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Check and summarize length distributions in a datras_raw object

Source: R/length.R
check_lengths.Rd

Create haul-by-length counts from the HL table of a datras_raw / DATRASraw object and inspect the resulting length distribution.

Usage

check_lengths(
  x,
  cm_breaks = NULL,
  by = get_accuracy_cm(x),
  length_percentile = 99.9999,
  plot = TRUE
)

Arguments

x

A datras_raw object.

cm_breaks

Numeric vector of break points for length classes in centimetres. If supplied, these are used directly to bin LngtCm.

by

Optional bin width in centimetres. If cm_breaks is not supplied, the bin width is determined from this argument or, if NULL, from the get_accuracy_cm() function.

length_percentile

Numeric percentile used to summarize the upper tail of the observed length distribution. Defaults to 99.9999.

plot

Logical. If TRUE (default), plot the length spectrum on raw and log count scales.

Value

A list with three elements:

  • N: a haul-by-length count matrix,

  • lPars: a data frame of summary statistics for the length distribution,

  • nAbove: a data frame with the number and percentage of observations above selected upper-length thresholds.

Details

The function bins fish lengths into user-defined or automatically derived length classes, constructs a haul-by-length count matrix, computes summary statistics of the overall length distribution, and optionally plots the observed spectrum on both raw and log scales.

Lengths are grouped into classes using cut() and counts are aggregated by haul and length class.

In addition to the haul-by-length matrix, the function calculates summary statistics for the pooled length distribution, including:

  • observed minimum length,

  • weighted mean length,

  • median length,

  • observed maximum length,

  • empirical maximum length from species_info, if available,

  • a user-defined upper percentile of the length distribution.

The function also reports the number and percentage of observations above the empirical maximum length and above the selected percentile threshold.

If multiple species are present in the HL table, the combined spectrum across all species is used and a warning is issued.

See also

check_weights()

Examples

if (FALSE) { # \dontrun{
res <- check_lengths(x)

## Use custom length bins
res <- check_lengths(x, cm_breaks = seq(0, 100, by = 1))

## Use an automatically generated spectrum with 0.5 cm bins
res <- check_lengths(x, by = 0.5)
} # }