BEQI2: Benthic Ecosystem Quality Index 2

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Tool for analysing benthos data. It estimates several quality indices like the total abundance of species, species richness, Margalef's d, AZTI Marine Biotic Index (AMBI), and the BEQI-2 index. Furthermore, additional (optional) features are provided that enhance data preprocessing: (1) genus to species conversion, i.e.,taxa counts at the taxonomic genus level can optionally be converted to the species level and (2) pooling: small samples are combined to bigger samples with a standardized size to (a) meet the data requirements of the AMBI, (b) generate comparable species richness values and (c) give a higher benthos signal to noise ratio.

Author
Willem van Loon [aut, cph], Dennis Walvoort [aut, cre]
Date of publication
2015-01-07 06:33:26
Maintainer
Dennis Walvoort <dennis.Walvoort@wur.nl>
License
GPL (>= 3)
Version
2.0-0

View on CRAN

Man pages

abundance
Abundance
beqi2
Perform BEQI-2 Analysis
BEQI2dir
Create BEQI-2 Directory Structure
BEQI2-pkg
Marine Benthic Ecosystem Quality Index
entropy
Shannon's Entropy
eqr
Ecological Quality Ratio (EQR)
genusToSpecies
Genus to Species Conversion
grapes-inInterval-grapes
Test if a Value is in an Interval
harmonize
Harmonize Case
isAzoic
Test for Azoic Samples
margalef
Margalef Index of Diversity
pool
Pooling
readAMBI
Read AMBI Sensitivity Data
readBEQI
Read BEQI input files
readERF
Read Ecotopes References File
readFIBI
Read Freshwater Inflow Biotic Index File
readITI
Read Infaunal Trophic Index File
readSettings
Read BEQI Settings File
readTWN
Read TWN Data
rename
Renaming Taxon Names
speciesRichness
Species Richness
stripSpaces
Remove Redundant Spaces

Files in this package

BEQI2
BEQI2/inst
BEQI2/inst/NEWS.Rd
BEQI2/inst/Rmd
BEQI2/inst/Rmd/user_ambi.Rmd
BEQI2/inst/Rmd/pooling.Rmd
BEQI2/inst/Rmd/genus_to_species.Rmd
BEQI2/inst/Rmd/nopooling.Rmd
BEQI2/inst/Rmd/beqi2.Rmd
BEQI2/inst/Rmd/default_ambi.Rmd
BEQI2/inst/Rmd/pooling_area.Rmd
BEQI2/inst/css
BEQI2/inst/css/beqi2.css
BEQI2/inst/extdata
BEQI2/inst/extdata/REF-FILES
BEQI2/inst/extdata/REF-FILES/AMBI-NL+.csv
BEQI2/inst/extdata/REF-FILES/TAXA-TWN-2013-11-27.csv
BEQI2/inst/extdata/REF-FILES/BEQI2-Ecotopes.csv
BEQI2/inst/extdata/INPUT-FILES
BEQI2/inst/extdata/INPUT-FILES/20140115-BEQI2-Data-Oosterschelde.csv
BEQI2/inst/extdata/AMBI.rds
BEQI2/inst/extdata/settings.json
BEQI2/inst/doc
BEQI2/inst/doc/BEQI2.Rnw
BEQI2/inst/doc/install.R
BEQI2/inst/doc/install.pdf
BEQI2/inst/doc/install.Rnw
BEQI2/inst/doc/BEQI2.R
BEQI2/inst/doc/BEQI2.pdf
BEQI2/tests
BEQI2/tests/testthat
BEQI2/tests/testthat/test-input.R
BEQI2/tests/testthat/test-poole.R
BEQI2/tests/testthat/BEQI2-FILES
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_WADDEN_SEA_BALGZDB-P5.csv
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_POOL_BALGZD-P5_PIETSVPT600-P10.csv
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_POOL_BALGZDB-P1_BALGZDB-P5.csv
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_WADDEN_COAST3.csv
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_WADDEN_SEA_PIETSVPT600-P10.csv
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_POOL_BALGZDB-P1_PIETSVPT600-P10.csv
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_DUTCH_COAST_NOORWIJK2.csv
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_DUTCH_COAST_EGMOND.csv
BEQI2/tests/testthat/BEQI2-FILES/INPUT-FILES/TEST_WADDEN_SEA_BALGZDB-P1.csv
BEQI2/tests/testthat/JSON
BEQI2/tests/testthat/JSON/TEST_DUTCH_COAST_EGMOND.json
BEQI2/tests/testthat/JSON/TEST_WADDEN_SEA_BALGZDB-P5.json
BEQI2/tests/testthat/JSON/TEST_WADDEN_SEA_PIETSVPT600-P10.json
BEQI2/tests/testthat/JSON/TEST_WADDEN_COAST3.json
BEQI2/tests/testthat/JSON/TEST_POOL_BALGZDB-P1_PIETSVPT600-P10.json
BEQI2/tests/testthat/JSON/TEST_WADDEN_SEA_BALGZDB-P1.json
BEQI2/tests/testthat/JSON/TEST_POOL_BALGZD-P5_PIETSVPT600-P10.json
BEQI2/tests/testthat/JSON/TEST_POOL_BALGZDB-P1_BALGZDB-P5.json
BEQI2/tests/testthat/JSON/TEST_DUTCH_COAST_NOORWIJK2.json
BEQI2/tests/testthat/REF-FILES
BEQI2/tests/testthat/REF-FILES/BEQI2-Ecotopes-2014-04-11.csv
BEQI2/tests/testthat/REF-FILES/AMBI-NL+.csv
BEQI2/tests/testthat/REF-FILES/ITI.csv
BEQI2/tests/testthat/REF-FILES/TAXA-TWN-2013-11-27.csv
BEQI2/tests/test-all.R
BEQI2/NAMESPACE
BEQI2/R
BEQI2/R/utils.R
BEQI2/R/onAttach.R
BEQI2/R/beqi2-pkg.R
BEQI2/R/beqi2.R
BEQI2/vignettes
BEQI2/vignettes/figures
BEQI2/vignettes/figures/intro_dir.png
BEQI2/vignettes/figures/install_mirror.png
BEQI2/vignettes/figures/install_package.png
BEQI2/vignettes/figures/install_gui.png
BEQI2/vignettes/BEQI2.Rnw
BEQI2/vignettes/install.Rnw
BEQI2/vignettes/tables
BEQI2/vignettes/tables/tabbeqi2input.csv
BEQI2/MD5
BEQI2/build
BEQI2/build/vignette.rds
BEQI2/DESCRIPTION
BEQI2/man
BEQI2/man/isAzoic.Rd
BEQI2/man/pool.Rd
BEQI2/man/entropy.Rd
BEQI2/man/readERF.Rd
BEQI2/man/readTWN.Rd
BEQI2/man/grapes-inInterval-grapes.Rd
BEQI2/man/BEQI2-pkg.Rd
BEQI2/man/stripSpaces.Rd
BEQI2/man/eqr.Rd
BEQI2/man/beqi2.Rd
BEQI2/man/readBEQI.Rd
BEQI2/man/harmonize.Rd
BEQI2/man/rename.Rd
BEQI2/man/margalef.Rd
BEQI2/man/readITI.Rd
BEQI2/man/readSettings.Rd
BEQI2/man/BEQI2dir.Rd
BEQI2/man/speciesRichness.Rd
BEQI2/man/abundance.Rd
BEQI2/man/readFIBI.Rd
BEQI2/man/readAMBI.Rd
BEQI2/man/genusToSpecies.Rd