bio.infer: Predict environmental conditions from biological observations

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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