R: Multiple Checks on MEDITS Trawl Survey Data

# Multiple Checks on MEDITS Trawl Survey Data

## Documentation for package ‘RoME’ version 0.2.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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