====== R Stuff ======

[[http://www.r-project.org|{{:tutoriais:rlogo-4.png  }}]] Some R-codes, class notes and tutorials produced by our team and collaborators. We are glad to share them as they are, of course without any warranty that they are all running properly.

Your feedback is very welcome.

===== R Packages =====
==== Species Abundance Distributions ====

  * Package [[http://cran.r-project.org/web/packages/sads|sads]] on CRAN
  
  * [[http://piklprado.github.io/sads/|Package site]] at GitHub

==== Parameter Space Exploration ====
  * R Package [[http://cran.r-project.org/web/packages/pse|pse]] on CRAN
  * Chalom, A. & Prado, P.I. 2012. Parameter space exploration of ecological models. [[http://arxiv.org/abs/1210.6278]]


=====Codes and tutorials=====
==== R programing and modelling ====

  * [[http://ecologia.ib.usp.br/bie5782/doku.php?id=bie5782:03_apostila:start|On line syllabus]] from our graduate course on using R in ecology. In portuguese.
  * [[http://ecologia.ib.usp.br/bie5782/doku.php?id=bie5782:02_tutoriais:start|Tutorials on basic use of the R environment]], from our graduate course on using R in ecology. In portuguese.
  * [[tutoriais:tut-mod|quick R tutorial on model fiting]] by the maximum likelihood method. In portuguese.
  * [[http://cmq.esalq.usp.br/LCF5877/|Our graduate course on statistical modelling]]: nice R tutorials and study notes. In portuguese.

==== Additive Diversity Partitioning ====

The R package vegan has [[http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adipart.html|functions]] for individual-based permutation tests of additive diversity partitioning (//sensu// Crist et al. 2003).

Here we provide a code for the sample-based tests (Crist et al. 2003), where sample units of a given level are shuffled within units of the level above. 

This code is an improved version of code used by Ribeiro et al. (2008). Apart code fine-tuning, in this version average diversity indexes are not weighted (see Crist et al. 2003).

  * {{:tutoriais:funcoes_partition.r|R code - Sample-based partition test}}
  * {{:didatico:quantif:bird.csv|Test data: birds in Southern Bahia}} (Pardini //et al.// 2009).
  * {{:tutoriais:partition_example.txt|Results of analysis of test data}}
  * {{:tutoriais:roteiro_particao.pdf|An introductory tutorial in R}} of additive diversity partitioning, from a graduate course (in portuguese).

==== Compound glm's ====

Compound generalized linear models of [[http://dx.doi.org/10.1371%2Fjournal.pone.0013666|Pardini et al. (2010)]]. 

Different combinations of Poisson and negative binomial linear models were used to predict number of species (or individuals) of small mammals in three landscapes that differ in the remaining forest cover. Each of these combinations represents alternative hypotheses on the interaction between landscape context and patch-area in fragmented landscapes. 

  * {{:engl:tutorials:pardini_etal_2010.r|R codes of the analysis}}
  * {{:engl:tutorials:datastruct.txt|Structure of the database used}}


===== References =====


<bibtex>
@ARTICLE{Alonso2008,
  author = {Alonso, D and Ostling, A and Etienne, R S},
  title = {The implicit assumption of symmetry and the species abundance distribution},
  journal = {Ecology Letters},
  year = {2008},
  volume = {11},
  pages = {93-105},
 url={http://www3.interscience.wiley.com/journal/119419803/suppinfo|SOM}
}
@ARTICLE{bulmer1974,
  author = {Bulmer, M. G.},
  title = {On fitting the Poisson lognormal distribution to species abundance
	data},
  journal = {Biometrics},
  year = {1974},
  volume = {30},
  pages = {651-660},
  owner = {paulo},
  timestamp = {2009.04.12}
}

@article{crist2003,
  title={Partitioning species diversity across landscapes and regions: a hierarchical analysis of $$\alpha$$, $$\beta$$, and $$\gamma$$ diversity},
  author={Crist, T.O. and Veech, J.A. and Gering, J.C. and Summerville, K.S.},
  journal={The American Naturalist},
  volume={162},
  pages={734--743},
  year={2003},
  publisher={Univ. Chicago Press}
}

@ARTICLE{fisher1947,
  author = {Fisher, R.A. and Corbet, A.S. and Williams, C.B.},
  title = {The relation between the number of the species and the number of
	individuals in a random sample from animal population},
  journal = {Journal of Animal Ecology},
  year = {1943},
  volume = {12},
  pages = {42-58},
  owner = {paulo},
  timestamp = {2009.04.12}
}
@ARTICLE{Green2007,
  author = {Jessica L. Green and Joshua B. Plotkin},
  title = {A statistical theory for sampling species abundances},
  journal = {Ecology Letters},
  year = {2007},
  volume = {10},
  pages = {1037 - 1045},
  owner = {paulo},
  timestamp = {2008.12.16},
  url={http://www3.interscience.wiley.com/journal/118545784/suppinfo}
 }

  @Manual{grotan2008,
    title = {poilog: Poisson lognormal and bivariate Poisson lognormal distribution},
    author = {Vidar Grøtan and Steinar Engen},
    year = {2008},
    note = {R package version 0.4},
    url={http://finzi.psych.upenn.edu/R/library/poilog/html/00Index.html}
  }


@ARTICLE{MacArthur1960,
  author = {MacArthur, R. H.},
  title = {On the relative abundance of species},
  journal = {American Naturalist},
  year = {1960},
  volume = {94},
  pages = {25-36},
  owner = {paulo},
  timestamp = {2009.04.11}
}

@ARTICLE{Motomura1932,
  author = {I Motomura},
  title = {On the statistical treatment of communities},
  journal = {Zoological Magazine, Tokyo},
  year = {1932},
  volume = {44},
  pages = {379-383},
  owner = {paulo},
  timestamp = {2009.04.14}
}

@ARTICLE{pardini2009,
  author = {Pardini, R. and Faria, D. and Accacio, G.M. and Laps, R.R. and Mariano-Neto, E. and Paciencia, M.L.B. and Dixo, M. and Baumgarten, J.},
  title = {The challenge of maintaining Atlantic forest biodiversity: A multi-taxa
	conservation assessment of specialist and generalist species in an
	agro-forestry mosaic in southern Bahia},
  journal = {Biological Conservation},
  year = {2009},
  volume = {142},
  pages = {1178--1190},
  number = {6},
  publisher = {Elsevier}
}

@article{pardini2010,
    author = {Pardini, Renata AND Bueno, Adriana de Arruda AND Gardner, Toby A. AND Prado, Paulo Inácio AND Metzger, Jean Paul},
    journal = {PLoS ONE},
    publisher = {Public Library of Science},
    title = {Beyond the Fragmentation Threshold Hypothesis: Regime Shifts in Biodiversity Across Fragmented Landscapes},
    year = {2010},
    month = {10},
    volume = {5},
    url = {http://dx.doi.org/10.1371%2Fjournal.pone.0013666},
    pages = {e13666},
    number = {10},
    doi = {10.1371/journal.pone.0013666}
}        

@ARTICLE{ribeiro2008,
  author = {Ribeiro, D.B. and Prado, P.I. and Brown Jr, K.S. and Freitas, A.V.L.},
  title = {Additive partitioning of butterfly diversity in a fragmented landscape:
	importance of scale and implications for conservation},
  journal = {Diversity and Distributions},
  year = {2008},
  volume = {14},
  pages = {961--968},
  number = {6},
  publisher = {John Wiley \& Sons},
  file={:prado:ribeiro2008.pdf}
}

</bibtex>