├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── CITATION ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── EcoSimR-package.r ├── algorithms.R ├── coccurrence_null.R ├── metrics.R ├── niche_overlap_null.R ├── null_model_engine.R ├── randomMatrixGenerator.R ├── reproduce_model.R ├── sim9fast.R └── sizeratio_null.R ├── README.md ├── appveyor.yml ├── data └── datasets.rda ├── inst ├── CITATION ├── burnin.png ├── cooc.png ├── cooc_hist.png ├── niche.png ├── niche_hist.png ├── size.png └── size_hist.png ├── man ├── EcoSimR.Rd ├── c_score.Rd ├── c_score_skew.Rd ├── c_score_var.Rd ├── checker.Rd ├── cooc_null_model.Rd ├── czekanowski.Rd ├── czekanowski_skew.Rd ├── czekanowski_var.Rd ├── dataMacWarb.Rd ├── dataRodents.Rd ├── dataWiFinches.Rd ├── min_diff.Rd ├── min_ratio.Rd ├── niche_null_model.Rd ├── null_model_engine.Rd ├── pianka.Rd ├── pianka_skew.Rd ├── pianka_var.Rd ├── plot.coocnullmod.Rd ├── plot.nichenullmod.Rd ├── plot.nullmod.Rd ├── plot.sizenullmod.Rd ├── ra1.Rd ├── ra2.Rd ├── ra3.Rd ├── ra4.Rd ├── ranMatGen.Rd ├── reproduce_model.Rd ├── sim1.Rd ├── sim10.Rd ├── sim2.Rd ├── sim3.Rd ├── sim4.Rd ├── sim5.Rd ├── sim6.Rd ├── sim7.Rd ├── sim8.Rd ├── sim9.Rd ├── sim9_single.Rd ├── size_gamma.Rd ├── size_null_model.Rd ├── size_source_pool.Rd ├── size_uniform.Rd ├── size_uniform_user.Rd ├── species_combo.Rd ├── summary.coocnullmod.Rd ├── summary.nichenullmod.Rd ├── summary.nullmod.Rd ├── summary.sizenullmod.Rd ├── v_ratio.Rd ├── var_diff.Rd ├── var_ratio.Rd └── vector_sample.Rd ├── tests ├── testthat.R └── testthat │ ├── test_cooccurrence.R │ ├── test_nichebreadth.R │ └── test_sizeratio.R └── vignettes ├── CoOccurrenceVignette.Rmd ├── SizeRatioVignette.Rmd ├── nicheOverlapVignette.Rmd └── nullModelPlug-Ins.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/.travis.yml -------------------------------------------------------------------------------- /CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/CITATION -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/LICENSE -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/EcoSimR-package.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/EcoSimR-package.r -------------------------------------------------------------------------------- /R/algorithms.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/algorithms.R -------------------------------------------------------------------------------- /R/coccurrence_null.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/coccurrence_null.R -------------------------------------------------------------------------------- /R/metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/metrics.R -------------------------------------------------------------------------------- /R/niche_overlap_null.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/niche_overlap_null.R -------------------------------------------------------------------------------- /R/null_model_engine.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/null_model_engine.R -------------------------------------------------------------------------------- /R/randomMatrixGenerator.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/randomMatrixGenerator.R -------------------------------------------------------------------------------- /R/reproduce_model.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/reproduce_model.R -------------------------------------------------------------------------------- /R/sim9fast.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/sim9fast.R -------------------------------------------------------------------------------- /R/sizeratio_null.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/R/sizeratio_null.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/README.md -------------------------------------------------------------------------------- /appveyor.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/appveyor.yml -------------------------------------------------------------------------------- /data/datasets.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/data/datasets.rda -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/inst/CITATION -------------------------------------------------------------------------------- /inst/burnin.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/inst/burnin.png -------------------------------------------------------------------------------- /inst/cooc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/inst/cooc.png -------------------------------------------------------------------------------- /inst/cooc_hist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/inst/cooc_hist.png -------------------------------------------------------------------------------- /inst/niche.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/inst/niche.png -------------------------------------------------------------------------------- /inst/niche_hist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/inst/niche_hist.png -------------------------------------------------------------------------------- /inst/size.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/inst/size.png -------------------------------------------------------------------------------- /inst/size_hist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/inst/size_hist.png -------------------------------------------------------------------------------- /man/EcoSimR.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/EcoSimR.Rd -------------------------------------------------------------------------------- /man/c_score.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/c_score.Rd -------------------------------------------------------------------------------- /man/c_score_skew.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/c_score_skew.Rd -------------------------------------------------------------------------------- /man/c_score_var.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/c_score_var.Rd -------------------------------------------------------------------------------- /man/checker.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/checker.Rd -------------------------------------------------------------------------------- /man/cooc_null_model.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/cooc_null_model.Rd -------------------------------------------------------------------------------- /man/czekanowski.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/czekanowski.Rd -------------------------------------------------------------------------------- /man/czekanowski_skew.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/czekanowski_skew.Rd -------------------------------------------------------------------------------- /man/czekanowski_var.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/czekanowski_var.Rd -------------------------------------------------------------------------------- /man/dataMacWarb.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/dataMacWarb.Rd -------------------------------------------------------------------------------- /man/dataRodents.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/dataRodents.Rd -------------------------------------------------------------------------------- /man/dataWiFinches.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/dataWiFinches.Rd -------------------------------------------------------------------------------- /man/min_diff.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/min_diff.Rd -------------------------------------------------------------------------------- /man/min_ratio.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/min_ratio.Rd -------------------------------------------------------------------------------- /man/niche_null_model.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/niche_null_model.Rd -------------------------------------------------------------------------------- /man/null_model_engine.