bot89-introR.bib

% Encoding: UTF-8
"

@Article{Vicentini2016,
  author        = {Vicentini, Alberto},
  title         = {{The evolutionary history of \textit{Pagamea} (Rubiaceae), a white-sand specialist lineage in tropical South America}},
  journal       = {Biotropica},
  year          = {2016},
  volume        = {48},
  number        = {1},
  pages         = {58--69},
  date-added    = {2016-03-12 04:21:41 +0000},
  date-modified = {2016-03-12 04:21:41 +0000},
  file          = {:/Users/ricoperdiz/Documents/CIENCIA/Vicentini_LAB-ECOEVOAMAZON/Vicentini2016.pdf:PDF},
  publisher     = {Wiley Online Library},
}
@Book{VenablesRipley2002,
  title     = {Modern Applied Statistics with {S}},
  publisher = {Springer},
  year      = {2002},
  author    = {Venables, W. N. and Ripley, B. D.},
  address   = {New York},
  note      = {ISBN 0-387-95457-0, fourth edition},
  keywords  = {R-project; MASS package},
  url       = {http://www.stats.ox.ac.uk/pub/MASS4},
}

@Article{APG,
  author  = {{APG}},
  title   = {{An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV}},
  journal = {Botanical Journal of the Linnean Society},
  year    = {2016},
  volume  = {181},
  pages   = {1-–20},
  file    = {:/Users/ricoperdiz/Documents/CIENCIA/Artigos_livros_afins/APG/APGIV2016.pdf:PDF},
}

@Manual{rstudio,
  title        = {RStudio: Integrated Development Environment for R},
  author       = {{RStudio Team}},
  organization = {RStudio, PBC.},
  address      = {Boston, MA},
  year         = {2020},
  url          = {http://www.rstudio.com/},
}

@Manual{R-ape,
  title = {ape: Analyses of Phylogenetics and Evolution},
  author = {Emmanuel Paradis and Simon Blomberg and Ben Bolker and Joseph Brown and Santiago Claramunt and Julien Claude and Hoa Sien Cuong and Richard Desper and Gilles Didier and Benoit Durand and Julien Dutheil and RJ Ewing and Olivier Gascuel and Thomas Guillerme and Christoph Heibl and Anthony Ives and Bradley Jones and Franz Krah and Daniel Lawson and Vincent Lefort and Pierre Legendre and Jim Lemon and Guillaume Louvel and Eric Marcon and Rosemary McCloskey and Johan Nylander and Rainer Opgen-Rhein and Andrei-Alin Popescu and Manuela Royer-Carenzi and Klaus Schliep and Korbinian Strimmer and Damien {de Vienne}},
  year = {2020},
  note = {R package version 5.4-1},
  url = {http://ape-package.ird.fr/},
}

@Manual{R-base,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2020},
  url = {https://www.R-project.org/},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 0.21.6},
  url = {https://github.com/rstudio/bookdown},
}

@Manual{R-datatable,
  title  = {data.table: Extension of `data.frame`},
  author = {Matt Dowle and Arun Srinivasan},
  year   = {2020},
  note   = {R package version 1.13.4},
  url    = {https://CRAN.R-project.org/package=data.table},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel {
             Henry} and Kirill Müller},
  year = {2020},
  note = {R package version 1.0.2},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},
  year = {2020},
  note = {R package version 3.3.3},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-kableExtra,
  title = {kableExtra: Construct Complex Table with kable and Pipe Syntax},
  author = {Hao Zhu},
  year = {2020},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=kableExtra},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 1.31},
  url = {https://yihui.org/knitr/},
}

@Manual{R-magrittr,
  title = {magrittr: A Forward-Pipe Operator for R},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2020},
  note = {R package version 2.0.1},
  url = {https://CRAN.R-project.org/package=magrittr},
}

@Manual{R-maps,
  title = {maps: Draw Geographical Maps},
  author = {Ray Brownrigg},
  year = {2018},
  note = {R package version 3.3.0},
  url = {https://CRAN.R-project.org/package=maps},
}

@Manual{R-printr,
  title = {printr: Automatically Print R Objects to Appropriate Formats According
to the knitr Output Format},
  author = {Yihui Xie},
  year = {2017},
  note = {R package version 0.1},
  url = {https://yihui.name/printr/},
}

