Fit and Compare Species-Area Relationship Models Using Multimodel Inference

Implements the basic elements of the multi-model inference paradigm for up to twenty species-area relationship models (SAR), using simple R list-objects and functions, as in Triantis et al. 2012 . The package is scalable and users can easily create their own model and data objects. Additional SAR related functions are provided.


The 'sars' R Package

Build Status Downloads CRAN

sars provides functionality to fit twenty SAR model using non-linear regression, and to calculate multi-model averaged curves using various information criteria. The software also provides easy to use functionality to plot multi-model SAR curves and to generate confidence intervals using bootstrapping. Additional SAR related functions include fitting the linear version of the power model and comparing parameters with the non-linear version, fitting the general dynamic model of island biogeography, and fitting the random placement model to a species abundance - site matrix.

As this is version 1.0.0 of the package, it is possible that there are some bugs in places. Please report any issues to us via GitHub.

Table of Contents

Installation

You can install the released version of sars from CRAN with:

install.packages("sars")

And the development version from GitHub with:

devtools::install_github("txm676/sars")

Example usage

Basic usage of sars will result in using two types of functions:

To fit the power sar model (Arrhenius 1921) to the 'galapagos' (Preston 1962) data set:

fit_pow <- sar_power(data = galap)

Attempting to fit all 20 sar models to the 'galapagos' (Preston 1962) data set and get a multi-model SAR:

mm_galap <- sar_multi(data = galap)
#> 
#>  Now attempting to fit the 20 SAR models: 
#>  
#> --  multi_sars ---------------------------------------------------------------------------- multi-model SAR --
#> > power    : v
#> > powerR   : v
#> > epm1     : v
#> > epm2     : v
#> > p1       : v
#> > p2       : v
#> > expo     : v
#> > koba     : v
#> > mmf      : v
#> > monod    : v
#> > negexpo  : v
#> > chapman  : Warning: could not compute parameters statistics
#> > weibull3 : v
#> > asymp    : v
#> > ratio    : v
#> > gompertz : v
#> > weibull4 : v
#> > betap    : v
#> > heleg    : v
#> > linear   : v
#> 
#>  Model fitting completed - all models succesfully fitted. Now undertaking model validation checks. 
#>  Additional models will be excluded if necessary:
#> 
#> 4 models failed the residuals normality test and have been excluded from the multi SAR:
#> Extended Power model 1, Asymptotic regression, Cumulative Weibull 4 par., Linear model
#> 
#> 1 models have negative fitted values and have been excluded from the multi SAR:
#> Exponential
#> 15 remaining models used to construct the multi SAR: 
#>  Power, PowerR, Extended Power model 2, Persistence function 1, Persistence function 2, Kobayashi, MMF, Monod, Negative exponential, Chapman Richards, Cumulative Weibull 3 par., Rational function, Gompertz, Beta-P cumulative, Heleg(Logistic) 
#> --------------------------------------------------------------------------------------------------------------

Each of the 'fitted' objects have corresponding plot methods:

to fit the exponential SAR model (Gleason 1922) to the 'galapagos' data set and plot it

fit_expo <- sar_expo(data = galap)
 
plot(fit_expo)

to fit a multimodel SAR curve to the 'galapagos' data set and plot it

mm_galap <- suppressMessages(sar_multi(data = galap, verb = FALSE))
 
plot(mm_galap, pLeg = FALSE)

Troubleshoutting

If, despite the ❤️ brought during the programming of this R 📦 and writing of this documentation, you have difficulties to install or run sars, if you have questions about the procedures or calculations, or if you want to report bugs 🐞, do not hesitate to connect with us on GitHub.

References

Arrhenius, Olof. 1921. “Species and Area.” The Journal of Ecology 9 (1). British Ecological Society: 95. doi:10.2307/2255763.

Gleason, Henry Allan. 1922. “On the Relation Between Species and Area.” Ecology 3 (2). Ecological Society of America: 158–62. doi:10.2307/1929150.

Preston, F. W. 1962. “The Canonical Distribution of Commonness and Rarity: Part I.” Ecology 43 (2). Ecological Society of America: 185. doi:10.2307/1931976.

News

Version 1.0.0

  • Initial version on CRAN

Reference manual

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install.packages("sars")

1.1.0 by Thomas J. Matthews, 21 days ago


https://github.com/txm676/sars


Report a bug at https://github.com/txm676/sars/issues


Browse source code at https://github.com/cran/sars


Authors: Thomas J. Matthews [aut, cre] , Francois Guilhaumon [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports dplyr, graphics, nortest, stats, utils, crayon, cli, numDeriv

Suggests knitr, rmarkdown, testthat


See at CRAN