Given a site by species interaction matrix, users can make inferences about species interactions by performance hypothesis comparing test statistics against a null distribution. The current package provides algorithms and metrics for niche-overlap, body size ratios and species co-occurrence. Users can also integrate their own algorithms and metrics within these frameworks or completely novel null models. Detailed explanations about the underlying assumptions of null model analysis in ecology can be found at http://ecosimr.org.

Author | Nick Gotelli [aut], Edmund Hart [aut, cre], Aaron Ellison [aut] |

Date of publication | 2015-04-03 22:09:00 |

Maintainer | Edmund Hart <edmund.m.hart@gmail.com> |

License | MIT + file LICENSE |

Version | 0.1.0 |

**checker:** Checker Co-occurrence Metric

**cooc_null_model:** Co-Occurrence Null model

**c_score:** CScore Co-occurrence Metric

**c_score_skew:** CScoreSkew Co-occurrence Metric

**c_score_var:** CScoreVariance Co-occurrence Metric

**czekanowski:** Czekanowski Niche Overlap Metric

**czekanowski_skew:** CzekanowskiSkew Niche Overlap Metric

**czekanowski_var:** CzekanowskiVariance Niche Overlap Metric

**dataMacWarb:** MacArthur's (1958) warbler data This data matrix is from...

**dataRodents:** Desert rodent data set This data vector is from Brown's...

**dataWiFinches:** West Indian Finches data This data frame is a binary...

**EcoSimR:** EcoSimR EcoSimR is a collection of functions for calculating...

**min_diff:** MinDiff Size Overlap Metric

**min_ratio:** MinRatio Size Overlap Ratio Metric

**niche_null_model:** Niche overlap null models

**null_model_engine:** Run null model

**pianka:** Pianka Niche Overlap Metric

**pianka_skew:** PiankaSkew Niche Overlap Metric

**pianka_var:** PiankaVariance Niche Overlap Metric

**plot.coocnullmod:** Co-Occurrence Model Plot Function

**plot.nichenullmod:** Niche Null Model Plot function

**plot.nullmod:** plot a histogram null model

**plot.sizenullmod:** Size Ratio Plot Function

**ra1:** RA1 Niche Overlap Randomization Algorithm

**ra2:** RA2 Niche Overlap Randomization Algorithm

**ra3:** RA3 Niche Overlap Randomization Algorithm

**ra4:** RA4 Niche Overlap Randomization Algorithm

**ranMatGen:** Random Matrix Generator

**reproduce_model:** Reproduce a result

**sim1:** Sim1 Co-occurrence Randomization Algorithm

**sim10:** Sim10 Co-occurrence Randomization Algorithm

**sim2:** Sim2 Co-occurrence Randomization Algorithm

**sim3:** Sim3 Co-occurrence Randomization Algorithm

**sim4:** Sim4 Co-occurrence Randomization Algorithm

**sim5:** Sim5 Co-occurrence Randomization Algorithm

**sim6:** Sim6 Co-occurrence Randomization Algorithm

**sim7:** Sim7 Co-occurrence Randomization Algorithm

**sim8:** Sim8 Co-occurrence Randomization Algorithm

**sim9:** Sim9 Co-occurrence Randomization Algorithm

**sim9_single:** sim9_single

**size_gamma:** SizeGamma Size Overlap Randomization Algorithm

**size_null_model:** Size Ratio

**size_source_pool:** SizeSourcePoolDraw Size Overlap Randomization Algorithm

**size_uniform:** SizeUniform Size Overlap Randomization Algorithm

**size_uniform_user:** SizeUser Size Overlap Randomization Algorithm

**species_combo:** SpeciesCombo Co-occurrence Metric

**summary.coocnullmod:** Generic function for calculating null model summary...

**summary.nichenullmod:** Generic function for calculating null model summary...

**summary.nullmod:** Generic function for calculating null model summary...

**summary.sizenullmod:** Generic function for calculating null model summary...

**var_diff:** VarDiff Size Overlap Ratio Metric

**var_ratio:** VarRatio Size Overlap Ratio Metric

**vector_sample:** Vector Sample Function

**v_ratio:** SchlutersVRatio Co-occurrence Metric

EcoSimR

