Diversity (“shannon”)
2. Simpson’s Diversity (“simpson”)
3. Margalef’s Diversity (“margalef”)
4. Menhinick’s Diversity (“menhinick”)
5. Pielou Evenness (“pielou”)

8.1 Community Diversity

div.df <- nest.df %>% 
  dplyr::mutate(
    shannon_genus = taxa_div(.dataframe = .,
                             .key_col = uid,
                             .counts_col = total,
                             .group_col = genus,
                             .job = "shannon",
                             .base_log = 2,
                             .unnest_col = data),
    simpson_genus = taxa_div(.dataframe = .,
                             .key_col = uid,
                             .counts_col = total,
                             .group_col = genus,
                             .job = "simpson",
                             .unnest_col = data),
    margalef_genus = taxa_div(.dataframe = .,
                              .key_col = uid,
                              .counts_col = total,
                              .group_col = genus,
                              .job = "margalef",
                              .unnest_col = data),
    menhinick_genus = taxa_div(.dataframe = .,
                               .key_col = uid,
                               .counts_col = total,
                               .group_col = genus,
                               .job = "menhinick",
                               .unnest_col = data),
    pielou_genus = taxa_div(.dataframe = .,
                            .key_col = uid,
                            .counts_col = total,
                            .group_col = genus,
                            .job = "pielou",
                            .unnest_col = data)
  )

8.2 Subset Diversity

sub_div.df <- nest.df %>% 
  dplyr::mutate(
    simpson_gen_ept = taxa_div(.dataframe = .,
                            .key_col = uid,
                            .counts_col = total,
                            .group_col = genus,
                            .filter = order %in% c("ephemeroptera",
                                                   "plecoptera",
                                                   "trichoptera"),
                            .job = "simpson",
                            .unnest_col = data))