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/null_model_engine.Rd -------------------------------------------------------------------------------- /man/pianka.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/pianka.Rd -------------------------------------------------------------------------------- /man/pianka_skew.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/pianka_skew.Rd -------------------------------------------------------------------------------- /man/pianka_var.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/pianka_var.Rd -------------------------------------------------------------------------------- /man/plot.coocnullmod.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/plot.coocnullmod.Rd -------------------------------------------------------------------------------- /man/plot.nichenullmod.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/plot.nichenullmod.Rd -------------------------------------------------------------------------------- /man/plot.nullmod.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/plot.nullmod.Rd -------------------------------------------------------------------------------- /man/plot.sizenullmod.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/plot.sizenullmod.Rd -------------------------------------------------------------------------------- /man/ra1.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/ra1.Rd -------------------------------------------------------------------------------- /man/ra2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/ra2.Rd -------------------------------------------------------------------------------- /man/ra3.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/ra3.Rd -------------------------------------------------------------------------------- /man/ra4.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/ra4.Rd -------------------------------------------------------------------------------- /man/ranMatGen.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/ranMatGen.Rd -------------------------------------------------------------------------------- /man/reproduce_model.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/reproduce_model.Rd -------------------------------------------------------------------------------- /man/sim1.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim1.Rd -------------------------------------------------------------------------------- /man/sim10.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim10.Rd -------------------------------------------------------------------------------- /man/sim2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim2.Rd -------------------------------------------------------------------------------- /man/sim3.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim3.Rd -------------------------------------------------------------------------------- /man/sim4.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim4.Rd -------------------------------------------------------------------------------- /man/sim5.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim5.Rd -------------------------------------------------------------------------------- /man/sim6.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim6.Rd -------------------------------------------------------------------------------- /man/sim7.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim7.Rd -------------------------------------------------------------------------------- /man/sim8.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim8.Rd -------------------------------------------------------------------------------- /man/sim9.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim9.Rd -------------------------------------------------------------------------------- /man/sim9_single.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/sim9_single.Rd -------------------------------------------------------------------------------- /man/size_gamma.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/size_gamma.Rd -------------------------------------------------------------------------------- /man/size_null_model.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/size_null_model.Rd -------------------------------------------------------------------------------- /man/size_source_pool.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/size_source_pool.Rd -------------------------------------------------------------------------------- /man/size_uniform.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/size_uniform.Rd -------------------------------------------------------------------------------- /man/size_uniform_user.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/size_uniform_user.Rd -------------------------------------------------------------------------------- /man/species_combo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/species_combo.Rd -------------------------------------------------------------------------------- /man/summary.coocnullmod.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/summary.coocnullmod.Rd -------------------------------------------------------------------------------- /man/summary.nichenullmod.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/summary.nichenullmod.Rd -------------------------------------------------------------------------------- /man/summary.nullmod.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/summary.nullmod.Rd -------------------------------------------------------------------------------- /man/summary.sizenullmod.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/summary.sizenullmod.Rd -------------------------------------------------------------------------------- /man/v_ratio.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/v_ratio.Rd -------------------------------------------------------------------------------- /man/var_diff.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/var_diff.Rd -------------------------------------------------------------------------------- /man/var_ratio.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/var_ratio.Rd -------------------------------------------------------------------------------- /man/vector_sample.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/man/vector_sample.Rd -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test_cooccurrence.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/tests/testthat/test_cooccurrence.R -------------------------------------------------------------------------------- /tests/testthat/test_nichebreadth.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/tests/testthat/test_nichebreadth.R -------------------------------------------------------------------------------- /tests/testthat/test_sizeratio.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/tests/testthat/test_sizeratio.R -------------------------------------------------------------------------------- /vignettes/CoOccurrenceVignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/vignettes/CoOccurrenceVignette.Rmd -------------------------------------------------------------------------------- /vignettes/SizeRatioVignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/vignettes/SizeRatioVignette.Rmd -------------------------------------------------------------------------------- /vignettes/nicheOverlapVignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/vignettes/nicheOverlapVignette.Rmd -------------------------------------------------------------------------------- /vignettes/nullModelPlug-Ins.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GotelliLab/EcoSimR/HEAD/vignettes/nullModelPlug-Ins.Rmd --------------------------------------------------------------------------------