Calculate zooplankton biomass from dry weight and abundance

Calculates zooplankton biomass by combining per-individual dry weight ("Dry weight (mean)", in ug) with abundance measurements in the same observation. Two biomass parameters are produced:

• Biomass concentration (mg/m3) from "Abundance" rows (ind/m3).

• Integrated biomass (mg/m2) from "Integrated abundance" rows (ind/m2).

Usage

calc_zooplankton_biomass(
  data,
  abundance_parameter = "Abundance",
  integrated_abundance_parameter = "Integrated abundance",
  dry_weight_parameter = "Dry weight (mean)",
  biomass_concentration_parameter = "Biomass concentration",
  integrated_biomass_parameter = "Integrated biomass",
  append = TRUE,
  drop_na_values = TRUE,
  keep_reference = FALSE
)

Arguments

data

A data frame or tibble in SHARK zooplankton format. Must contain the observation-key columns listed in the Observation key section, plus parameter and value.

abundance_parameter

Character string giving the parameter name for abundance in ind/m3. Defaults to "Abundance".

integrated_abundance_parameter

Character string giving the parameter name for integrated abundance in ind/m2. Defaults to "Integrated abundance".

dry_weight_parameter

Character string giving the parameter name for per-individual dry weight in ug. Defaults to "Dry weight (mean)".

biomass_concentration_parameter

Character string used for calculated biomass concentration rows. Defaults to "Biomass concentration".

integrated_biomass_parameter

Character string used for calculated integrated biomass rows. Defaults to "Integrated biomass".

append

Logical. If TRUE (default), append calculated biomass rows to data. If FALSE, return only the calculated biomass rows.

drop_na_values

Logical. If TRUE (default), drop calculated rows where biomass could not be calculated and value is NA.

keep_reference

Logical. If TRUE, keep the dry-weight coefficient and reference columns used to compute biomass in the output.

Value

A tibble. By default, the original data are returned with calculated biomass rows appended. If append = FALSE, only the calculated rows are returned.

Details

The conversion is biomass = dry_weight_ug * abundance / 1000 so that the result is expressed in mg/m3 or mg/m2.

Observation key

Dry-weight and abundance rows are matched one-to-one using the following columns, which together identify a single zooplankton observation in SHARK:

• platform_code

• station_name

• sample_date

• sample_time

• sample_min_depth_m

• sample_max_depth_m

• aphia_id

• sex_code

• dev_stage_code

• size_class

One biomass row is produced per matching abundance row (no aggregation across size classes or development stages). Abundance rows without a matching dry-weight value yield NA biomass and are dropped by default.

If no "Dry weight (mean)" rows are present in data, the function calls calc_zooplankton_dry_weight() internally to compute them from "Length (mean)" before calculating biomass.

See also

calc_zooplankton_dry_weight()

Examples

zoo <- dplyr::tibble(
  platform_code = "77SE",
  station_name = "ANHOLT E",
  sample_date = as.Date("2023-06-01"),
  sample_time = "10:00",
  sample_min_depth_m = 0,
  sample_max_depth_m = 30,
  aphia_id = 104251,
  sex_code = NA_character_,
  dev_stage_code = "AD",
  size_class = NA_character_,
  parameter = c("Length (mean)", "Abundance", "Integrated abundance"),
  value = c(800, 120, 3600),
  unit = c("um", "ind/m3", "ind/m2")
)

calc_zooplankton_biomass(zoo, append = FALSE)
#> # A tibble: 2 × 13
#>   platform_code station_name sample_date sample_time sample_min_depth_m
#>   <chr>         <chr>        <date>      <chr>                    <dbl>
#> 1 77SE          ANHOLT E     2023-06-01  10:00                        0
#> 2 77SE          ANHOLT E     2023-06-01  10:00                        0
#> # ℹ 8 more variables: sample_max_depth_m <dbl>, aphia_id <dbl>, sex_code <chr>,
#> #   dev_stage_code <chr>, size_class <chr>, parameter <chr>, value <dbl>,
#> #   unit <chr>