Package: BioIndex 0.6.4

Walter Zupa

BioIndex: Biological Indicators and Indices for MEDITS Survey Data

Supports the standardized analysis of Mediterranean International Bottom Trawl Survey (MEDITS) data and the calculation of biological indicators for selected species and population components. The package provides functions to estimate abundance and biomass indices, analyse size structure and length frequency distributions, derive sex ratio and maturity related metrics, explore spatial patterns, and assess temporal trends across surveys. Developed for integration within the Regional Database for Fisheries (RDBFIS) framework, it is intended to work on quality checked input data and to produce reproducible outputs that can support monitoring, comparative analyses among Geographical Sub-Areas (GSAs) and countries, and fishery management.

Authors:Walter Zupa [aut, cre], Loredana Casciaro [rev], Cosmidano Neglia [rev], Isabella Bitetto [rev], Maria Teresa Spedicato [aut]

BioIndex_0.6.4.tar.gz
BioIndex_0.6.4.tar.gz(r-4.7-any)BioIndex_0.6.4.tar.gz(r-4.6-any)
BioIndex_0.6.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BioIndex/json (API)

# Install 'BioIndex' in R:

install.packages('BioIndex', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

centroidi - Centroidi
cgpmgrid - Cgpmgrid
continent - Continent
med_bathy - Mediterranean and Black Sea bathymetry
strata_scheme - Stratification scheme
strata_scheme_rapana - Stratification scheme
stratification - Stratification
stratification_rapana - Stratification
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

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 7 scripts 391 downloads 31 exports 90 dependencies

Last updated from:3d7cdc81e8. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	347
source / vignettes	OK	284
linux-release-x86_64	OK	350
wasm-release	OK	173

Exports:aggregate_gsas BioIndex bubble_plot_by_haul_indexes bubbleplot_RS_by_hauls check_date_haul check_dictionary check_hauls_TBTA check_numeric_range convert_coordinates dd.distance dd.to.MEDITS hauls_position index_on_grid index_recr index_spawn index_ts_F index_ts_M indices_ts LFD MEDITS.distance MEDITS.to.dd merge_TATB merge_TATBTC merge_TATC MIW overlayGrid run_BioIndex_app sex_ratio sex_ratio_on_grid spear spearman

Dependencies:adehabitatMA base64enc bit bit64 blob bslib cachem class classInt cli commonmark cpp11 data.table DBI digest dplyr e1071 farver fastmap fontawesome fs gdistance generics geosphere ggplot2 glue gridExtra gtable hms htmltools httpuv igraph isoband jquerylib jsonlite KernSmooth labeling later lattice lifecycle magrittr marmap MASS Matrix memoise mgcv mime ncdf4 nlme otel pillar pkgconfig plotrix plyr promises proxy purrr R6 rappdirs raster RColorBrewer Rcpp reshape2 rlang RSQLite s2 S7 sass scales sf shape shiny shinyjs sourcetools sp stringi stringr terra tibble tidyr tidyselect tidyterra units utf8 vctrs viridisLite withr wk xtable zip

BioIndex

Description | Installation | Use

Rendered fromBioIndex.Rmdusingknitr::rmarkdown

Last update: 2026-05-29
Started: 2026-05-29

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

Package: BioIndex 0.6.4

BioIndex: Biological Indicators and Indices for MEDITS Survey Data

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)