Extract numbers or biomass 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 total numbers and weight by haul, 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 number 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 weight:

surv <- add_total_weight_by_haul(surv)

This adds HaulWgt to the HH table, containing the total estimated weight by haul. As for abundance, custom length-group summaries can be generated when length_cuts is used.