@Manual{R-purrr,
  title = {purrr: Functional Programming Tools},
  author = {Lionel Henry and Hadley Wickham},
  year = {2020},
  note = {R package version 0.3.4},
  url = {https://CRAN.R-project.org/package=purrr},
}

@Manual{R-readr,
  title = {readr: Read Rectangular Text Data},
  author = {Hadley Wickham and Jim Hester},
  year = {2020},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=readr},
}

@Manual{R-readxl,
  title = {readxl: Read Excel Files},
  author = {Hadley Wickham and Jennifer Bryan},
  year = {2019},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=readxl},
}

@Manual{R-rgdal,
  title = {rgdal: Bindings for the Geospatial Data Abstraction Library},
  author = {Roger Bivand and Tim Keitt and Barry Rowlingson},
  year = {2020},
  note = {R package version 1.5-18},
  url = {https://CRAN.R-project.org/package=rgdal},
}

@Manual{R-taxize,
  title = {taxize: Taxonomic Information from Around the Web},
  author = {Scott Chamberlain and Eduard Szoecs and Zachary Foster and Zebulun Arendsee},
  year = {2020},
  note = {R package version 0.9.99},
  url = {https://CRAN.R-project.org/package=taxize},
}

@Article{ape2019,
  title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
  author = {E. Paradis and K. Schliep},
  journal = {Bioinformatics},
  year = {2019},
  volume = {35},
  pages = {526-528},
}

@Book{bookdown2016,
  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2016},
  note = {ISBN 978-1138700109},
  url = {https://github.com/rstudio/bookdown},
}

@Book{ggplot22016,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2016},
  isbn = {978-3-319-24277-4},
  url = {https://ggplot2.tidyverse.org},
}

@Book{knitr2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.org/knitr/},
}

@InCollection{knitr2014,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

@Article{taxize2013,
  title = {taxize - taxonomic search and retrieval in R},
  journal = {F1000Research},
  author = {{Scott Chamberlain} and {Eduard Szocs}},
  year = {2013},
  url = {https://f1000research.com/articles/2-191/v2},
}

@Article{Zuuretal2010,
  author   = {Zuur, Alain F. and Ieno, Elena N. and Elphick, Chris S.},
  title    = {A protocol for data exploration to avoid common statistical problems},
  journal  = {Methods in Ecology and Evolution},
  year     = {2010},
  volume   = {1},
  number   = {1},
  pages    = {3-14},
  abstract = {Summary 1. While teaching statistics to ecologists, the lead authors of this paper have noticed common statistical problems. If a random sample of their work (including scientific papers) produced before doing these courses were selected, half would probably contain violations of the underlying assumptions of the statistical techniques employed. 2. Some violations have little impact on the results or ecological conclusions; yet others increase type I or type II errors, potentially resulting in wrong ecological conclusions. Most of these violations can be avoided by applying better data exploration. These problems are especially troublesome in applied ecology, where management and policy decisions are often at stake. 3. Here, we provide a protocol for data exploration; discuss current tools to detect outliers, heterogeneity of variance, collinearity, dependence of observations, problems with interactions, double zeros in multivariate analysis, zero inflation in generalized linear modelling, and the correct type of relationships between dependent and independent variables; and provide advice on how to address these problems when they arise. We also address misconceptions about normality, and provide advice on data transformations. 4. Data exploration avoids type I and type II errors, among other problems, thereby reducing the chance of making wrong ecological conclusions and poor recommendations. It is therefore essential for good quality management and policy based on statistical analyses.},
  doi      = {10.1111/j.2041-210X.2009.00001.x},
  eprint   = {https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-210X.2009.00001.x},
  file     = {:/Users/ricoperdiz/Documents/CIENCIA/Artigos_livros_afins/Zuuretal2010.pdf:PDF},
  keywords = {collinearity, data exploration, independence, transformations, type I and II errors, zero inflation},
  url      = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.2041-210X.2009.00001.x},
}

