Relative Abundance

rel_taxa() provides a quick way to get relative abundance based solely off observations. Note this approach does not consider the volume sampled in acquiring observations. To get a better quantitative estimate, use uvp_zoo_conc(). This function will work either for a single zoo_df for multiple provided as either a zoo_list or ecopart_obj.

Use with UVP Data:

For multiple casts:

To get the relative abundance of all living categories:

library(EcotaxaTools)
rel_data <- ecopart_example |> 
    mod_zoo(names_drop, drop_names = 'not-living', drop_children = T) |>
    add_zoo(names_to, col_name = 'name', new_names = c('Rhizaria', 'Copepoda', 'Chaetognatha', 'Eumalacostraca', 'living',
                                                       'Trichodesmium'), suppress_print = T) |>
    rel_taxa()
# this produces a list for all casts with df of relative abundance
# Single list element:
rel_data[[1]]

# A tibble: 6 × 2
  taxa           rel_abundance
  <chr>                  <dbl>
1 Chaetognatha          0.0588
2 Copepoda              0.118 
3 Eumalacostraca        0.206 
4 living                0.0294
5 Rhizaria              0.309 
6 Trichodesmium         0.279 

Across all observations:

Zooplankton data are stored in individual zoo_df by each cast. So to quickly visualize the relative abundance across all casts, casts must be combined into one. This is best done with merge_casts():

name_map = list(
    all_casts = ecopart_example$meta$profileid
)

rel_data <- ecopart_example |>
    merge_casts(name_map = name_map) |>
    rel_taxa()

head(rel_data$all_casts, 15)

# A tibble: 15 × 2
   taxa              rel_abundance
   <chr>                     <dbl>
 1 Acantharea            0.00591  
 2 Actinopterygii        0.000279 
 3 Alciopidae            0.000559 
 4 Annelida              0.0000399
 5 artefact              0.0000399
 6 Aulacantha            0.00303  
 7 Aulacanthidae         0.00204  
 8 Aulatractus           0.0000399
 9 Aulosphaeridae        0.00339  
10 badfocus<artefact     0.337    
11 bubble                0.000599 
12 Cannosphaeridae       0.0000399
13 Castanellidae         0.00184  
14 Chaetognatha          0.00196  
15 Cnidaria<Hydrozoa     0.000279 

Use with a single zoo_df

To use with zooscan or planktoscope data, you can simply feed-in th zoo_df as the sole argument.