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ecosimr

Repository for EcoSimR, by Gotelli, N.J. , Hart E. M. and A.M. Ellison. 2014. EcoSimR 0.1.0

https://github.com/gotellilab/ecosimr

Science Score: 41.0%

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    .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
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    Links to: zenodo.org
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    Low similarity (9.2%) to scientific vocabulary
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Repository

Repository for EcoSimR, by Gotelli, N.J. , Hart E. M. and A.M. Ellison. 2014. EcoSimR 0.1.0

Basic Info
  • Host: GitHub
  • Owner: GotelliLab
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage: http://ecosimr.org
  • Size: 7.95 MB
Statistics
  • Stars: 24
  • Watchers: 6
  • Forks: 10
  • Open Issues: 10
  • Releases: 0
Created over 12 years ago · Last pushed about 11 years ago
Metadata Files
Readme License Citation

README.md

Build Status Build status Coverage Status DOI License Downloads

EcoSimR

Repository for EcoSimR, by Gotelli, N.J. and A.M. Ellison. 2015. EcoSimR 0.1.0 http://ecosimr.org

QuickStart

First install the dev branch r install.packages("EcoSimR") Currently null models can be run on niche data, co-occurrence data, and size ratio data

Niche null models ```r library(EcoSimR)

warbMod <- nichenullmodel(macwarb) summary(warbMod) plot(warbMod,type="niche") plot(warbMod, type="hist") r Time Stamp: Thu Jul 24 22:29:52 2014 Random Number Seed: -418884223 Number of Replications: 1000 Elapsed Time: 0.46 secs Metric: pianka Algorithm: ra3 Observed Index: 0.55514 Mean Of Simulated Index: 0.39145 Variance Of Simulated Index: 0.0022785 Lower 95% (1-tail): 0.32365 Upper 95% (1-tail): 0.47571 Lower 95% (2-tail): 0.31274 Upper 95% (2-tail): 0.50608 P(Obs <= null) = 0.997 P(Obs >= null) = 0.003 P(Obs = null) = 0 Standardized Effect Size (SES): 3.4293

```

Niche plots

Niche Null models

Histogram

Niche Null models

Co-Occurrence Null Models

r finchMod <- cooc_null_model(wiFinches, algo="sim3") summary(finchMod) plot(finchMod, typ="cooc") plot(finchMod, type="hist")

```r Time Stamp: Thu Jul 24 22:42:17 2014 Random Number Seed: 1969414287 Number of Replications: 1000 Elapsed Time: 2.7 secs Metric: c_score Algorithm: sim3 Observed Index: 3.7941 Mean Of Simulated Index: 7.2588 Variance Of Simulated Index: 0.25058 Lower 95% (1-tail): 6.6324 Upper 95% (1-tail): 8.1905 Lower 95% (2-tail): 6.5294 Upper 95% (2-tail): 8.3912 P(Obs <= null) = 0 P(Obs >= null) = 1 P(Obs = null) = 0 Standardized Effect Size (SES): -6.9214

```

Sample of shuffled matrix

Co-Occurrence null models

Histogram

Co-Occurrence null models

Also when we run with the simFast algorithm we can get a burn in plot

r finchMod <- cooc_null_model(wiFinches, algo="simFast",burnin=500) plot(finchMod,type="burnin") Co-Occurrence

Size Ratio null models

Lastly we can run null models on size ratios, and produce two different kinds of plots

r rodentMod <- size_null_model(rodents) summary(rodentMod) plot(rodentMode,type="size") plot(rodentMode,type="hist") Time Stamp: Thu Jul 24 22:45:34 2014 Random Number Seed: -438432393 Number of Replications: 1000 Elapsed Time: 0.15 secs Metric: var_ratio Algorithm: uniform_size Observed Index: 0.071826 Mean Of Simulated Index: 0.18809 Variance Of Simulated Index: 0.012434 Lower 95% (1-tail): 0.055043 Upper 95% (1-tail): 0.41076 Lower 95% (2-tail): 0.044767 Upper 95% (2-tail): 0.45634 P(Obs <= null) = 0.097 P(Obs >= null) = 0.903 P(Obs = null) = 0 Standardized Effect Size (SES): -1.0427

Size null model

Co-Occurrence null models

Histogram

Co-Occurrence null models

Owner

  • Name: Gotelli Lab
  • Login: GotelliLab
  • Kind: organization
  • Email: ngotelli@uvm.edu
  • Location: Department of Biology, University of Vermont

Pitcher plants, ants, null models, and more...

Citation (CITATION) 

citEntry(entry = "Manual",
  title   = "EcoSimR: Null model analysis for ecological data",
  author  = "Nicholas J. Gotelli and Edmund M. Hart and Aaron M. Ellison",
  year    = "2015",
  note    = "R package version 0.1.0",
  url     = "http://github.com/gotellilab/EcoSimR",
  doi     = "10.5281/zenodo.16522",

  textVersion =
  paste("Nicholas J. Gotelli, Edmund M. Hart and Aaron M. Ellison (2015) EcoSimR:  Null model analysis for ecological data. R package version 0.1.0. http://github.com/gotellilab/EcoSimR DOI: 10.5281/zenodo.16522")
)

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Dependencies

DESCRIPTION cran
  • MASS * depends
  • knitr * suggests
  • testthat * suggests