uvp_zoo_conc: Calculate UVP Zooplankton Concentration from an Ecopart...

In TheAlexBarth/EcotaxaTools: Data wrangling and post-validation processing programs

Calculate UVP Zooplankton Concentration from an Ecopart Object

Description

This function takes in an ecopart object and will calculate the concentration for zooplankton data. This is a big wrapper function to build and add functionality to uvp_conc().

Usage

uvp_zoo_conc(ecopart_obj, cast_name = NULL, breaks, ...)

Arguments

ecopart_obj	an ecopart object list
cast_name	the name (or names of a cast)
breaks	a vector to break on
...	pass into bin_taxa()

Examples

#concentration of a whole projects
zoo_conc <- ecopart_example |> uvp_zoo_conc(breaks = seq(0,1200,100))

# concentration for particular  taxa
zoo_conc <- ecopart_example |>
  add_zoo(func = names_to, col_name = 'name', 
          new_names = c('Chaetognatha','Copepoda',
                        'Eumalacostraca','living','not-living'),
          suppress_print = TRUE) |> # rename for simplicity
  mod_zoo(names_drop, drop_names = 'not-living') |> #remove detritus & artifact
  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$bats361_ctd1,8)
head(zoo_conc$bats361_ctd2,8)


#volumetric concentraiton for a single cast
cast1_copepod_conc <- ecopart_example |>
  mod_zoo(names_keep, keep_names = 'Copepoda', keep_children = TRUE) |>
  add_zoo(func = names_to, col_name = 'name', new_names = 'Copepoda', 
          suppress_print = TRUE) |>
  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)) |>
  bin_format()

cast1_copepod_conc

TheAlexBarth/EcotaxaTools documentation built on Nov. 14, 2024, 8:27 p.m.