Package: bio.infer 1.3-6

Lester L. Yuan

bio.infer: Predict Environmental Conditions from Biological Observations

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

Authors:Lester L. Yuan

bio.infer_1.3-6.tar.gz
bio.infer_1.3-6.tar.gz(r-4.5-noble)bio.infer_1.3-6.tar.gz(r-4.4-noble)
bio.infer_1.3-6.tgz(r-4.4-emscripten)bio.infer_1.3-6.tgz(r-4.3-emscripten)
bio.infer.pdf |bio.infer.html✨
bio.infer/json (API)

# Install 'bio.infer' in R:
install.packages('bio.infer', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

30 exports 0.00 score 0 dependencies 24 scripts 466 downloads

Last updated 4 years agofrom:7bb78e99d6. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 29 2024
R-4.5-linuxOKAug 29 2024

Exports:correct.taxanamesflist.dataflist.matchformtomatget.dupe.selget.otuget.taxon.namesget.taxonomicget.valid.namesin.ITISincorp.correctinferguiload.itisload.revised.otuload.revised.specieslocate.dupesmake.fulltab1make.speciesmakessmlsolvemodalDialogoutput.tax.tableparse.taxon.nameremove.dupesresolve.multsel.coeffiletaxon.envtklist.modaltrait.statview.te

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Scripts for computing biological inferencesbio.infer-package bio.infer
Benthic count data for the western United Statesbcnt.emapw
Benthic count data for western Oregonbcnt.OR
Benthic count data with OTUbcnt.otu.OR
Benthic count with taxonomic hierarchybcnt.tax.OR
Regression coefficients for eastern U.S. sedimentcoef.east.sed
Weighted regression coefficients for western U.S.coef.west.wt
Correct unrecognized taxon namescorrect.taxanames
Environmental data from the western United Statesenvdata.emapw
Environmental data from western ORenvdata.OR
List available dataflist.data
Selects data files matching search stringflist.match
Analyze formula stringformtomat
Get duplicate selectionget.dupe.sel
Defines operational taxonomic units (OTUs)get.otu
Get taxon names from benthic count fileget.taxon.names
Merge benthic count data with the ITIS taxonomy tableget.taxonomic
Get taxon names from benthic count fileget.valid.names
Check to see if taxon name is in ITISin.ITIS
Incorporate taxon name revisionsincorp.correct
Graphical User Interface for biological inferencesinfergui
ITIS taxonomic hierarchy tableitis.ttable
Load ITIS taxon tableload.itis
Loads a user-revised OTU tableload.revised.otu
Loads a user-revised list of species namesload.revised.species
Locate duplicated taxon nameslocate.dupes
Make full taxonomic tablemake.fulltab1
Generate species namesmake.species
Make a site-OTU matrixmakess
Maximum likelihood inferencesmlsolve
Modal dialog box using TclTKmodalDialog
Output final taxonomic tableoutput.tax.table
Parse taxon nameparse.taxon.name
Remove unselected duplicates from taxon tableremove.dupes
Resolve cases in which two taxa are found in ITISresolve.mult
Select coefficient filesel.coeffile
site-OTU matrix for western Oregonss.OR
Estimate taxon-environment relationshipstaxon.env
Modal select list dialog using TclTktklist.modal
Feeding traits for benthic invertebratestrait.feeding
Habit traits for benthic invertebratestrait.habit
Compute trait metricstrait.stat
View taxon-environment relationshipsview.te