Quality check functions for RDBFIS

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Documentation for package ‘RDBqc’ version 0.0.17.25

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A C D F G L M R S T

-- A --

aer_catch AER catch table
ALK_tab_example ALK table in MED&BS datacall format

-- C --

Catch_tab_example Catch table in MED&BS datacall format
catfau_check catfau_check in GFCM datacall format
check_age_MEDBS_AR Cross check of number of age measurements between MED&BS ALK table and AR Table 2.2
check_cs_header Headers check for CS table
check_EF_FDI_A Check empty fields in FDI A table
check_EF_FDI_G Check empty fields in FDI G table
check_EF_FDI_H Check empty fields in FDI H table
check_EF_FDI_I Check empty fields in FDI I table
check_EF_FDI_J Check empty fields in FDI J table
check_EF_taskII2 Check empty fields in GFCM Task II.2 table
check_EF_taskIII Check empty fields in GFCM Task III table
check_EF_taskVII2 Check empty fields in GFCM Task VII.2 table
check_EF_TaskVII31 Check empty fields in GFCM Task VII.3.1 table
check_EF_TaskVII32 Check empty fields in GFCM Task VII.3.2 table
check_gfcm_header Headers check for GFCM tables
check_l50_TaskVII.3.1 Consistency of L50 values in Task VII.3.1 table
check_ldf_TaskVII.2 Consistency of length frequency distributions
check_lengths_MEDBS_AR Cross check of number of lengths between MED&BS catch table and AR Table 2.1
check_lmat_TaskVII.3.2 Plot of the maturity stages per length for each sex and species
check_lw_TaskVII.2 Plot of the length-weight relationship
check_lw_TaskVII.3.2 Plot of the length-weight relationship by sex
check_maturity_MEDBS_AR Cross check of number of maturity measurements between MED&BS ML table and AR Table 2.2
check_minmaxl50_TaskVII.3.1 Comparison between min/max L50 observed for each species and sex with theoretical values
check_minmaxl_TaskVII.2 Comparison between min/max observed for each species with theoretical values
check_n_trips_MEDBS_AR Cross check of number of trips between MED&BS catch table and AR Table 2.5
check_presence_taskII2 Check of missing combination GSA/Fleet segment per year
check_RD_FDI_A Check duplicated records in FDI A table
check_RD_FDI_G Check duplicated records in FDI G table
check_RD_FDI_H Check duplicated records in FDI H table
check_RD_FDI_I Check duplicated records in FDI I table
check_RD_FDI_J Check duplicated records in FDI J table
check_RD_taskII2 Check duplicated records in GFCM Task II.2 table
check_RD_taskIII Check duplicated records in GFCM Task III table
check_RD_taskVII2 Check duplicated records in GFCM Task VII.2 table
check_RD_taskVII31 Check duplicated records in GFCM Task VII.3.1 table
check_RD_TaskVII32 Check duplicated records in GFCM Task VII.3.2 table
check_species_catfau_TaskVII.3.2 Check mismatching species/Catfau and Sex per maturity stages for Task VII.3.2 table
Check_Tot_Disc Comparing total discards in weight between MEDBS and FDI EU Data Calls
Check_Tot_Disc_gear Comparing total discards in weight between MEDBS and FDI EU Data Calls by Country, GSA, Species and Gear
Check_Tot_Disc_gear_Q Comparing total discards in weight between MEDBS and FDI EU Data Calls by Country, GSA, Species and Gear
Check_Tot_Disc_metier Comparing total discards in weight between MEDBS and FDI EU Data Calls by Country, GSA, Species and Metier
Check_Tot_Land Comparing total landings in weight between MEDBS and FDI EU Data Calls
Check_Tot_Land2 Comparing total landings in weight between MEDBS, FDI and AER EU Data Calls
Check_Tot_Land3 Comparing total landings in weight between MEDBS, FDI and AER EU Data Calls
Check_Tot_Land_gear Comparing total landings in weight between MEDBS and FDI EU Data Calls by Country, GSA, Species and Gear
Check_Tot_Land_gear_Q Comparing total landings in weight between MEDBS and FDI EU Data Calls by Country, GSA, Species and Gear
Check_Tot_Land_metier Comparing total landings in weight between MEDBS and FDI EU Data Calls by Country, GSA, Species and Metier
check_weights_MEDBS_AR Cross check of number of weight measurements between MED&BS GP table and AR Table 2.2
circabc Ports coordinates according to codification CIRCABC
combination_taskII2 combination_taskII2 in GFCM datacall format

-- D --

data_ex RCG CS example
data_exampleCL RCG CL example
Discard_tab_example Discard table in MED&BS datacall format

