Retrieve Species Larval Abundance Data from Database

Source: R/functions.R

Queries species, larva, net, tow, and site tables with temporal filters, computing standardized tally values. Returns a dbplyr lazy table for efficient downstream processing.

get_sp(sp_name, qtr, date_range, ck_children = T)

Arguments

sp_name

Character vector of species names (format: "Common Name (Scientific Name)")

qtr

Numeric vector of quarters to include (1-4)

date_range

Date vector of length 2 (start date, end date)

ck_children

Boolean (TRUE or FALSE) whether to include taxonomic children

Value

dbplyr lazy table with columns:

  • name - species name (common + scientific)

  • tally - raw larval count

  • std_tally - standardized tally (adjusted for haul factor and sorting proportion)

  • time_start - tow start datetime

  • longitude, latitude - spatial coordinates

  • quarter - quarter (1-4)

  • hex_h3res* - H3 hexagon indices at multiple resolutions

Details

The standardized tally accounts for differences in haul efficiency and subsampling: std_tally = std_haul_factor * tally / prop_sorted. Only records with non-NA tally values are returned.

See also

prep_sp_hex for spatial aggregation

prep_ts_sp for temporal aggregation

Examples

if (FALSE) { # \dontrun{
# retrieve anchovy data for all quarters 2010-2020
df_sp <- get_sp(
  sp_name    = "Anchovy (Engraulis mordax)",
  qtr        = 1:4,
  date_range = as.Date(c("2010-01-01", "2020-12-31"))
)
df_sp |> collect()
} # }