Add total haul biomass to HH

Calculate total biomass by haul and add it to the HH component of a datras_raw / DATRASraw object.

Usage

add_total_weight_by_haul(
  x,
  max_length = NULL,
  max_weight = NULL,
  plus_group = FALSE,
  lw_source = c("lookup", "ca"),
  lw_pars = NULL,
  length_cuts = NULL,
  per_minute = FALSE
)

Arguments

x

A datras_raw object.

max_length

Optional numeric value giving the maximum length in centimetres to retain when fitting the length-weight relationship. Observations above this value are excluded.

max_weight

Optional numeric value giving the maximum individual weight in grams to retain when fitting the length-weight relationship. Observations above this value are excluded.

plus_group

Logical. If TRUE, all fish at or above the largest length class are accumulated into that class. Passed to add_weight_at_length().

lw_source

Character string specifying the source of length-weight parameters. One of "ca" or "lookup".

lw_pars

Optional custom length-weight parameters passed to add_weight_at_length(). See that function for the accepted forms.

length_cuts

Optional numeric vector of break points for aggregating the original length classes into coarser bins. Must be strictly increasing.

per_minute

Logical. If TRUE, add HaulWgtPerMin, calculated as HaulWgt divided by haul duration in minutes. If FALSE, only HaulWgt is added.

Value

A datras_raw object with HaulWgt added to HH. If per_minute = TRUE, HaulWgtPerMin is also added.

Details

Optionally, total biomass can be standardized by haul duration and returned as biomass per minute. Length classes can also be aggregated into coarser bins via length_cuts.

If weight-at-length information is not already present, the function first calls add_weight_at_length() to create x[["HH"]][["Wgt"]].

Weight-at-length is calculated as: $$ W = a \times L^b $$

Total biomass for each haul is calculated by summing estimated weight-at-length across length classes and is stored in x[["HH"]][["HaulWgt"]].

If length_cuts is supplied, HaulWgt is a matrix with one column per aggregated length bin. Otherwise, HaulWgt is a vector with one value per haul.

If per_minute = TRUE, the function also adds x[["HH"]][["HaulWgtPerMin"]], calculated by dividing HaulWgt by HaulDur. If HaulWgt is a matrix, each row is divided by the corresponding haul duration.

See also

add_weight_at_length()

Examples

## Add numbers at length
dab <- add_numbers_at_length(dab)
#> Warning: Mixed accuracies found in var[[3]]$LngtCode - worst chosen: 1 cm
#> Warning: NAs found in var[[3]]$LngtCode - assumed to be 1 cm

## Add total haul biomass
x <- add_total_weight_by_haul(dab)

## Add total haul biomass and biomass per minute
x <- add_total_weight_by_haul(dab, per_minute = TRUE)

## Use length-weight parameters from the species_info table
x <- add_total_weight_by_haul(dab, lw_source = "lookup")