Package: BioMonTools 1.2.4.9026

BioMonTools: Biomonitoring and Bioassessment Calculations

An aid for manipulating data associated with biomonitoring and bioassessment. Calculations include metric calculation, marking of excluded taxa, subsampling, and multimetric index calculation. Targeted communities are benthic macroinvertebrates, fish, periphyton, and coral. As described in the Revised Rapid Bioassessment Protocols (Barbour et al. 1999) <https://archive.epa.gov/water/archive/web/html/index-14.html>.

Authors:Erik W. Leppo [aut, cre], Jen Stamp [ctb], John van Sickles [ctb], Ben Block [ctb]

BioMonTools_1.2.4.9026.tar.gz
BioMonTools_1.2.4.9026.zip(r-4.7)BioMonTools_1.2.4.9026.zip(r-4.6)BioMonTools_1.2.4.9026.zip(r-4.5)
BioMonTools_1.2.4.9026.tgz(r-4.6-any)BioMonTools_1.2.4.9026.tgz(r-4.5-any)
BioMonTools_1.2.4.9026.tar.gz(r-4.7-any)BioMonTools_1.2.4.9026.tar.gz(r-4.6-any)
BioMonTools_1.2.4.9026.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BioMonTools/json (API)

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

Bug tracker:https://github.com/leppott/biomontools/issues

Datasets:

On CRAN:

Conda:

benthicbioassessmentbiomonitoringfishmacorinvertebratesmetricperiphytonrbp

5.87 score 15 stars 52 scripts 237 downloads 22 exports 21 dependencies

Last updated from:d5f62da0a2. Checks:8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR266
source / vignettesERROR286
linux-release-x86_64ERROR216
macos-release-arm64ERROR158
macos-oldrel-arm64ERROR185
windows-develERROR138
windows-releaseERROR158
windows-oldrelERROR130
wasm-releaseOK154

Exports:assign_IndexClassMapTaxaObsmarkExcludedmetric.scoresmetric.statsmetric.stats2metric.valuesmetric.values.algaemetric.values.bugsmetric.values.coralmetric.values.fishmetvalgrpxlqc_taxaqc_taxa_match_officialqc_taxa_names_proofqc_taxa_phyloqc_taxa_values_charqc_taxa_values_logicalqc_taxa_values_numericqc.checksrarifytaxa_translate

Dependencies:clicpp11dplyrgenericsgluelifecyclemagrittrmapspillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
BioMonTools: Biomonitoring and Bioassessment CalculationsBioMonTools-package BioMonTools
Assign Index_Classassign_IndexClass
Benthic macroinvertebrate taxa data; MBSSdata_benthos_MBSS
Benthic macroinvertebrate taxa data; Pacific Northwestdata_benthos_PacNW
rarify example datadata_bio2rarify
Coral taxa data; Florida BCG.data_coral_bcg_metric_dev
Coral metric value data; Florida BCG.data_coral_bcg_metric_qc
Diatom taxa data; Indiana DEMdata_diatom_mmi_dev
Diatom metric value data; Indiana DEMdata_diatom_mmi_qc
Fish data, MBSSdata_fish_MBSS
data_metval_scmb_ibidata_metval_scmb_ibi
Metric data for metric stats for mmi developmentdata_mmi_dev
Metric data for metric stats for mmi developmentdata_mmi_dev_small
Estuary taxa datadata_Taxa_MA
Taxa Observation MapsMapTaxaObs
Mark "exclude" (non-distinct / non-unique / ambiguous) taxamarkExcluded
Score metricsmetric.scores
Calculate metric statisticsmetric.stats
Secondary metric statisticsmetric.stats2
Calculate metric valuesmetric.values
Metric values Groups to Excelmetvalgrpxl
Quality Control Check on User Data Against Master Taxa Listqc_taxa
Quality Control Check on User Data Against Master Taxa Listqc_taxa_match_official
QC Taxa List Proofreadingqc_taxa_names_proof
QC Taxa Phyloqc_taxa_phylo
QC Autecological Character Valuesqc_taxa_values_char
QC Autecological Logical Valuesqc_taxa_values_logical
QC Autecological Numeric Valuesqc_taxa_values_numeric
QC checks on metric valuesqc.checks
Rarify (subsample) biological sample to fixed countrarify
Taxa Translatetaxa_translate
TaxaMaster_Ben_BCG_PacNWTaxaMaster_Ben_BCG_PacNW