-- F --

FDI_AER_land_landvalue Cross check of landings or landings' value between the FDI and AER databases
fdi_a_catch fdi_a_catch in FDI DGMAREMED&BS datacall format
FDI_checks_spatial_HI check NA values in spatial columns of both table H and I
FDI_check_coord Compatibility of the geographical coordinates with rectangle type
FDI_coverage Coverage of data by GSA and year (reporting the number of records)
FDI_cov_tableA Check number of record in FDI A table
FDI_cov_tableG Check FDI G table coverage
FDI_cov_tableJ Check number of record in FDI J table
FDI_cross_checks_AG Cross check between FDI tables A and G
FDI_cross_checks_AH Cross check between FDI tables A and H
FDI_cross_checks_IG Cross check between FDI tables I and G
FDI_cross_checks_JG Cross check between FDI tables J and G
FDI_disc_coverage Coverage of FDI discard data
FDI_fishdays_cov Coverage comparison of totfishdays between FDI tables G and I
fdi_g_effort fdi_g_effort in FDI DGMAREMED&BS datacall format
fdi_h_spatial_land fdi_h_spatial_land in FDI DGMAREMED&BS datacall format
fdi_h_spatial_landings fdi_h_spatial_landings in FDI DGMAREMED&BS datacall format
fdi_i_spatial_effort fdi_i_spatial_effort in FDI DGMAREMED&BS datacall format
fdi_j_capacity fdi_j_capacity in FDI DGMAREMED&BS datacall format
FDI_landweight_cov Coverage of weight of landings in FDI table A and H
FDI_prices_cov Check prices trend in FDI A table
FDI_prices_not_null Check of species value
FDI_vessel_lenth Check of vessel lenght in FDI table J
FDI_vessel_numbers Check number of vessels in FDI table J and G

-- G --

GFCM_check_headers Check headers of GFCM tables
GFCM_cov_II2 Check coverage of GFCM task II.2 table
GFCM_cov_task_iii Check number of individuals in GFCM Task III table
GP_tab_example GP table in MED&BS datacall format
GSAlist GSAlist table

-- L --

Landing_tab_example Landing table in MED&BS datacall format

-- M --

MA_tab_example MA table in MED&BS datacall format
MEDBSSP MEDBSSP table
MEDBS_ALK Plot of Age-Length Keys
MEDBS_Catch_coverage Check the coverage of Catch table
MEDBS_check_disaggregated Check for disaggregated data rows in landings, discards and catch tables
MEDBS_check_duplicates Check for duplicated data rows in MED & BS tables
MEDBS_check_missing_years Check for missing years in MED & BS tables
MEDBS_comp_disc_YQ Comparison between discards in weight by quarter and -1
MEDBS_comp_disc_YQ_fishery Comparison between discards in weight by quarter, quarter -1 and by fishery
MEDBS_comp_land_Q_VL Comparison between landings in weight by quarter accounting for vessel length
MEDBS_comp_land_Q_VL_fishery Comparison between landings in weight by quarter and fishery, accounting for vessel length
MEDBS_comp_land_YQ Comparison between landings in weight by quarter and -1
MEDBS_comp_land_YQ_fishery Comparison between landings in weight by quarter, quarter -1 and by fishery
MEDBS_discard_coverage Check the coverage of discard data
MEDBS_disc_mean_weight Check of mean discard weight aggregations by year, gear and fishery
MEDBS_GP_check Check of growth parameters table
MEDBS_ks Kolmogorov-Smirnov test
MEDBS_Landing_coverage Check the coverage of Landing table
MEDBS_land_mean_weight Mean weight by year, gear and fishery aggregation
MEDBS_lengthclass_0 Checks length classes numbers with zeros in landings and discards
MEDBS_length_ind Main length size indicators
MEDBS_LFD LFD of MED & BS landing and discard data
MEDBS_LW_check Check LW parameters in GP table
MEDBS_MA_check Check of MA_tab (maturity at age) table
MEDBS_ML_check Check of ML_tab (maturity at length) table
MEDBS_plot_discard_ts Plot of total discards
MEDBS_plot_disc_vol Plot of total discards by gear and fishery
MEDBS_plot_landing_ts Plot of total landing time series
MEDBS_plot_land_vol Plot of total landing by gear and fishery
MEDBS_SA_check Check of SA_tab (sex ratio at age) table
MEDBS_SL_check Check of SL_tab (sex ratio at length) table
MEDBS_SOP check of the sum of products
MEDBS_weight_0 Check of weights 0 in landings and discards
MEDBS_weight_minus1 Check weights -1 in landings
MEDBS_yr_missing_length Years with missing length distributions
minmaxLtaskVII2 minmaxLtaskVII2 in GFCM datacall format
minmaxLtaskVII31 minmaxLtaskVII31 in GFCM datacall format
ML_tab_example ML table in MED&BS datacall format

-- R --

RCG_check_AL Check consistency of age-length relationship
RCG_check_CL Quality checks on CL RCG table
RCG_check_LFD Consistency check of LFDs
RCG_check_LFD_comm_cat Check consistency of LFD by year and commercial category
RCG_check_loc Check trip location
RCG_check_lw Consistency check of length-weight relationship
RCG_check_mat Check consistency sex and maturity stage
RCG_check_mat_ogive check_mat_ogive
RCG_summarize_ind_meas Number of individual by trip for which biological data have been collected (length, sex, maturity, weight and age)
RCG_summarize_trips summarizing the number of trips/hauls monitored by year by port, metier, sampling method;

-- S --

SA_tab_example SA table in MED&BS datacall format
sex_mat sex_mat in GFCM datacall format
SL_tab_example SL table in MED&BS datacall format
SSPP SSPP table

-- T --

task_ii2 task_ii2 in GFCM DCRF datacall format
task_iii task_iii in GFCM DCRF datacall format
task_vii2 task_vii2 in GFCM DCRF datacall format
task_vii31 task_vii31 in GFCM datacall format
task_vii32 task_vii32 in GFCM DCRF datacall format