BioMonTools1.2.4 package

Biomonitoring and Bioassessment Calculations

assign_IndexClass

Assign Index_Class

MapTaxaObs

Taxa Observation Maps

markExcluded

Mark "exclude" (non-distinct / non-unique / ambiguous) taxa

metric.scores

Score metrics

metric.stats

Calculate metric statistics

metric.stats2

Secondary metric statistics

metric.values.algae

Calculate metric values, Algae

metric.values.bugs

Calculate metric values, Bugs

metric.values.coral

Calculate metric values, coral

metric.values.fish

Calculate metric values, Fish

metric.values

Calculate metric values

metvalgrpxl

Metric values Groups to Excel

qc_taxa

Quality Control Check on User Data Against Master Taxa List

qc.checks

QC checks on metric values

rarify

Rarify (subsample) biological sample to fixed count

taxa_translate

Taxa Translate

Download source packageRead PDF manual

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>.

  • Maintainer: Erik W. Leppo
  • License: MIT + file LICENSE
  • Last published: 2025-10-09

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