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Read ICES DATRAS survey data from zipped exchange files

Source: R/read_write.R
read_datras.Rd

Read one or more ICES DATRAS exchange files, or all zipped exchange files in one or more directories, into a single datras_raw / DATRASraw object.

Usage

read_datras(
  paths,
  years = NULL,
  recursive = TRUE,
  min_file_size = 10000,
  prune = FALSE,
  verbose = TRUE
)

Arguments

paths

A character vector of file paths or directory paths. Paths can point either to individual DATRAS .zip exchange files or to directories containing such files.

years

Optional integer vector of years to read. When supplied and paths contains directories, only zip files matching those years are read.

recursive

logical. Should the listing recurse into directories? (Default: TRUE).

min_file_size

Minimum file size in bytes. Files smaller than this threshold are excluded because they are likely incomplete or invalid and may cause errors when being read. Defaults to 1e4.

prune

Logical. If TRUE, only core columns are retained using prune_datras() before combining files. This can substantially reduce memory use when reading many files.

verbose

Logical. If TRUE (default), progress messages are printed.

Value

A combined DATRAS survey object with classes datras_raw and DATRASraw.

Details

The function can read:

  • one or more individual .zip files,

  • one or more directories containing .zip files,

  • optionally only files matching selected years.

Small zip files can be excluded using min_file_size, as unusually small files are often incomplete or corrupted and may fail in the underlying DATRAS reader functions.

DATRAS zip archives are typically much larger than a few kilobytes, so very small files are often suspicious and may represent failed downloads or damaged archives.

Reading a large number of DATRAS files into R can require substantial memory, especially when combining multiple surveys or many years. Setting prune = TRUE can reduce memory use by removing non-essential columns before merging files.

If you need a different set of retained columns than provided by prune_datras(), you may wish to apply your own pruning function after reading or adapt the pruning code.

See also

download_datras(), prune_datras()

Examples

if (FALSE) { # \dontrun{
## Read all zip files from a survey folder
x <- read_datras("data/NS-IBTS")

## Read selected years from a folder
x <- read_datras("data/NS-IBTS", years = 2018:2020)

## Read multiple zip files directly
files <- c("data/NS-IBTS/NS-IBTS_2020.zip",
           "data/NS-IBTS/NS-IBTS_2021.zip")
x <- read_datras(files)

## Read and prune to reduce memory use
x <- read_datras("data/NS-IBTS", prune = TRUE)
} # }