# Biological Indicators and Indices for MEDITS Survey Data

## Documentation for package ‘BioIndex’ version 0.6.4

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

## 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 (0â€“1000 m, bathy object)
merge_TATB | Merge TA and TB tables (haul-level catches)
merge_TATBTC | Merge TAâ€“TB and TAâ€“TC tables (MEDITS protocol)
merge_TATC | Merge TA and TC tables (haul-level lengthâ€“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