Zooplankton Concentration

A key feature of EcotaxaTools is easily getting the concentration of the zooplankton taxa from an ecopart_obj. This is done with uvp_zoo_conc(). You must provide an ecopart_obj as the first argument, then there is the option to specify which cast_name the calculation should be done on. This can be a single cast or multiple in a char vector. If not specified, it will be done on all casts. Finally, breaks must be provided as a numeric vector with limits on which to break. These should be the limits of each bin: breaks = c(0,200,1000) or breaks = seq(0,1200,10). Additionally, if a bin’s limits is outside the maximum range of observations, it will be trimmed to the maximum observation. There are additional arguments which can then be passed to bin_taxa(). For ecopart_obj, the applicable arguments are: - cat_col the category to bin by. Default is set to ‘name’, or the taxonomic labels. However, if there is a new column/labelling it can be set with this category. - func_col the column to apply the function to. Again by default this is ‘name’ but it could be changed if there is a need. For example, if there was a user-defined column for biomass it could be selected here - func the function to apply to func_col. Default is set to length. This is used rather than sum because bin_taxa() will count each observation of that category. However, if calculating the total biomass of each category, sum would be appropriate.

Taxa Warning

uvp_zoo_conc() has a runtime O(N x M x P) where N is the number of casts and M is the number of unique taxa and P is the number of depth-bins. Loops are still done within lapply() but there is the potential for very slow preformance. Especially if there are many casts or many taxa-labels. Consider simplifying taxanomic categories prior to using. Also, this is a good opportunity for a coffee break!

use bin_format()

uvp_zoo_conc() will return a $db column which is a character vector with the depth limits. This is not very useful for down-stream use. bin_format() will take a etx_conc_obj and add columns for the min, max, and midpoint for each depth bin.

Examples:

Getting concentration for certain taxa:

library(EcotaxaTools)
zoo_conc <- ecopart_example |>
    add_zoo(func = names_to, col_name = 'name', new_names = c('Chaetognatha','Copepoda','Eumalacostraca','living','not-living'), suppress_print = T) |> # rename for simplicity
    mod_zoo(names_drop, drop_names = 'not-living') |> #remove detritus & artefact
    uvp_zoo_conc(cast_name = c('bats361_ctd1', 'bats361_ctd2'), breaks = seq(0,1200,100)) |> # get concentration
    lapply(bin_format) #formatting

#take a peek:
head(zoo_conc$bats361_ctd1,8)

         db          group   conc_m3 min_d max_d  mp
1   (0,100]       Copepoda 1.1281843     0   100  50
2   (0,100] Eumalacostraca 2.4820055     0   100  50
3   (0,100]   Chaetognatha 0.4512737     0   100  50
4   (0,100]         living 4.5127372     0   100  50
5 (100,200]   Chaetognatha 0.4280089   100   200 150
6 (100,200]       Copepoda 0.4280089   100   200 150
7 (100,200] Eumalacostraca 0.4280089   100   200 150
8 (100,200]         living 3.8520801   100   200 150

head(zoo_conc$bats361_ctd2,8)

         db          group   conc_m3 min_d max_d  mp
1   (0,100]   Chaetognatha 0.2419726     0   100  50
2   (0,100]       Copepoda 1.2098628     0   100  50
3   (0,100] Eumalacostraca 0.2419726     0   100  50
4   (0,100]         living 6.2912866     0   100  50
5 (100,200]   Chaetognatha 0.9084096   100   200 150
6 (100,200]       Copepoda 1.5897168   100   200 150
7 (100,200]         living 9.0840960   100   200 150
8 (100,200] Eumalacostraca 0.0000000   100   200 150

Calcuting biovolume concentration:

Let’s say you were interested in getting the volumetric concentration of all copepods for a single cast:

cast1_copepod_conc <- ecopart_example |>
    mod_zoo(names_keep, keep_names = 'Copepoda', keep_children = T) |>
    add_zoo(func = names_to, col_name = 'name', new_names = 'Copepoda', suppress_print = T) |>
    add_zoo(func = biovolume, col_name = 'biovol', shape = 'ellipsoid', pixel_mm = unique(ecopart_example$meta$acq_pixel)) |>
    uvp_zoo_conc(cast_name = 'bats361_ctd12', breaks = seq(0,500,100), 
                 func_col = 'biovol', func = sum) |>
    bin_format()

cast1_copepod_conc

         db    group   conc_m3 min_d max_d  mp
1   (0,100] Copepoda 0.3706134     0   100  50
2 (100,200] Copepoda 0.7869312   100   200 150
3 (200,300] Copepoda 0.0000000   200   300 250
4 (300,400] Copepoda 0.0000000   300   400 350
5 (400,500] Copepoda 1.6664027   400   500 450

There are several more options on how this feature can be used and customized for different projects. Look into the structure of bin_taxa() to futher understand this process. Additionally feel free to discuss any questions with Alex Barth.