Predict Environmental Conditions from Biological Observations

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

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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 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 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 final taxonomic table 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