Package: benthos 1.3-8

Dennis Walvoort

benthos: Marine Benthic Ecosystem Analysis

Preprocessing tools and biodiversity measures (species abundance, species richness, population heterogeneity and sensitivity) for analysing marine benthic data. See Van Loon et al. (2015) <doi:10.1016/j.seares.2015.05.002> for an application of these tools.

Authors:Dennis Walvoort [aut, cre, cph]

benthos_1.3-8.tar.gz
benthos_1.3-8.tar.gz(r-4.5-noble)benthos_1.3-8.tar.gz(r-4.4-noble)
benthos_1.3-8.tgz(r-4.4-emscripten)benthos_1.3-8.tgz(r-4.3-emscripten)
benthos.pdf |benthos.html✨
benthos/json (API)
NEWS

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

Peer review:

Datasets:

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

3.01 score 1 packages 34 scripts 329 downloads 62 exports 28 dependencies

Last updated 2 years agofrom:6615e8093e. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-linuxNOTEOct 28 2024

Exports:abundanceabundance_ambiambi_as_acceptedbray_curtiseqrgeneric_namegenus_to_speciesget_ambiget_itiget_taxaget_wormsharmonizehas_ambihas_ambi_has_itihas_iti_hillhill_hill0hill0_hill1hill1_hill2hill2_hpiehpie_hurlberthurlbert_is_acceptedis_accepted_is_azoicis_binomenis_wormsis_worms_itiiti_lnnlnn_margalefmargalef_poolread_ambiread_beqi2read_itiread_refread_taxaread_twnryggrygg_shannonshannon_simpsonsimpson_species_richnessspecies_richness_specific_namestrip_spto_wormstotal_abundancetotal_abundance_

Dependencies:bitbit64clicliprcpp11crayondplyrfansigenericsgluehmslazyevallifecyclemagrittrpillarpkgconfigprettyunitsprogressR6readrrlangtibbletidyselecttzdbutf8vctrsvroomwithr

Introduction to the benthos-package

Dennis Walvoort

Rendered frombenthos.Rmdusingknitr::rmarkdownon Oct 28 2024.

Last update: 2022-08-22
Started: 2017-11-22

Readme and manuals

Help Manual

Help pageTopics
Marine Benthic Ecosystem Analysisbenthos-package benthos
Abundanceabundance abundance_
AZTI Marine Biotic Index (AMBI)ambi ambi_ has_ambi has_ambi_
Convert Taxon Names to Comply with WoRMS/TWNas_accepted
Bray-Curtis Dissimilaritybray_curtis
Ecological Quality Ratio (EQR)eqr
Genus to Species Conversiongenus_to_species
Get Supplementary AMBI Sensitivity Groupsget_ambi
Get Infaunal Trophic Indexget_iti
Harmonize Caseharmonize
Hill's Diversity Numbershill hill0 hill0_ hill1 hill1_ hill2 hill2_ hill_
Hurlbert's Probability of Interspecific Encounter (PIE)hpie hpie_
Hurlbert's Expected Number of Specieshurlbert hurlbert_
Test for Azoic Samplesis_azoic
Binomial Names 'is_binomial' tests for valid binomial names, 'generic_name' extracts the genus to which the species belongs, 'specific_name' extracts the species within the genus.generic_name is_binomen specific_name strip_sp
Infaunal Trophic Index (ITI)has_iti has_iti_ iti iti_
Margalef Index of Diversitymargalef margalef_
MWTL North Sea Bentos Datanorthsea
Oosterschelde Marine Benthos Dataoosterschelde
Pooling.pool pool
Read and Validate AMBI Sensitivity Dataread_ambi validate_ambi
Read and Validate BEQI2 Input Filesread_beqi2 validate_beqi2
Read and Validate Infaunal Trophic Index Filesread_iti validate_iti
Read and Validate Habitat References Filesread_ref validate_ref
Read and Validate Taxa Dataget_taxa read_taxa validate_taxa
Read and Validate Taxa Waterbeheer Nederland (TWN) Dataget_worms read_twn validate_twn
Rygg's Index of Diversityrygg rygg_
Shannon's Index or Entropyshannon shannon_
Simpson's Measure of Concentrationsimpson simpson_
Species Richnessspecies_richness species_richness_
Remove Redundant Spacesstrip_spaces
Convert Taxon Names to Comply with WoRMSis_accepted is_accepted_ is_worms is_worms_ to_worms
Total Abundancelnn lnn_ total_abundance total_abundance_