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.

Install the latest version of this package by entering the following in R:
install.packages("BEQI2")
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

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