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RoME (version 0.2.4)

Multiple Checks on MEDITS Trawl Survey Data

Description

Provides quality checks for MEDITS (International Bottom Trawl Survey in the Mediterranean) trawl survey exchange data tables (TA (Haul data), TB (Catch data), TC (Biological data), TE (Biological individual data), TL (Litter data)). The main function RoME() calls all check functions in a defined sequence to perform a complete quality control of TX (Generic exchange data) data, including header validation, controlled-vocabulary checks, cross-table consistency tests, and biological plausibility checks. No automatic correction is applied: the package detects errors, warns the user, and specifies the type of error to ease data correction. Checks can be run simultaneously on multi-year datasets. An embedded 'shiny' application is also provided via run_RoME_app(). References describing the methods: MEDITS Working Group (2017).

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Version

Install

install.packages('RoME')

Monthly Downloads

257

Version

0.2.4

License

GPL-3

Maintainer

Walter Zupa

Last Published

July 23rd, 2026

Functions in RoME (0.2.4)

Check if TX files have the same area

check_associations_category_TL

Check correctness of TL categories

TL association between categories and sub-categories

check_identical_records

Check of identical records in TX tables

check_haul_species_TCTB

Check species of TC in TB

Check of "WING_OPENING" and "VERTICAL_OPENING" fields

check_individual_weightTC

Check of observed and estimated total weight in the haul

check_length_class_codeTC

Consistency check of LENGTH_CLASS

Consistency of number of individuals sampled for weight and ageing in TE

Check of consistency in number per sex set "not mandatory" in TB

check_species_TBTC

Function checking if all the target species in the catch data table (TB) are in Biological data table (TC)

Check total number of individuals in TB

check_mat_stages

Consistency of maturity stages

check_numeric_range

Check of the values range in specific fields

check_position_in_Med

Check of haul position in Mediterranean Sea

check_nb_per_sexTC

Consistency check of number of individuals

check_dictionary

Check of the dictionary of specific fields

Comprehensive consistency checks between MEDITS TB and TC files

check_step_length_distr

The function verifies that in TC the length measures are reported with the correct precision.

Plot of haul positions

check_hauls_TLTA

Check presence of TL hauls in TA

check_individual_weightTE

Consistency of individual weights (according to length-weight relationship)

check_hauls_TATB

Check of TA hauls in TB

Check of distance consistency

check_no_empty_fields

Check empty fields in TA, TB, TC, TE and TL

check_hauls_TATL

Check presence of TA hauls in TL

check_smallest_mature

Check for mature individuals below literature thresholds in TC data

Check of length classes in TC

check_rubincode

Function checking the correctness of species MEDITS code and faunistic category according to TM reference list

check_quasiidentical_records

Function checking the presence of quasi-identical records.

Check start and end quadrant for each haul

check_spawning_period

Check consistency of maturity stages with respect to the spawning period

check_hauls_TBTA

Check of TB hauls in TA

check_consistencyTA_duration

Consistency check of hauls duration in TA

Consistency check of TYPE_OF_FILE field

Function that checks the consistency between start and end depth according to the stratum.

check_stratum_code

Function to check the correct codification of the strata in haul data table (TA).

check_temperature

Function to check the consistency of the temperature data stored in haul data table (TA).

check_unique_valid_haul

Function checking that among hauls with the same code, only one must be valid.

check_subsampling

Function to warn the user about the presence of subsamples <0.1 of the total catch.

Function to create R-sufi file containing haul data.

headers.conversion

Headers conversion for MEDITS tables

check_swept_area

Check Swept Area Calculation and Plot

Summary table of the errors

Class of fields

Function for qualitative checks of shooting depth, warp length and wing opening in Haul data table (TA).

Check consistency between total weight and number of individuals in MEDITS TB data.

Consistency check of YEAR field

Run the RoME Shiny application

Function to create the R-sufi file taille.

Estimation of haul distance

stratification_scheme

stratification_scheme

scheme_individual_data

Summary of the individual data collected by species

Table of maturity stages

Management of the error in logfile.

Management of the error in logfile.

Check of haul position on sea area

stratification_scheme_rapana

stratification_scheme_rapana

check_weight_tot_nb

Function to check if, when the weight is not null, also the number is not null.

Function to create the R-sufi file capt.

Function to create R-sufi file containing strata surface data.

allowed values for SHOOTING_TIME and HAULING_TIME

List of G1 and G2 species

Template biological data table (TC).

Template individual data table (TE).

Template haul data table (TA).

TL table template

Template catch data table (TB).

Maturity_parameters

Maturity parameters

Table of the Length-Weight parameters

Continuous Quality Checks on MEDITS Trawl Survey Data

Function to check the correctness of the headers.

List of GFCM Geographical subareas (GSAs)

Multiple Checks on MEDITS Trawl Survey Data

Conversion of MEDITS format coordinates in decimal degrees format

Function to concatenate the R-sufi files of the different years.

check_abundance

Box-plots of swept-area-standardised abundance indices

check_bridles_length

check of bridles length correctness

Check of length measurements for G1 and G2 species

check_consistencyTA_distance

Consistency check of distance in TA

DataTargetSpecies

Length and weight ranges for relevant species

Continuous Quality Checks on Black Sea trawl Survey Data

Check of field's class

check_0_fieldsTA

Checks the presence of 0 fields in TA

Check between start depth and end depth

Shapefile of Mediterranean and Black Sea area

check_date_haul

Check of date consistency

Function to verify the consistency between individual data table (TE) and biological data table (TC) respect to number of individuals.