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Calculate zooplankton dry weight from mean length

Source: R/zooplankton.R
calc_zooplankton_dry_weight.Rd

Calculates zooplankton dry weight from rows where parameter equals "Length (mean)" using bundled taxa-specific coefficients for mesozooplankton from Kattegat and Skagerrak.

Usage

calc_zooplankton_dry_weight(
  data,
  length_parameter = "Length (mean)",
  dry_weight_parameter = "Dry weight (mean)",
  append = TRUE,
  drop_na_values = TRUE,
  keep_reference = FALSE
)

Arguments

data

A data frame or tibble in SHARK zooplankton format. Must contain the columns parameter, value, aphia_id, and dev_stage_code.

length_parameter

Character string giving the parameter name used for mean length. Defaults to "Length (mean)".

dry_weight_parameter

Character string used for the calculated dry weight rows. Defaults to "Dry weight (mean)".

append

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

drop_na_values

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

keep_reference

Logical. If TRUE, keep additional columns with the selected coefficients and reference metadata in the output.

Value

A tibble. By default, the original data are returned with calculated "Dry weight (mean)" rows appended. If append = FALSE, only the calculated rows are returned.

Details

The dry weight calculation follows:

DW = 10^((B * log10(length)) - A)

For nauplii (dev_stage_code == "NP"), taxon-specific nauplii coefficients are used when available. Otherwise, the general coefficients for "copepod nauplii *all copepod species" are used. All other development stages use the non-nauplii coefficients. In practice, these coefficients are used for adults as well as copepodite stages and other non-NP stages.

The calculation assumes that SHARK "Length (mean)" values are reported in um. Calculated dry-weight rows are assigned the unit ug.

The bundled coefficient workbook used by this function can be accessed with: system.file("extdata", "Mesozooplankton_Kattegat_Skagerrak_taxa_and_biomass_calculations.xlsx", package = "SHARK4R").

Matching is performed using aphia_id, as preferred for SHARK data. Taxa with no matching coefficient keep NA dry-weight values.

Reference coefficient table

The bundled workbook used for these coefficients can be downloaded directly: Download coefficient workbook (.xlsx)

Reference taxonAphiaIDDevelopment stageABReference
Acartia bifilosa345919all stages except nauplii7.712.96Hay 1991¹
Acartia clausi149755all stages except nauplii7.712.96Hay 1991¹
Acartia longiremis346037all stages except nauplii7.712.96Hay 1991¹
Acartia104108all stages except nauplii7.712.96Hay 1991¹
Calanus finmarchicus104464all stages except nauplii6.882.69Hay 1991¹
Calanus finmarchicus104464nauplii5.382.03Hygum et al. 2000²
Centropages hamatus104496all stages except nauplii6.092.45Hay 1991¹
Centropages104159all stages except nauplii6.102.45Hay 1991¹
Centropages typicus104499all stages except nauplii6.102.45Hay 1991¹
Clausocalanus104161all stages except nauplii8.903.35Hay et al. 1988³
Corycaeus128634all stages except nauplii6.072.63Satapoomin 1999⁴
Cyclopoida106415all stages except nauplii6.722.71Uye 1982⁵
Evadne nordmanni106273all stages except nauplii5.792.80Hernroth 1985⁶
Fritillaria103358all stages except nauplii4.512.66Paffenhofer 1976¹⁰
Harpacticoid copepod1102all stages except nauplii7.242.89Uye 1982⁵
copepod nauplii *all copepod species1080nauplii5.482.23Hay 1991¹
Metridia104190all stages except nauplii7.122.68Hirche and Mumm 1992⁹
Microcalanus104164all stages except nauplii7.862.91Hay 1991¹
Microsetella115341all stages except nauplii7.662.88Satapoomin 1999⁴
Oikopleura dioica103407all stages except nauplii4.512.66Paffenhofer 1976¹⁰
Oithona106485nauplii2.682.14Almeda et al. 2010⁸
Oithona similis106656all stages except nauplii6.722.71Uye 1982⁵
Oncaea128690all stages except nauplii6.282.63Satapoomin 1999⁴
Paracalanus parvus104685all stages except nauplii6.162.45Hay 1991¹
Penilia avirostris106272all stages except nauplii4.952.38Atienza et al. 2006⁷
Podon leukarti106277all stages except nauplii7.523.02Uye 1982⁵
Podon polyphemoides159919all stages except nauplii6.602.75Uye 1982⁵
Pseudocalanus104165all stages except nauplii8.373.00Hay et al. 1988³
Temora longicornis104878all stages except nauplii8.373.00Hay et al. 1988³

For a local copy within an installed package, use: system.file("extdata", "Mesozooplankton_Kattegat_Skagerrak_taxa_and_biomass_calculations.xlsx", package = "SHARK4R")

To download the latest version directly: Download from GitHub

References

  1. Hay SJ, Kiørboe T, Matthews A (1991) Zooplankton biomass and production in the North Sea during the Autumn Circulation experiment, October 1987-March 1988. Continental Shelf Research 11(12):1453-1476. https://doi.org/10.1016/0278-4343(91)90021-W

