Extract abundance or biomass per unit effort for a single species

library(DATRASextra)

# select survey

survey <- "NS-IBTS"

# create temporary directory

tmp <- file.path(tempdir(), "DATRASextra")

dir.create(tmp, recursive = TRUE, showWarnings = FALSE)

# download data

download_datras(
  surveys = survey,
  years = 2021,
  dir = tmp
)

# read in
surv0 <- read_datras(file.path(tmp, survey))

# clean data
surv <- clean_datras(surv0)

# subset for your species
surv <- subset(surv, Valid_Aphia == "126822") # Horse mackerel

To calculate abundance or biomass per unit effort, the information in the HL table first needs to be raised to the haul level. A convenient first step is to add numbers-at-length:

surv <- add_numbers_at_length(surv)

This adds a matrix N to the HH table, containing the estimated numbers in each length class for each haul. The length classes can be modified with the cm_breaks or by arguments. The total abundance by haul can then be obtained by summing over length classes:

surv <- add_total_numbers_by_haul(surv)

By default, this adds a single column HaulN to the HH table. More generally, custom bins can be specified via length_cuts. In that case, the result may contain separate totals for broader user-defined length groups.

If species-specific length and weight information are available in CA, or suitable length-weight relationships are available in the species_info table, the numbers can also be converted to biomass:

surv <- add_total_weight_by_haul(surv)

This adds HaulWgt to the HH table, containing the total estimated biomass by haul. To standardize abundance and biomass by swept area, a swept-area estimate can be added to each haul:

surv <- add_swept_area_simple(surv)

This adds swept-area estimates to the HH table based on haul distance and gear width information. When gear information is missing, values are imputed automatically (see ?add_swept_area_simple). Abundance per unit effort and biomass per unit effort can then be calculated by dividing haul-level totals by swept area:

# convert swept area from m2 to km2
surv[['HH']]$SweptArea_km2 <- surv$HH$SweptArea / 1e6

# abundance per km2
surv[['HH']]$CPUE_N <- surv$HH$HaulN / surv$HH$SweptArea_km2

# biomass per km2
surv[['HH']]$CPUE_W <- surv$HH$HaulWgt / surv$HH$SweptArea_km2

The resulting variables contain standardized density estimates expressed as:

• numbers per \(km^2\) (CPUE_N)

• biomass per \(km^2\) (CPUE_W)