Calculate zooplankton dry weight from mean length — calc_zooplankton_dry

Calculates zooplankton dry weight from rows where parameter equals "Length (mean)" using taxa-specific coefficients from inst/extdata/Mesozooplankton_Kattegat_Skagerrak_taxa_and_biomass_calculations.xlsx.

Usage

calc_zooplankton_dry_weight(
  data,
  length_parameter = "Length (mean)",
  dry_weight_parameter = "Dry weight",
  append = 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".
append: Logical. If TRUE (default), append calculated dry-weight rows to data. If FALSE, return only the calculated dry-weight rows.
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" 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 adult coefficients, defined in the reference list as rows with missing Stadium (NA in the workbook).

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

Reference coefficient table

Reference taxon	AphiaID	Stadium	B	A	Reference
Acartia bifilosa	345919	adult	2.96	7.71	Hay 1991 (same as for A.clausi)
Acartia clausi	149755	adult	2.96	7.71	Hay 1991
Acartia longiremis	346037	adult	2.96	7.71	Hay 1991 (same as for A.clausi)
Acartia	104108	adult	2.96	7.71	Hay 1991 (same as for A.clausi)
Calanus finmarchicus	104464	adult	2.69	6.88	Hay 1991 (same as for C. helgolandicus)
Calanus finmarchicus	104464	NP	2.03	5.38	Hygum et al 2000
Centropages hamatus	104496	adult	2.45	6.09	Hay 1991
Centropages	104159	adult	2.45	6.10	Hay 1991
Centropages typicus	104499	adult	2.45	6.10	Hay 1991
Clausocalanus	104161	adult	3.35	8.90	Hay et al 1988
Corycaeus	128634	adult	2.63	6.07	Satapoomin 1999
Cyclopoida	106415	adult	2.71	6.72	Uye 1982 (Oithona)
Evadne nordmanni	106273	adult	2.80	5.79	Hernroth 1985
Fritillaria	103358	adult	2.66	4.51	Paffenhofer 1976 (same as for Oikopleura)
Harpacticoid copepod	1102	adult	2.89	7.24	Uye (equation "for all copepods")
copepod nauplii *all copepod species	1080	NP	2.23	5.48	Hay 1991 (same as for Pseudocalanus)
Metridia	104190	adult	2.68	7.12	Hirche & Mumm 1992
Microcalanus	104164	adult	2.91	7.86	Hay 1991 (same as for Temora, se Koski 2012)
Microsetella	115341	adult	2.88	7.66	Satapoomin 1999
Oikopleura dioica	103407	adult	2.66	4.51	Paffenhofer 1976
Oithona	106485	NP	2.14	2.68	Almeda et al 2010
Oithona similis	106656	adult	2.71	6.72	Uye 1982
Oncaea	128690	adult	2.63	6.28	Satapoomin 1999
Paracalanus parvus	104685	adult	2.45	6.16	Hay 1991
Penilia avirostris	106272	adult	2.38	4.95	Atienza et al 2006
Podon leukarti	106277	adult	3.02	7.52	Uye 1982
Podon polyphemoides	159919	adult	2.75	6.60	Uye 1982
Pseudocalanus	104165	adult	3.00	8.37	Hay et al 1988
Temora longicornis	104878	adult	3.00	8.37	Hay et al 1988

Examples

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(149755, 104464, 999999),
  dev_stage_code = c("AD", "NP", "NP")
)

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 0.129   149755 AD            
#> 2 Calanus finmarchicus Dry weight 0.307   104464 NP            
#> 3 Unknown taxon        Dry weight 0.272   999999 NP