Calculate zooplankton dry weight from mean length

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 taxon	AphiaID	Development stage	A	B	Reference
Acartia bifilosa	345919	all stages except nauplii	7.71	2.96	Hay 1991(1)
Acartia clausi	149755	all stages except nauplii	7.71	2.96	Hay 1991(1)
Acartia longiremis	346037	all stages except nauplii	7.71	2.96	Hay 1991(1)
Acartia	104108	all stages except nauplii	7.71	2.96	Hay 1991(1)
Calanus finmarchicus	104464	all stages except nauplii	6.88	2.69	Hay 1991(1)
Calanus finmarchicus	104464	nauplii	5.38	2.03	Hygum et al. 2000(2)
Centropages hamatus	104496	all stages except nauplii	6.09	2.45	Hay 1991(1)
Centropages	104159	all stages except nauplii	6.10	2.45	Hay 1991(1)
Centropages typicus	104499	all stages except nauplii	6.10	2.45	Hay 1991(1)
Clausocalanus	104161	all stages except nauplii	8.90	3.35	Hay et al. 1988(3)
Corycaeus	128634	all stages except nauplii	6.07	2.63	Satapoomin 1999(4)
Cyclopoida	106415	all stages except nauplii	6.72	2.71	Uye 1982(5)
Evadne nordmanni	106273	all stages except nauplii	5.79	2.80	Hernroth 1985(6)
Fritillaria	103358	all stages except nauplii	4.51	2.66	Paffenhofer 1976(10)
Harpacticoid copepod	1102	all stages except nauplii	7.24	2.89	Uye 1982(5)
copepod nauplii *all copepod species	1080	nauplii	5.48	2.23	Hay 1991(1)
Metridia	104190	all stages except nauplii	7.12	2.68	Hirche and Mumm 1992(9)
Microcalanus	104164	all stages except nauplii	7.86	2.91	Hay 1991(1)
Microsetella	115341	all stages except nauplii	7.66	2.88	Satapoomin 1999(4)
Oikopleura dioica	103407	all stages except nauplii	4.51	2.66	Paffenhofer 1976(10)
Oithona	106485	nauplii	2.68	2.14	Almeda et al. 2010(8)
Oithona similis	106656	all stages except nauplii	6.72	2.71	Uye 1982(5)
Oncaea	128690	all stages except nauplii	6.28	2.63	Satapoomin 1999(4)
Paracalanus parvus	104685	all stages except nauplii	6.16	2.45	Hay 1991(1)
Penilia avirostris	106272	all stages except nauplii	4.95	2.38	Atienza et al. 2006(7)
Podon leukarti	106277	all stages except nauplii	7.52	3.02	Uye 1982(5)
Podon polyphemoides	159919	all stages except nauplii	6.60	2.75	Uye 1982(5)
Pseudocalanus	104165	all stages except nauplii	8.37	3.00	Hay et al. 1988(3)
Temora longicornis	104878	all stages except nauplii	8.37	3.00	Hay et al. 1988(3)

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. doi: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. doi: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. doi: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. doi: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. doi: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. doi: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. doi: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. doi: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>, …
# }