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  "Description": "Supports the standardized analysis of Mediterranean\nInternational Bottom Trawl Survey (MEDITS) data and the\ncalculation of biological indicators for selected species and\npopulation components. The package provides functions to\nestimate abundance and biomass indices, analyse size structure\nand length frequency distributions, derive sex ratio and\nmaturity related metrics, explore spatial patterns, and assess\ntemporal trends across surveys. Developed for integration\nwithin the Regional Database for Fisheries (RDBFIS) framework,\nit is intended to work on quality checked input data and to\nproduce reproducible outputs that can support monitoring,\ncomparative analyses among Geographical Sub-Areas (GSAs) and\ncountries, and fishery management.",
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      "fields": [
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        "COUNTRY",
        "CODE",
        "MIN_DEPTH",
        "MAX_DEPTH"
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      "rows": 7,
      "table": true,
      "tojson": true
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      "name": "stratification",
      "title": "stratification",
      "object": "stratification",
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        "CODE",
        "SURF",
        "UNIT"
      ],
      "rows": 276,
      "table": true,
      "tojson": true
    },
    {
      "name": "stratification_rapana",
      "title": "stratification (rapa whelk)",
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        "SURF",
        "UNIT"
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      "tojson": true
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      "name": "stratum_0_125",
      "title": "stratum_0_125",
      "object": "stratum_0_125",
      "class": [
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      ],
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      "tojson": false
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    {
      "name": "stratum_0_200",
      "title": "stratum_0_200",
      "object": "stratum_0_200",
      "class": [
        "PackedSpatVector"
      ],
      "fields": [],
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      "tojson": false
    },
    {
      "name": "stratum_0_35",
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      ],
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      "table": false,
      "tojson": false
    },
    {
      "name": "stratum_0_800",
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      ],
      "fields": [],
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      "tojson": false
    },
    {
      "name": "stratum_200_800",
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      "object": "stratum_200_800",
      "class": [
        "PackedSpatVector"
      ],
      "fields": [],
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      "tojson": false
    },
    {
      "name": "TA",
      "title": "TA table example",
      "object": "TA",
      "class": [
        "data.frame"
      ],
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        "TYPE_OF_FILE",
        "COUNTRY",
        "AREA",
        "VESSEL",
        "GEAR",
        "RIGGING",
        "DOORS",
        "YEAR",
        "MONTH",
        "DAY",
        "HAUL_NUMBER",
        "CODEND_CLOSING",
        "PART_OF_THE_CODEND",
        "SHOOTING_TIME",
        "SHOOTING_QUADRANT",
        "SHOOTING_LATITUDE",
        "SHOOTING_LONGITUDE",
        "SHOOTING_DEPTH",
        "HAULING_TIME",
        "HAULING_QUADRANT",
        "HAULING_LATITUDE",
        "HAULING_LONGITUDE",
        "HAULING_DEPTH",
        "HAUL_DURATION",
        "VALIDITY",
        "COURSE",
        "RECORDED_SPECIES",
        "DISTANCE",
        "VERTICAL_OPENING",
        "WING_OPENING",
        "GEOMETRICAL_PRECISION",
        "BRIDLES_LENGTH",
        "WARP_LENGTH",
        "WARP_DIAMETER",
        "HYDROLOGICAL_STATION",
        "OBSERVATIONS",
        "BOTTOM_TEMPERATURE_BEGINNING",
        "BOTTOM_TEMPERATURE_END",
        "MEASURING_SYSTEM",
        "NUMBER_OF_THE_STRATUM",
        "BOTTOM_SALINITY_BEGINNING",
        "BOTTOM_SALINITY_END",
        "MEASURING_SYSTEM_SALINITY"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "TA_cols",
      "title": "TA table headings",
      "object": "TA_cols",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "TB",
      "title": "TB table example",
      "object": "TB",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TYPE_OF_FILE",
        "COUNTRY",
        "AREA",
        "VESSEL",
        "YEAR",
        "MONTH",
        "DAY",
        "HAUL_NUMBER",
        "CODEND_CLOSING",
        "PART_OF_THE_CODEND",
        "FAUNISTIC_CATEGORY",
        "GENUS",
        "SPECIES",
        "NAME_OF_THE_REFERENCE_LIST",
        "TOTAL_WEIGHT_IN_THE_HAUL",
        "TOTAL_NUMBER_IN_THE_HAUL",
        "NB_OF_FEMALES",
        "NB_OF_MALES",
        "NB_OF_UNDETERMINED"
