Biological Indicators and Indices for MEDITS Survey Data
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Documentation for package ‘BioIndex’ version 0.6.4
Help Pages
| aggregate_gsas | Aggregate MEDITS data across multiple GSAs |
| ALK | ALK (Age Length Key) |
| ALKf | Estimation of ALK |
| BioIndex | Main function to perform BioIndex analysis |
| bubbleplot_RS_by_hauls | Bubbleplot of abundance indices for recruits and spawners |
| bubble_plot_by_haul_indexes | Bubble plot of abundance and biomass indices by haul |
| centroidi | centroidi |
| cgpmgrid | cgpmgrid |
| check_date_haul | Check date haul (RoME) |
| check_dictionary | Check dictionary (RoME) |
| check_hauls_TBTA | Check hauls TB TA (RoME) |
| check_numeric_range | Check numeric range (RoME) |
| continent | continent |
| convert_coordinates | MEDITS coordinates in decimal degrees |
| dd.distance | Estimate hauls distances (decimal degrees) |
| dd.to.MEDITS | Conversion of decimal degrees coordinates in MEDITS format |
| hauls_position | Plot of hauls time series |
| index_on_grid | Generating maps of indexes |
| index_recr | Estimation of abundance indices for recruits |
| index_spawn | Estimation of abundance indices for spawners (females) |
| index_ts_F | Estimation of abundance indices for females |
| index_ts_M | Estimation of abundance indices for males |
| indices_ts | Estimation of abundance and biomass indices |
| IUT | Interception Union Tets |
| LFD | Length Frequency Distribution (LFD) Estimation and Plotting |
| Lquant | Estimation of L50 and L95 |
| LW | LW (Length-Weight relationship) |
| LWf | Estimation of LW relationship |
| MEDITS.distance | Estimation of haul distance |
| MEDITS.to.dd | Conversion of MEDITS format coordinates in decimal degrees format |
| med_bathy | Mediterranean and Black Sea bathymetry (0–1000 m, bathy object) |
| merge_TATB | Merge TA and TB tables (haul-level catches) |
| merge_TATBTC | Merge TA–TB and TA–TC tables (MEDITS protocol) |
| merge_TATC | Merge TA and TC tables (haul-level length–frequency data) |
| MIW | Estimation of Mean Individual Weight (MIW) time series |
| overlayGrid | Overlay mTATB and mTATC on GFCM spatial grid |
| quant | Quantile estimation |
| run_BioIndex_app | launches the embedded Shiny application included in the package. |
| sex_ratio | Sex ratio |
| sex_ratio_on_grid | Plot sex ratio spatial distribution |
| spear | Spearman test for timeseries |
| spearman | Spearman test |
| strata_scheme | stratification scheme |
| strata_scheme_rapana | stratification scheme (rapa whelk) |
| stratification | stratification |
| stratification_rapana | stratification (rapa whelk) |
| stratum_0_125 | stratum_0_125 |
| stratum_0_200 | stratum_0_200 |
| stratum_0_35 | stratum_0_35 |
| stratum_0_45 | stratum_0_45 |
| stratum_0_800 | stratum_0_800 |
| stratum_200_800 | stratum_200_800 |
| TA | TA table example |
| TA_cols | TA table headings |
| TB | TB table example |
| TB_cols | TB table headings |
| TC | TC table example |
| TC_cols | TC table headings |