BEQI2: Benthic Ecosystem Quality Index 2

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.

AuthorWillem van Loon [aut, cph], Dennis Walvoort [aut, cre]
Date of publication2015-01-07 06:33:26
MaintainerDennis Walvoort <dennis.Walvoort@wur.nl>
LicenseGPL (>= 3)
Version2.0-0

View on CRAN

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.