      ],
      "rows": 3059,
      "table": true,
      "tojson": true
    },
    {
      "name": "TB_cols",
      "title": "TB table headings",
      "object": "TB_cols",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "TC",
      "title": "TC table example",
      "object": "TC",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TYPE_OF_FILE",
        "COUNTRY",
        "AREA",
        "VESSEL",
        "YEAR",
        "MONTH",
        "DAY",
        "HAUL_NUMBER",
        "CODEND_CLOSING",
        "PART_OF_THE_CODEND",
        "FAUNISTIC_CATEGORY",
        "GENUS",
        "SPECIES",
        "LENGTH_CLASSES_CODE",
        "WEIGHT_OF_THE_FRACTION",
        "WEIGHT_OF_THE_SAMPLE_MEASURED",
        "SEX",
        "NO_OF_INDIVIDUAL_OF_THE_ABOVE_SEX_MEASURED",
        "LENGTH_CLASS",
        "MATURITY",
        "MATSUB",
        "NUMBER_OF_INDIVIDUALS_IN_THE_LENGTH_CLASS_AND_MATURITY_STAGE"
      ],
      "rows": 11185,
      "table": true,
      "tojson": true
    },
    {
      "name": "TC_cols",
      "title": "TC table headings",
      "object": "TC_cols",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aggregate_gsas",
      "title": "Aggregate MEDITS data across multiple GSAs",
      "topics": [
        "aggregate_gsas"
      ]
    },
    {
      "page": "ALK",
      "title": "ALK (Age Length Key)",
      "topics": [
        "ALK"
      ]
    },
    {
      "page": "ALKf",
      "title": "Estimation of ALK",
      "topics": [
        "ALKf"
      ]
    },
    {
      "page": "BioIndex",
      "title": "Main function to perform BioIndex analysis",
      "topics": [
        "BioIndex"
      ]
    },
    {
      "page": "bubble_plot_by_haul_indexes",
      "title": "Bubble plot of abundance and biomass indices by haul",
      "topics": [
        "bubble_plot_by_haul_indexes"
      ]
    },
    {
      "page": "bubbleplot_RS_by_hauls",
      "title": "Bubbleplot of abundance indices for recruits and spawners",
      "topics": [
        "bubbleplot_RS_by_hauls"
      ]
    },
    {
      "page": "centroidi",
      "title": "centroidi",
      "topics": [
        "centroidi"
      ]
    },
    {
      "page": "cgpmgrid",
      "title": "cgpmgrid",
      "topics": [
        "cgpmgrid"
      ]
    },
    {
      "page": "check_date_haul",
      "title": "Check date haul (RoME)",
      "topics": [
        "check_date_haul"
      ]
    },
    {
      "page": "check_dictionary",
      "title": "Check dictionary (RoME)",
      "topics": [
        "check_dictionary"
      ]
    },
    {
      "page": "check_hauls_TBTA",
      "title": "Check hauls TB TA (RoME)",
      "topics": [
        "check_hauls_TBTA"
      ]
    },
    {
      "page": "check_numeric_range",
      "title": "Check numeric range (RoME)",
      "topics": [
        "check_numeric_range"
      ]
    },
    {
      "page": "continent",
      "title": "continent",
      "topics": [
        "continent"
      ]
    },
    {
      "page": "convert_coordinates",
      "title": "MEDITS coordinates in decimal degrees",
      "topics": [
        "convert_coordinates"
      ]
    },
    {
      "page": "dd.distance",
      "title": "Estimate hauls distances (decimal degrees)",
      "topics": [
        "dd.distance"
      ]
    },
    {
      "page": "dd.to.MEDITS",
      "title": "Conversion of decimal degrees coordinates in MEDITS format",
      "topics": [
        "dd.to.MEDITS"
      ]
    },
    {
      "page": "hauls_position",
      "title": "Plot of hauls time series",
      "topics": [
        "hauls_position"
      ]
    },
    {
      "page": "index_on_grid",
      "title": "Generating maps of indexes",
      "topics": [
        "index_on_grid"
      ]
    },
    {
      "page": "index_recr",
      "title": "Estimation of abundance indices for recruits",
      "topics": [
        "index_recr"
      ]
    },
    {
      "page": "index_spawn",
      "title": "Estimation of abundance indices for spawners (females)",
      "topics": [
        "index_spawn"
      ]
    },
    {
      "page": "index_ts_F",
      "title": "Estimation of abundance indices for females",
      "topics": [
        "index_ts_F"
      ]
    },
    {
      "page": "index_ts_M",
      "title": "Estimation of abundance indices for males",
      "topics": [
        "index_ts_M"
      ]
    },
    {
      "page": "indices_ts",
      "title": "Estimation of abundance and biomass indices",
      "topics": [
        "indices_ts"
      ]
    },
    {
      "page": "IUT",
      "title": "Interception Union Tets",
      "topics": [
        "IUT"
      ]
    },
    {
      "page": "LFD",
      "title": "Length Frequency Distribution (LFD) Estimation and Plotting",
      "topics": [
        "LFD"
      ]
    },
    {
      "page": "Lquant",
      "title": "Estimation of L50 and L95",
      "topics": [
        "Lquant"
      ]
    },
    {
      "page": "LW",
      "title": "LW (Length-Weight relationship)",
      "topics": [
        "LW"
      ]
    },
    {
      "page": "LWf",
      "title": "Estimation of LW relationship",