@Article{Tukey1980,
  author    = {John W. Tukey},
  title     = {We need both exploratory and confirmatory},
  journal   = {The American Statistician},
  year      = {1980},
  volume    = {34},
  number    = {1},
  pages     = {23--25},
  abstract  = { Abstract We often forget how science and engineering function. Ideas come from previous exploration more often than from lightning strokes. Important questions can demand the most careful planning for confirmatory analysis. Broad general inquiries are also important. Finding the question is often more important than finding the answer. Exploratory data analysis is an attitude, a flexibility, and a reliance on display, NOT a bundle of techniques, and should be so taught. Confirmatory data analysis, by contrast, is easier to teach and easier to computerize. We need to teach both; to think about science and engineering more broadly; to be prepared to randomize and avoid multiplicity. },
  doi       = {10.1080/00031305.1980.10482706},
  eprint    = {https://www.tandfonline.com/doi/pdf/10.1080/00031305.1980.10482706},
  file      = {:/Users/ricoperdiz/Documents/CIENCIA/Artigos_livros_afins/Tukey1980.pdf:PDF},
  publisher = {Taylor \& Francis},
  url       = {https://www.tandfonline.com/doi/abs/10.1080/00031305.1980.10482706},
}

@Book{Burns2012_rinferno,
  title     = {{The R Inferno}},
  publisher = {Lulu.com},
  year      = {2012},
  author    = {Burns, Patrick},
  isbn      = {9781471046520},
  abstract  = {A book about trouble spots, oddities, traps, glitches in R. If you are using R and you think you’re in hell, this is a map for you.},
  file      = {:/Users/ricoperdiz/Documents/CIENCIA/Artigos_livros_afins/Burns2012_rinferno.pdf:PDF},
  url       = {https://www.burns-stat.com/documents/books/the-r-inferno/},
}

@Book{Chambers2008,
  title     = {Programming with R},
  publisher = {Springer},
  year      = {2008},
  author    = {Chambers, John M.},
  editor    = {Härdle, W. and Hand, David},
  isbn      = {978-0-387-75935-7},
  doi       = {10.1007/978-0-387-75936-4},
  file      = {:/Users/ricoperdiz/Documents/CIENCIA/Artigos_livros_afins/Chambers2008.pdf:PDF},
}

@Book{Crawley2007,
  title     = {{The R book}},
  publisher = {John Wiley \& Sons, Ltd},
  year      = {2007},
  author    = {Crawley, Michael J.},
  isbn      = {978-0-470-97392-9},
  doi       = {10.1002/9780470515075},
  file      = {:/Users/ricoperdiz/Documents/CIENCIA/Artigos_livros_afins/Crawley2007.pdf:PDF},
}

@Book{Gotelli2013,
  title     = {{A Primer of Ecological Statistics}},
  publisher = {Sinauer Associates},
  year      = {2013},
  author    = {Gotelli, Nicholas J. and Ellison, Aaron M.},
  edition   = {2},
}

@Manual{R-labdsv,
  title  = {labdsv: Ordination and Multivariate Analysis for Ecology},
  author = {David W. Roberts},
  year   = {2019},
  note   = {R package version 2.0-1},
  url    = {http://ecology.msu.montana.edu/labdsv/R},
}

@Manual{R-vegan,
  title  = {vegan: Community Ecology Package},
  author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
  year   = {2020},
  note   = {R package version 2.5-7},
  url    = {https://CRAN.R-project.org/package=vegan},
}

@Manual{R-lattice,
  title  = {lattice: Trellis Graphics for R},
  author = {Deepayan Sarkar},
  year   = {2020},
  note   = {R package version 0.20-41},
  url    = {http://lattice.r-forge.r-project.org/},
}

@Manual{Chalometal2012,
  title  = {notaR - Um sistema para notas automatizadas em cursos que utilizam a linguagem R (Version 2.0)},
  author = {Chalom, A. and Salles, M. and Prado, P. I. and Adalardo, A.},
  year   = {2012},
  url    = {https://github.com/lageIBUSP/notaR},
}

@Manual{Batista2009,
  title  = {{Introdução ao R - Uma Apostila online}},
  author = {Batista, J.L.F. and Prado P.I. and Oliveira, A. A.},
  year   = {2009},
  url    = {http://ecologia.ib.usp.br/bie5782},
}

@Comment{jabref-meta: databaseType:bibtex;}

"