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.

Install the latest version of this package by entering the following in R:
install.packages("EcoSimR")
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

Functions

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

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

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.