      "topics": [
        "LWf"
      ]
    },
    {
      "page": "med_bathy",
      "title": "Mediterranean and Black Sea bathymetry (0â€“1000 m, bathy object)",
      "topics": [
        "med_bathy"
      ]
    },
    {
      "page": "MEDITS.distance",
      "title": "Estimation of haul distance",
      "topics": [
        "MEDITS.distance"
      ]
    },
    {
      "page": "MEDITS.to.dd",
      "title": "Conversion of MEDITS format coordinates in decimal degrees format",
      "topics": [
        "MEDITS.to.dd"
      ]
    },
    {
      "page": "merge_TATB",
      "title": "Merge TA and TB tables (haul-level catches)",
      "topics": [
        "merge_TATB"
      ]
    },
    {
      "page": "merge_TATBTC",
      "title": "Merge TAâ€“TB and TAâ€“TC tables (MEDITS protocol)",
      "topics": [
        "merge_TATBTC"
      ]
    },
    {
      "page": "merge_TATC",
      "title": "Merge TA and TC tables (haul-level lengthâ€“frequency data)",
      "topics": [
        "merge_TATC"
      ]
    },
    {
      "page": "MIW",
      "title": "Estimation of Mean Individual Weight (MIW) time series",
      "topics": [
        "MIW"
      ]
    },
    {
      "page": "overlayGrid",
      "title": "Overlay mTATB and mTATC on GFCM spatial grid",
      "topics": [
        "overlayGrid"
      ]
    },
    {
      "page": "quant",
      "title": "Quantile estimation",
      "topics": [
        "quant"
      ]
    },
    {
      "page": "run_BioIndex_app",
      "title": "launches the embedded Shiny application included in the package.",
      "topics": [
        "run_BioIndex_app"
      ]
    },
    {
      "page": "sex_ratio",
      "title": "Sex ratio",
      "topics": [
        "sex_ratio"
      ]
    },
    {
      "page": "sex_ratio_on_grid",
      "title": "Plot sex ratio spatial distribution",
      "topics": [
        "sex_ratio_on_grid"
      ]
    },
    {
      "page": "spear",
      "title": "Spearman test for timeseries",
      "topics": [
        "spear"
      ]
    },
    {
      "page": "spearman",
      "title": "Spearman test",
      "topics": [
        "spearman"
      ]
    },
    {
      "page": "strata_scheme",
      "title": "stratification scheme",
      "topics": [
        "strata_scheme"
      ]
    },
    {
      "page": "strata_scheme_rapana",
      "title": "stratification scheme (rapa whelk)",
      "topics": [
        "strata_scheme_rapana"
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    },
    {
      "page": "stratification",
      "title": "stratification",
      "topics": [
        "stratification"
      ]
    },
    {
      "page": "stratification_rapana",
      "title": "stratification (rapa whelk)",
      "topics": [
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      "page": "stratum_0_125",
      "title": "stratum_0_125",
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      "page": "stratum_0_200",
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      "page": "stratum_0_45",
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        "stratum_0_45"
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      "page": "stratum_0_800",
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      "topics": [
        "stratum_0_800"
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      "page": "stratum_200_800",
      "title": "stratum_200_800",
      "topics": [
        "stratum_200_800"
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    },
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      "page": "TA",
      "title": "TA table example",
      "topics": [
        "TA"
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    },
    {
      "page": "TA_cols",
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      "topics": [
        "TA_cols"
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    },
    {
      "page": "TB",
      "title": "TB table example",
      "topics": [
        "TB"
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    },
    {
      "page": "TB_cols",
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      "topics": [
        "TB_cols"
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    },
    {
      "page": "TC",
      "title": "TC table example",
      "topics": [
        "TC"
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    {
      "page": "TC_cols",
      "title": "TC table headings",
      "topics": [
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  "_vignettes": [
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      "source": "BioIndex.Rmd",
      "filename": "BioIndex.html",
      "title": "BioIndex",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Description",
        "Installation",
        "Use"
      ],
      "created": "2026-05-29 12:29:29",
      "modified": "2026-05-29 12:29:29",
      "commits": 1
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  "_indexed": true,
  "_nocasepkg": "bioindex",
  "_universes": [
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}