bio.infer: Predict environmental conditions from biological observations

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

Install the latest version of this package by entering the following in R:
install.packages("bio.infer")
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

Functions

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.