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Prune a datras_raw object to selected columns

Source: R/clean_prune.R
prune_datras.Rd

Reduce a datras_raw / DATRASraw object to a smaller set of columns in the HH, HL, and CA tables.

Usage

prune_datras(
  x,
  keep = NULL,
  add = NULL,
  drop = NULL,
  do_fishglob = FALSE,
  warn_missing = TRUE
)

Arguments

x

A datras_raw object.

keep

Optional named list of columns to keep. List names should be HH, HL, and/or CA. If supplied, these columns replace the default columns for the named table(s).

add

Optional named list of columns to add to the default columns. List names should be HH, HL, and/or CA.

drop

Optional named list of columns to remove from the selected columns. List names should be HH, HL, and/or CA.

do_fishglob

Logical. If TRUE, apply prune_fishglob() instead of the standard DATRAS pruning rules.

warn_missing

Logical. If TRUE, warn when requested columns are not present in the corresponding table.

Value

A pruned datras_raw object.

Details

This is mainly intended to reduce memory use when working with large DATRAS data sets, while still allowing users to modify which columns are retained.

If do_fishglob = TRUE, pruning is delegated to prune_fishglob().

By default, the function keeps a predefined set of core columns in each of the HH, HL, and CA tables. These defaults are intended to retain the most commonly used haul metadata, length-frequency data, and biological sampling information.

The default columns can be inspected with list_prune_datras_defaults(). The available columns in a specific object can be inspected with list_prune_datras_available().

Column selection can be modified in three ways:

  • keep replaces the default columns for the named table(s),

  • add adds columns to the default or selected columns,

  • drop removes columns from the default or selected columns.

Columns listed in keep, add, or drop for tables not present in x are ignored. Requested columns that are not present in a table are ignored, with an optional warning controlled by warn_missing.

See also

list_prune_datras_defaults(), list_prune_datras_available(), clean_datras(), prune_fishglob()

Examples

if (FALSE) { # \dontrun{
## Inspect default columns retained by prune_datras()
list_prune_datras_defaults()

## Inspect available columns in a specific object
list_prune_datras_available(x)

## Reduce a DATRAS object to the default core columns
x_small <- prune_datras(x)

## Keep defaults, but retain additional environmental variables in HH
x_small <- prune_datras(
  x,
  add = list(HH = c("SurTemp", "BotTemp", "SurSal", "BotSal"))
)

## Keep defaults, but remove selected columns
x_small <- prune_datras(
  x,
  drop = list(HH = c("Roundfish", "timeOfYear"),
              HL = "Count")
)

## Fully override the columns retained for HH
x_small <- prune_datras(
  x,
  keep = list(HH = c("Survey", "Year", "haul.id", "lon", "lat", "Depth"))
)
} # }