# Biomonitoring and Bioassessment Calculations

## Documentation for package ‘BioMonTools’ version 1.3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BioMonTools-package | BioMonTools: Biomonitoring and Bioassessment Calculations
assign_IndexClass | Assign Index_Class
BioMonTools | BioMonTools: Biomonitoring and Bioassessment Calculations
data_algae_names_official | Algae Taxa Names, Official
data_algae_names_user | Algae Taxa Names, User
data_benthos_MBSS | Benthic macroinvertebrate taxa data; MBSS
data_benthos_PacNW | Benthic macroinvertebrate taxa data; Pacific Northwest
data_bio2rarify | rarify example data
data_coral_bcg_metric_dev | Coral taxa data; Florida BCG.
data_coral_bcg_metric_qc | Coral metric value data; Florida BCG.
data_diatom_mmi_dev | Diatom taxa data; Indiana DEM
data_diatom_mmi_qc | Diatom metric value data; Indiana DEM
data_fish_MBSS | Fish data, MBSS
data_metval_scmb_ibi | data_metval_scmb_ibi
data_mmi_dev | Metric data for metric stats for mmi development
data_mmi_dev_small | Metric data for metric stats for mmi development
data_Taxa_MA | Estuary taxa data
data_taxa_names_issues | Taxa name data frame with issues
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 | Calculate metric values
metvalgrpxl | Metric values Groups to Excel
qc.checks | QC checks on metric values
qc_taxa | Quality Control Check on User Data Against Master Taxa List
qc_taxa_match_official | Quality Control Check on User Data Against Master Taxa List
qc_taxa_names_proof | QC Taxa List Proofreading
qc_taxa_phylo | QC Taxa Phylo
qc_taxa_values_character | QC Autecological Character Values
qc_taxa_values_logical | QC Autecological Logical Values
qc_taxa_values_numeric | QC Autecological Numeric Values
rarify | Rarify (subsample) biological sample to fixed count
TaxaMaster_Ben_BCG_PacNW | TaxaMaster_Ben_BCG_PacNW
taxa_translate | Taxa Translate