bio.infer: Predict environmental conditions from biological observations

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

Author
Lester L. Yuan
Date of publication
2014-02-12 07:23:36
Maintainer
Lester L. Yuan <yuan.lester@epa.gov>
License
GPL (>= 2)
Version
1.3-3

View on CRAN

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

Files in this package

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