EcoSimR: Null Model Analysis for Ecological Data

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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

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