Package: RoME 0.2.3

Walter Zupa

RoME: Multiple Checks on MEDITS Trawl Survey Data

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) <https://www.sibm.it/MEDITS%202011/principaledownload.htm>.

Authors:Walter Zupa [aut, cre], Isabella Bitetto [aut], Maria Teresa Spedicato [aut], Loredana Casciaro [rev], Cosmidano Neglia [rev]

RoME_0.2.3.tar.gz
RoME_0.2.3.tar.gz(r-4.7-any)RoME_0.2.3.tar.gz(r-4.6-any)
RoME_0.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RoME/json (API)

# Install 'RoME' in R:

install.packages('RoME', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

assTL - TL association between categories and sub-categories
classes - Class of fields
DataTargetSpecies - Length and weight ranges for relevant species
GSAs - List of GFCM Geographical subareas
list_g1_g2 - List of G1 and G2 species
LW - Table of the Length-Weight parameters
mat_stages - Table of maturity stages
Maturity_parameters - Maturity parameters
MedSea - Shapefile of Mediterranean and Black Sea area
stratification_scheme - Stratification_scheme
stratification_scheme_rapana - Stratification_scheme_rapana
TA - TA
TB - TB
TC - TC
TE - TE
templateTA - Template haul data table (TA).
templateTB - Template catch data table (TB).
templateTC - Template biological data table (TC).
templateTE - Template individual data table (TE).
templateTL - TL table template
time - Allowed values for SHOOTING_TIME and HAULING_TIME
TL - TL
TM_list - TM list

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.18 score 15 scripts 462 downloads 71 exports 76 dependencies

Last updated from:5675f8e691. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	165
source / vignettes	OK	188
linux-release-x86_64	OK	186
wasm-release	OK	136

Exports:check_0_fieldsTA check_abundance check_area check_associations_category_TL check_bridles_length check_class check_consistencyTA_distance check_consistencyTA_duration check_date_haul check_depth check_dictionary check_distance check_dm check_G1_G2 check_haul_species_TCTB check_hauls_TATB check_hauls_TATL check_hauls_TBTA check_hauls_TLTA check_identical_records check_individual_weightTC check_individual_weightTE check_length check_length_class_codeTC check_mat_stages check_nb_per_sexTC check_nb_TE check_nbtotTB check_nm_TB check_no_empty_fields check_numeric_range check_position check_position_in_Med check_quadrant check_quasiidentical_records check_raising check_rubincode check_smallest_mature check_spawning_period check_species_TBTC check_step_length_distr check_stratum check_stratum_code check_subsampling check_swept_area check_TE_TC check_temperature check_type check_unique_valid_haul check_weight check_weight_tot_nb check_year checkHeader create_catch create_haul create_length create_strata dd.distance error.table graphs_TA haul_at_sea headers.conversion MEDITS.to.dd printError printError_cc RoME RoMEBScc RoMEcc RSufi_files run_RoME_app scheme_individual_data

Dependencies:askpass base64enc bslib cachem class classInt cli commonmark cpp11 curl DBI digest dplyr e1071 farver fastmap fontawesome fs generics geosphere ggplot2 ggrepel glue gtable htmltools httpuv httr isoband jquerylib jsonlite KernSmooth labeling later lattice lifecycle magrittr maps MASS memoise mime openssl otel pillar pkgconfig promises proxy R6 rappdirs RColorBrewer Rcpp rlang rnaturalearth rnaturalearthdata s2 S7 sass scales sf shiny sourcetools sp stringi stringr sys terra tibble tidyselect timeDate units utf8 vctrs viridisLite withr wk xtable zip

RoME

Installation | References | Use of RoME function | Use of RoMEcc function | Graphical interface

