Package: ambiR 0.1.1

Ciarán J. Murray

ambiR: Calculate AZTI’s Marine Biotic Index

Calculate AZTI’s Marine Biotic Index - AMBI. The included list of benthic fauna species according to their sensitivity to pollution. Matching species in sample data to the list allows the calculation of fractions of individuals in the different sensitivity categories and thereafter the AMBI index. The Shannon Diversity Index H' and the Danish benthic fauna quality index DKI (Dansk Kvalitetsindeks) can also be calculated, as well as the multivariate M-AMBI index. Borja, A., Franco, J., Pérez, V. (2000) "A marine biotic index to establish the ecological quality of soft bottom benthos within European estuarine and coastal environments" <doi:10.1016/S0025-326X(00)00061-8>.

Authors:Ciarán J. Murray [aut, cre, cph], Ángel Borja [aut], Sarai Pouso [aut], Iñigo Muxika [aut], Joxe Mikel Garmendia [aut], Steen Knudsen [ctb], GES4SEAS [fnd]

ambiR_0.1.1.tar.gz
ambiR_0.1.1.zip(r-4.7)ambiR_0.1.1.zip(r-4.6)ambiR_0.1.1.zip(r-4.5)
ambiR_0.1.1.tgz(r-4.6-any)ambiR_0.1.1.tgz(r-4.5-any)
ambiR_0.1.1.tar.gz(r-4.7-any)ambiR_0.1.1.tar.gz(r-4.6-any)
ambiR_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ambiR/json (API)

# Install 'ambiR' in R:
install.packages('ambiR', repos = c('https://niva-denmark.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/niva-denmark/ambir/issues

Pkgdown/docs site:https://niva-denmark.github.io

Datasets:

On CRAN:

Conda:

4.78 score 9 scripts 267 downloads 9 exports 20 dependencies

Last updated from:4e75b9ce51. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK147
source / vignettesOK269
linux-release-x86_64OK146
macos-release-arm64OK132
macos-oldrel-arm64OK200
windows-develOK100
windows-releaseOK98
windows-oldrelOK123
wasm-releaseOK119

Exports:%>%AMBIAMBI_salAMBI_speciesDKIDKI2H_salHdashMAMBI

Dependencies:clicpp11dplyrgenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr

AMBI figures
Bar chart from original AMBI software | Bar chart using ggplot | Bar chart with AMBI theme
Rendered fromambi-figures.Rmdusingknitr::rmarkdown

Last update: 2025-12-10
Started: 2025-12-04

Interactive mode
Test data | Instructions | Interactive AMBI calculation | Results | Aborting interactive mode
Rendered frominteractive.Rmdusingknitr::rmarkdown

Last update: 2025-12-10
Started: 2025-02-25

The AMBI index
Species Groups | M-AMBI - the multivariate AMBI index | AMBI software | References
Rendered frombackground.Rmdusingknitr::rmarkdown

Last update: 2025-12-10
Started: 2025-12-04

Get started
Structuring species observation data | Species names in columns | Stations and replicates in columns | Combine station and replicate values | Transpose using the combined station/replicate variable | Retrieve station and replicate variables from the transposed data | Calculate AMBI | Results | Calculate M-AMBI | Limit values | Status class boundaries | Call MAMBI() | M-AMBI results | EQR values | References
Rendered fromambiR.Rmdusingknitr::rmarkdown

Last update: 2025-12-08
Started: 2025-02-25