R Code to Perform Multiple Checks on MEDITS Survey Data


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Documentation for package ‘RoMEBS’ version 0.2.02

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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_area Check if TX files have the same area
check_associations_category_TL Check corretness of TL categories
check_bridles_length check of bridles length correctness
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_nb_TE_rapa Consistency of number of individuals sampled for weight and ageing in rapa whelk TE table
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 Function checking if, in case of sub-sampling in TC, the Total number and the number per sex in TB is raised correctly
check_rubincode Function checking the correctness of species MEDITS code and faunistic category according to TM reference list
check_sex_inversion Function to verify the consistency of sex information about hermaphrodite species.
check_smallest_mature Function to verify the consistency of maturity information respect to the smallest mature individual observed in literature.
check_spawning_period Function to check the consistency of the maturity stages according 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_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 Function that checks if number of individuals and total weight collected in the haul are consistent.
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
cood.conv Coordinates conversion tool
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
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
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
MedSea Shapefile of Mediterranean and Black Sea area
printError Management of the error in logfile.
RoMEBS R code to perform multiple checks on MEDITS-like Survey data (TA, TB, TC, TE and TL files)
RoMEBS.wizard Wizard function for RoMEBS
RSufi_files Function to concatenate the R-sufi files of the different years.
scheme_individual_data Summary of the individual data collected by species
Stratification Stratification
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
TL TL
TM_list TM list