Rendered fromRoME_vignettes.Rmdusingknitr::rmarkdown

Last update: 2026-04-23
Started: 2026-04-23

Help page	Topics
TL association between categories and sub-categories	assTL
Checks the presence of 0 fields in TA	check_0_fieldsTA
Box-plots of swept-area-standardised abundance indices	check_abundance
Check if TX files have the same area	check_area
Check correctness of TL categories	check_associations_category_TL
check of bridles length correctness	check_bridles_length
Check of field's class	check_class
Consistency check of distance in TA	check_consistencyTA_distance
Consistency check of hauls duration in TA	check_consistencyTA_duration
Check of date consistency	check_date_haul
Check between start depth and end depth	check_depth
Check of the dictionary of specific fields	check_dictionary
Check of distance consistency	check_distance
Check of "WING_OPENING" and "VERTICAL_OPENING" fields	check_dm
Check of length measurements for G1 and G2 species	check_G1_G2
Check species of TC in TB	check_haul_species_TCTB
Check of TA hauls in TB	check_hauls_TATB
Check presence of TA hauls in TL	check_hauls_TATL
Check of TB hauls in TA	check_hauls_TBTA
Check presence of TL hauls in TA	check_hauls_TLTA
Check of identical records in TX tables	check_identical_records
Check of observed and estimated total weight in the haul	check_individual_weightTC
Consistency of individual weights (according to length-weight relationship)	check_individual_weightTE
Check of length classes in TC	check_length
Consistency check of LENGTH_CLASS	check_length_class_codeTC
Consistency of maturity stages	check_mat_stages
Consistency check of number of individuals	check_nb_per_sexTC
Consistency of number of individuals sampled for weight and ageing in TE	check_nb_TE
Check total number of individuals in TB	check_nbtotTB
Check of consistency in number per sex set "not mandatory" in TB	check_nm_TB
Check empty fields in TA, TB, TC, TE and TL	check_no_empty_fields
Check of the values range in specific fields	check_numeric_range
Plot of haul positions	check_position
Check of haul position in Mediterranean Sea	check_position_in_Med
Check start and end quadrant for each haul	check_quadrant
Function checking the presence of quasi-identical records.	check_quasiidentical_records
Comprehensive consistency checks between MEDITS 'TB' and 'TC' files	check_raising
Function checking the correctness of species MEDITS code and faunistic category according to TM reference list	check_rubincode
Check for mature individuals below literature thresholds in TC data	check_smallest_mature
Check consistency of maturity stages with respect to the spawning period	check_spawning_period
Function checking if all the target species in the catch data table (TB) are in Biological data table (TC)	check_species_TBTC
The function verifies that in TC the length measures are reported with the correct precision.	check_step_length_distr
Function that checks the consistency between start and end depth according to the stratum.	check_stratum
Function to check the correct codification of the strata in haul data table (TA).	check_stratum_code
Function to warn the user about the presence of subsamples <0.1 of the total catch.	check_subsampling
Check Swept Area Calculation and Plot	check_swept_area
Function to verify the consistency between individual data table (TE) and biological data table (TC) respect to number of individuals.	check_TE_TC
Function to check the consistency of the temperature data stored in haul data table (TA).	check_temperature
Consistency check of TYPE_OF_FILE field	check_type
Function checking that among hauls with the same code, only one must be valid.	check_unique_valid_haul
Check consistency between total weight and number of individuals in MEDITS TB data.	check_weight
Function to check if, when the weight is not null, also the number is not null.	check_weight_tot_nb
Consistency check of YEAR field	check_year
Function to check the correctness of the headers.	checkHeader
Class of fields	classes
Function to create the R-sufi file capt.	create_catch
Function to create R-sufi file containing haul data.	create_haul
Function to create the R-sufi file taille.	create_length
Function to create R-sufi file containing strata surface data.	create_strata
Length and weight ranges for relevant species	DataTargetSpecies
Estimation of haul distance	dd.distance
Summary table of the errors	error.table
Function for qualitative checks of shooting depth, warp length and wing opening in Haul data table (TA).	graphs_TA
List of GFCM Geographical subareas (GSAs)	GSAs
Check of haul position on sea area	haul_at_sea
Headers conversion for MEDITS tables	headers.conversion
List of G1 and G2 species	list_g1_g2
Table of the Length-Weight parameters	LW
Table of maturity stages	mat_stages
Maturity parameters	Maturity_parameters
Conversion of MEDITS format coordinates in decimal degrees format	MEDITS.to.dd
Shapefile of Mediterranean and Black Sea area	MedSea
Management of the error in logfile.	printError
Management of the error in logfile.	printError_cc
Multiple Checks on MEDITS Trawl Survey Data	RoME
Continuous Quality Checks on Black Sea trawl Survey Data	RoMEBScc
Continuous Quality Checks on MEDITS Trawl Survey Data	RoMEcc
Function to concatenate the R-sufi files of the different years.	RSufi_files
Run the RoME Shiny application	run_RoME_app
Summary of the individual data collected by species	scheme_individual_data
stratification_scheme	stratification_scheme
stratification_scheme_rapana	stratification_scheme_rapana
TA	TA
TB	TB
TC	TC
TE	TE
Template haul data table (TA).	templateTA
Template catch data table (TB).	templateTB
Template biological data table (TC).	templateTC
Template individual data table (TE).	templateTE
TL table template	templateTL
allowed values for SHOOTING_TIME and HAULING_TIME	time
TL	TL
TM list	TM_list

Package: RoME 0.2.3

RoME: Multiple Checks on MEDITS Trawl Survey Data

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)