# Predict Environmental Conditions from Biological Observations

## Documentation for package ‘bio.infer’ version 1.3-6

- DESCRIPTION file.

## Help Pages

bio.infer-package | Scripts for computing biological inferences
bcnt.emapw | Benthic count data for the western United States
bcnt.OR | Benthic count data for western Oregon
bcnt.otu.OR | Benthic count data with OTU
bcnt.tax.OR | Benthic count with taxonomic hierarchy
bio.infer | Scripts for computing biological inferences
coef.east.sed | Regression coefficients for eastern U.S. sediment
coef.west.wt | Weighted regression coefficients for western U.S.
correct.taxanames | Correct unrecognized taxon names
envdata.emapw | Environmental data from the western United States
envdata.OR | Environmental data from western OR
flist.data | List available data
flist.match | Selects data files matching search string
formtomat | Analyze formula string
get.dupe.sel | Get duplicate selection
get.otu | Defines operational taxonomic units (OTUs)
get.taxon.names | Get taxon names from benthic count file
get.taxonomic | Merge benthic count data with the ITIS taxonomy table
get.valid.names | Get taxon names from benthic count file
in.ITIS | Check to see if taxon name is in ITIS
incorp.correct | Incorporate taxon name revisions
infergui | Graphical User Interface for biological inferences
itis.ttable | ITIS taxonomic hierarchy table
load.itis | Load ITIS taxon table
load.revised.otu | Loads a user-revised OTU table
load.revised.species | Loads a user-revised list of species names
locate.dupes | Locate duplicated taxon names
make.fulltab1 | Make full taxonomic table
make.species | Generate species names
makess | Make a site-OTU matrix
mlsolve | Maximum likelihood inferences
modalDialog | Modal dialog box using TclTK
output.tax.table | Output final taxonomic table
parse.taxon.name | Parse taxon name
remove.dupes | Remove unselected duplicates from taxon table
resolve.mult | Resolve cases in which two taxa are found in ITIS
sel.coeffile | Select coefficient file
ss.OR | site-OTU matrix for western Oregon
taxon.env | Estimate taxon-environment relationships
tklist.modal | Modal select list dialog using TclTk
trait.feeding | Feeding traits for benthic invertebrates
trait.habit | Habit traits for benthic invertebrates
trait.stat | Compute trait metrics
view.te | View taxon-environment relationships