EcoSimR/inst

EcoSimR/inst/cooc_hist.png

EcoSimR/inst/CITATION

EcoSimR/inst/niche.png

EcoSimR/inst/cooc.png

EcoSimR/inst/size.png

EcoSimR/inst/doc

EcoSimR/inst/doc/CoOccurrenceVignette.html

EcoSimR/inst/doc/nullModelPlug-Ins.R

EcoSimR/inst/doc/SizeRatioVignette.R

EcoSimR/inst/doc/nullModelPlug-Ins.Rmd

EcoSimR/inst/doc/nullModelPlug-Ins.html

EcoSimR/inst/doc/CoOccurrenceVignette.R

EcoSimR/inst/doc/nicheOverlapVignette.R

EcoSimR/inst/doc/SizeRatioVignette.html

EcoSimR/inst/doc/nicheOverlapVignette.html

EcoSimR/inst/doc/SizeRatioVignette.Rmd

EcoSimR/inst/doc/CoOccurrenceVignette.Rmd

EcoSimR/inst/doc/nicheOverlapVignette.Rmd

EcoSimR/inst/niche_hist.png

EcoSimR/inst/size_hist.png

EcoSimR/inst/burnin.png

EcoSimR/tests

EcoSimR/tests/testthat.R

EcoSimR/tests/testthat

EcoSimR/tests/testthat/test_nichebreadth.R

EcoSimR/tests/testthat/test_cooccurrence.R

EcoSimR/tests/testthat/test_sizeratio.R

EcoSimR/NAMESPACE

EcoSimR/data

EcoSimR/data/datasets.rda

EcoSimR/R

EcoSimR/R/coccurrence_null.R
EcoSimR/R/metrics.R
EcoSimR/R/sim9fast.R
EcoSimR/R/algorithms.R
EcoSimR/R/randomMatrixGenerator.R
EcoSimR/R/null_model_engine.R
EcoSimR/R/sizeratio_null.R
EcoSimR/R/reproduce_model.R
EcoSimR/R/EcoSimR-package.r

EcoSimR/R/niche_overlap_null.R
EcoSimR/vignettes

EcoSimR/vignettes/nullModelPlug-Ins.Rmd

EcoSimR/vignettes/SizeRatioVignette.Rmd

EcoSimR/vignettes/CoOccurrenceVignette.Rmd

EcoSimR/vignettes/nicheOverlapVignette.Rmd

EcoSimR/MD5

EcoSimR/build

EcoSimR/build/vignette.rds

EcoSimR/DESCRIPTION

EcoSimR/man

EcoSimR/man/czekanowski_skew.Rd
EcoSimR/man/ranMatGen.Rd
EcoSimR/man/czekanowski_var.Rd
EcoSimR/man/sim10.Rd
EcoSimR/man/sim5.Rd
EcoSimR/man/var_diff.Rd
EcoSimR/man/dataRodents.Rd
EcoSimR/man/vector_sample.Rd
EcoSimR/man/summary.nullmod.Rd
EcoSimR/man/dataMacWarb.Rd
EcoSimR/man/sim2.Rd
EcoSimR/man/summary.nichenullmod.Rd
EcoSimR/man/pianka.Rd
EcoSimR/man/c_score.Rd
EcoSimR/man/pianka_var.Rd
EcoSimR/man/plot.nichenullmod.Rd
EcoSimR/man/size_uniform_user.Rd
EcoSimR/man/reproduce_model.Rd
EcoSimR/man/ra4.Rd
EcoSimR/man/sim4.Rd
EcoSimR/man/plot.coocnullmod.Rd
EcoSimR/man/size_gamma.Rd
EcoSimR/man/v_ratio.Rd
EcoSimR/man/sim6.Rd
EcoSimR/man/ra2.Rd
EcoSimR/man/czekanowski.Rd
EcoSimR/man/min_diff.Rd
EcoSimR/man/size_source_pool.Rd
EcoSimR/man/plot.sizenullmod.Rd
EcoSimR/man/sim3.Rd
EcoSimR/man/species_combo.Rd
EcoSimR/man/ra1.Rd
EcoSimR/man/var_ratio.Rd
EcoSimR/man/summary.sizenullmod.Rd
EcoSimR/man/c_score_var.Rd
EcoSimR/man/c_score_skew.Rd
EcoSimR/man/pianka_skew.Rd
EcoSimR/man/plot.nullmod.Rd
EcoSimR/man/size_null_model.Rd
EcoSimR/man/sim7.Rd
EcoSimR/man/size_uniform.Rd
EcoSimR/man/dataWiFinches.Rd
EcoSimR/man/checker.Rd
EcoSimR/man/summary.coocnullmod.Rd
EcoSimR/man/sim8.Rd
EcoSimR/man/min_ratio.Rd
EcoSimR/man/ra3.Rd
EcoSimR/man/sim9.Rd
EcoSimR/man/null_model_engine.Rd
EcoSimR/man/EcoSimR.Rd
EcoSimR/man/sim1.Rd
EcoSimR/man/sim9_single.Rd
EcoSimR/man/niche_null_model.Rd
EcoSimR/man/cooc_null_model.Rd
EcoSimR/LICENSE

Questions? Problems? Suggestions? Tweet to @rdrrHQ 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.