EcoSimR: Null Model Analysis for Ecological Data

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.

AuthorNick Gotelli [aut], Edmund Hart [aut, cre], Aaron Ellison [aut]
Date of publication2015-04-03 22:09:00
MaintainerEdmund Hart <edmund.m.hart@gmail.com>
LicenseMIT + file LICENSE
Version0.1.0

View on CRAN

Man pages

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

Files in this package

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? 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.