check_smallest_mature: Check for mature individuals below literature thresholds in...

In RoME: Multiple Checks on MEDITS Trawl Survey Data

Check for mature individuals below literature thresholds in TC data

Description

This function verifies the consistency of maturity information in TC data by detecting mature individuals whose lengths are smaller than the smallest mature size reported in the literature for each species and sex. Detected inconsistencies are saved in a CSV file for traceability and further review, while a concise summary is written in the log file.

Usage

check_smallest_mature(ResultData, year, MaturityParameters, TargetSpecies,
  wd, suffix)

Arguments

ResultData	Biological data table (TC) formatted according to the MEDITS protocol. This table should contain length-class, sex, and maturity stage information for all recorded hauls.
year	Reference year for the analysis. Only records from the specified year are processed.
MaturityParameters	Table with bibliographic parameters describing the smallest mature individual observed for each species and sex, and the related reference sources.
TargetSpecies	Table containing information on target species, including taxonomic codes and faunistic categories used to identify relevant maturity checks.
wd	Working directory where the function writes log files and CSV outputs.
suffix	String appended to filenames of log and CSV files to distinguish outputs from different runs.

Details

The function processes the TC data for the selected year and examines each species listed in the MaturityParameters table. For each mature individual (i.e.\ not coded as immature stages), it checks whether the length class is smaller than the bibliographic minimum threshold, allowing a 10% tolerance buffer to account for biological variability. If such individuals are detected, they are recorded in a CSV file including:

• GSA

• Year

• Species

• Sex

• Haul number

• Length class (mm)

• Threshold applied (mm)

• Literature threshold (mm)

• Bibliographic reference

• Type of file

• Type of warning

A concise message summarizing how many records were written to the CSV is printed to the log file (.dat). If no inconsistencies are found, the function logs a message indicating that all maturity stages are above bibliographic thresholds.

The check uses the updated DataTargetSpecies table for consistency with current species definitions and codes.

Value

The function always returns TRUE. Its purpose is to perform quality checks and log potential issues, but it does not interrupt the execution of other routines in the RoME package.

Author(s)

W. Zupa, I. Bitetto

References

Anonymus. 2017. MEDITS-Handbook. Version n. 9. MEDITS Working Group. 106 pp.https://www.sibm.it/MEDITS%202011/principaledownload.htm

Examples

  wd <- tempdir()
  suffix <- "2020-03-05_time_h17m44s55"
  TC <- RoME::TC
  year <- 2007
  check_smallest_mature(
    TC,
    year,
    RoME::Maturity_parameters,
    RoME::DataTargetSpecies,
    wd,
    suffix
  )

RoME documentation built on April 24, 2026, 1:07 a.m.