bio.infer: Predict environmental conditions from biological observations
Version 1.3-3

Imports benthic count data, reformats this data, and computes environmental inferences from this data.

AuthorLester L. Yuan
Date of publication2014-02-12 07:23:36
MaintainerLester L. Yuan <yuan.lester@epa.gov>
LicenseGPL (>= 2)
Version1.3-3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bio.infer")

Popular man pages

bcnt.tax.OR: Benthic count with taxonomic hierarchy
correct.taxanames: Correct unrecognized taxon names
get.valid.names: Get taxon names from benthic count file
load.itis: Load ITIS taxon table
make.species: Generate species names
output.tax.table: Output final taxonomic table
taxon.env: Estimate taxon-environment relationships
See all...

All man pages Function index File listing

Man pages

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.package: 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
incorp.correct: Incorporate taxon name revisions
infergui: Graphical User Interface for biological inferences
in.ITIS: Check to see if taxon name is in ITIS
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

Functions

bcnt.OR Man page
bcnt.emapw Man page
bcnt.otu.OR Man page
bcnt.tax.OR Man page
bio.infer Man page
bio.infer-package Man page
coef.east.sed Man page
coef.west.wt Man page
correct.taxanames Man page Source code
envdata.OR Man page
envdata.emapw Man page
flist.data Man page
flist.match Man page
formtomat Man page
get.dupe.sel Man page Source code
get.otu Man page
get.taxon.names Man page Source code
get.taxonomic Man page Source code
get.valid.names Man page Source code
in.ITIS Man page Source code
incorp.correct Man page Source code
infergui Man page
itis.ttable Man page
load.itis Man page Source code
load.revised.otu Man page
load.revised.species Man page
locate.dupes Man page Source code
make.fulltab1 Man page Source code
make.species Man page Source code
makess Man page
mlsolve Man page
modalDialog Man page
output.tax.table Man page Source code
parse.taxon.name Man page Source code
remove.dupes Man page Source code
resolve.mult Man page Source code
sel.coeffile Man page Source code
ss.OR Man page
taxon.env Man page
tklist.modal Man page Source code
trait.feeding Man page
trait.habit Man page
trait.stat Man page Source code
view.te Man page

Files

NAMESPACE
data
data/trait.habit.rda
data/bcnt.emapw.rda
data/itis.ttable.old.rda
data/coef.west.wt.rda
data/bcnt.otu.OR.rda
data/coef.east.sed.rda
data/itis.ttable.rda
data/trait.feeding.rda
data/envdata.OR.rda
data/ss.OR.rda
data/envdata.emapw.rda
data/datalist
data/bcnt.OR.rda
data/bcnt.tax.OR.rda
R
R/trait.stat.R
R/get.otu.R
R/formtomat.R
R/tklist.modal.R
R/infergui.R
R/makess.R
R/load.revised.otu.R
R/load.revised.species.R
R/get.taxonomic.R
R/view.te.R
R/parse.taxon.name.R
R/mlsolve.R
R/flist.data.R
R/flist.match.R
R/sel.coeffile.R
R/modaldialog.R
R/taxon.env.R
MD5
DESCRIPTION
man
man/incorp.correct.Rd
man/bcnt.tax.OR.Rd
man/locate.dupes.Rd
man/flist.match.Rd
man/output.tax.table.Rd
man/modaldialog.Rd
man/trait.habit.Rd
man/bio.infer.package.Rd
man/trait.feeding.Rd
man/flist.data.Rd
man/load.itis.Rd
man/coef.west.wt.Rd
man/taxon.env.Rd
man/itis.ttable.Rd
man/bcnt.emapw.Rd
man/coef.east.sed.Rd
man/mlsolve.Rd
man/envdata.emapw.Rd
man/in.ITIS.Rd
man/correct.taxanames.Rd
man/get.valid.names.Rd
man/formtomat.Rd
man/remove.dupes.Rd
man/view.te.Rd
man/get.otu.Rd
man/bcnt.otu.OR.Rd
man/parse.taxon.name.Rd
man/make.species.Rd
man/load.revised.otu.Rd
man/resolve.mult.Rd
man/trait.stat.Rd
man/bcnt.OR.Rd
man/get.dupe.sel.Rd
man/get.taxon.names.Rd
man/tklist.modal.Rd
man/ss.OR.Rd
man/get.taxonomic.Rd
man/infergui.Rd
man/load.revised.species.Rd
man/makess.Rd
man/envdata.OR.Rd
man/sel.coeffile.Rd
man/make.fulltab1.Rd
bio.infer documentation built on May 19, 2017, 12:40 p.m.