  2. Hygum BH, Rey C, Hansen BW (2000) Growth and development rates of Calanus finmarchicus nauplii during a diatom spring bloom. Marine Biology 136:1075-1085. https://doi.org/10.1007/s002270000313

  3. Hay SJ, Evans GT, Gamble JC (1988) Birth, growth and death rates for enclosed populations of calanoid copepods. Journal of Plankton Research 10(3):431-454. https://doi.org/10.1093/plankt/10.3.431

  4. Satapoomin S (1999) Carbon content of some common tropical Andaman Sea copepods. Journal of Plankton Research 21(11):2117-2123. https://doi.org/10.1093/plankt/21.11.2117

  5. Uye SI (1982) Length-weight relationships of important zooplankton from the Inland Sea of Japan. Journal of the Oceanographical Society of Japan 38:149-158. https://doi.org/10.1007/BF02110286

  6. Hernroth L, ed. (1985) Recommendations on methods for marine biological studies in the Baltic Sea: mesozooplankton biomass assessment / individual volume technique. Publication / The Baltic Marine Biologists - BMB, 10. Lysekil: Institute of Marine Research.

  7. Atienza D, Saiz E, Calbet A (2006) Feeding ecology of the marine cladoceran Penilia avirostris: natural diet, prey selectivity and daily ration. Marine Ecology Progress Series 315:211-220. https://doi.org/10.3354/meps315211

  8. Almeda R, Calbet A, Alcaraz M, Yebra L, Saiz E (2010) Effects of temperature and food concentration on the survival, development and growth rates of naupliar stages of Oithona davisae (Copepoda, Cyclopoida). Marine Ecology Progress Series 410:97-109. https://doi.org/10.3354/meps08625

  9. Hirche HJ, Mumm N (1992) Distribution of dominant copepods in the Nansen Basin, Arctic Ocean, in summer. Deep-Sea Research Part A. Oceanographic Research Papers 39(Suppl. 2):S485-S505. https://doi.org/10.1016/S0198-0149(06)80017-8

  10. Paffenhöfer GA (1976) On the biology of appendicularia of the southeastern North Sea. In: 10th European Symposium on Marine Biology, Ostend, Belgium, 17-23 September 1975, Vol. 2, pp. 437-455.

See also

calc_zooplankton_biomass()

Examples

# Minimal example with a few rows
zoo <- dplyr::tibble(
  scientific_name = c("Acartia clausi", "Calanus finmarchicus", "Unknown taxon"),
  parameter = c("Length (mean)", "Length (mean)", "Length (mean)"),
  value = c(200, 250, 160),
  aphia_id = c(104251, 104464, 999999),
  dev_stage_code = c("AD", "NP", "NP")
)

# Calculate dry weight rows only
calc_zooplankton_dry_weight(zoo, append = FALSE)
#> # A tibble: 3 × 5
#>   scientific_name      parameter         value aphia_id dev_stage_code
#>   <chr>                <chr>             <dbl>    <dbl> <chr>         
#> 1 Acartia clausi       Dry weight (mean) 0.129   104251 AD            
#> 2 Calanus finmarchicus Dry weight (mean) 0.307   104464 NP            
#> 3 Unknown taxon        Dry weight (mean) 0.272   999999 NP            

# \donttest{
# Download zooplankton data from SHARK
zoo_shark <- get_shark_data(
  "sharkdata_zooplankton",
  dataTypes = "Zooplankton",
  fromYear = 2023,
  toYear = 2023,
  stationName = "ANHOLT E",
  verbose = FALSE,
)

# Calculate dry weight from "Length (mean)" and return only the new rows
calc_zooplankton_dry_weight(
  zoo_shark,
  append = FALSE
)
#> # A tibble: 463 × 109
#>    delivery_datatype check_status_sv data_checked_by_sv visit_year visit_month
#>    <chr>             <chr>           <chr>                   <dbl>       <dbl>
#>  1 Zooplankton       Klar            Leverantör               2023          12
#>  2 Zooplankton       Klar            Leverantör               2023          12
#>  3 Zooplankton       Klar            Leverantör               2023          12
#>  4 Zooplankton       Klar            Leverantör               2023          12
#>  5 Zooplankton       Klar            Leverantör               2023          12
#>  6 Zooplankton       Klar            Leverantör               2023          12
#>  7 Zooplankton       Klar            Leverantör               2023          12
#>  8 Zooplankton       Klar            Leverantör               2023          12
#>  9 Zooplankton       Klar            Leverantör               2023          12
#> 10 Zooplankton       Klar            Leverantör               2023          12
#> # ℹ 453 more rows
#> # ℹ 104 more variables: station_name <chr>, reported_station_name <chr>,
#> #   sample_location_id <dbl>, station_id <dbl>, sample_project_name_sv <chr>,
#> #   sample_orderer_name_sv <chr>, platform_code <chr>, visit_id <dbl>,
#> #   expedition_id <dbl>, shark_sample_id_md5 <chr>, sample_date <date>,
#> #   sample_time <time>, sample_latitude_dm <chr>, sample_longitude_dm <chr>,
#> #   sample_latitude_dd <dbl>, sample_longitude_dd <dbl>, …
# }