EcoSimR: Null Model Analysis for Ecological Data
Version 0.1.0

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.

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("EcoSimR")

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

Functions

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

Files

inst
inst/cooc_hist.png
inst/CITATION
inst/niche.png
inst/cooc.png
inst/size.png
inst/doc
inst/doc/CoOccurrenceVignette.html
inst/doc/nullModelPlug-Ins.R
inst/doc/SizeRatioVignette.R
inst/doc/nullModelPlug-Ins.Rmd
inst/doc/nullModelPlug-Ins.html
inst/doc/CoOccurrenceVignette.R
inst/doc/nicheOverlapVignette.R
inst/doc/SizeRatioVignette.html
inst/doc/nicheOverlapVignette.html
inst/doc/SizeRatioVignette.Rmd
inst/doc/CoOccurrenceVignette.Rmd
inst/doc/nicheOverlapVignette.Rmd
inst/niche_hist.png
inst/size_hist.png
inst/burnin.png
tests
tests/testthat.R
tests/testthat
tests/testthat/test_nichebreadth.R
tests/testthat/test_cooccurrence.R
tests/testthat/test_sizeratio.R
NAMESPACE
data
data/datasets.rda
R
R/coccurrence_null.R
R/metrics.R
R/sim9fast.R
R/algorithms.R
R/randomMatrixGenerator.R
R/null_model_engine.R
R/sizeratio_null.R
R/reproduce_model.R
R/EcoSimR-package.r
R/niche_overlap_null.R
vignettes
vignettes/nullModelPlug-Ins.Rmd
vignettes/SizeRatioVignette.Rmd
vignettes/CoOccurrenceVignette.Rmd
vignettes/nicheOverlapVignette.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/czekanowski_skew.Rd
man/ranMatGen.Rd
man/czekanowski_var.Rd
man/sim10.Rd
man/sim5.Rd
man/var_diff.Rd
man/dataRodents.Rd
man/vector_sample.Rd
man/summary.nullmod.Rd
man/dataMacWarb.Rd
man/sim2.Rd
man/summary.nichenullmod.Rd
man/pianka.Rd
man/c_score.Rd
man/pianka_var.Rd
man/plot.nichenullmod.Rd
man/size_uniform_user.Rd
man/reproduce_model.Rd
man/ra4.Rd
man/sim4.Rd
man/plot.coocnullmod.Rd
man/size_gamma.Rd
man/v_ratio.Rd
man/sim6.Rd
man/ra2.Rd
man/czekanowski.Rd
man/min_diff.Rd
man/size_source_pool.Rd
man/plot.sizenullmod.Rd
man/sim3.Rd
man/species_combo.Rd
man/ra1.Rd
man/var_ratio.Rd
man/summary.sizenullmod.Rd
man/c_score_var.Rd
man/c_score_skew.Rd
man/pianka_skew.Rd
man/plot.nullmod.Rd
man/size_null_model.Rd
man/sim7.Rd
man/size_uniform.Rd
man/dataWiFinches.Rd
man/checker.Rd
man/summary.coocnullmod.Rd
man/sim8.Rd
man/min_ratio.Rd
man/ra3.Rd
man/sim9.Rd
man/null_model_engine.Rd
man/EcoSimR.Rd
man/sim1.Rd
man/sim9_single.Rd
man/niche_null_model.Rd
man/cooc_null_model.Rd
LICENSE
EcoSimR documentation built on May 19, 2017, 7:40 p.m.