Preface

This book will be a manual for the R package papaja. It is currently in the process of being written; I’m publishing new sections of the book as I’m writing them. If you have suggestions for improvements or additional topics you would like to see covered, please let me know by opening an issue on GitHub or creating a pull request.

papaja has not yet been submitted to CRAN because it is under active development. Currently, there are still a couple of loose ends we would like to tie up before we release the package to a larger audience. If you would like to contribute to speed up the process, have a look at the chapters Limitations and Future directions.

If you are interested in reproducible research with R more generally, I recommend the books by Xie (2015) and Gandrud (2013). Furthermore, Stodden, Leisch, & Peng (2014) give an overview of tools, practices, and platforms to implement reproducible research.

This manual is fully reproducible and was written in R (Version 3.4.4; R Core Team, 2016) and the R-packages afex (Version 0.20.2; Singmann, Bolker, Westfall, & Aust, 2016), bindrcpp (Version 0.2.2; Müller, 2017), car (Version 2.1.6; Fox & Weisberg, 2011), citr (Version 0.2.0.9055; Aust, 2016), DiagrammeR (Version 0.9.2; Sveidqvist et al., 2016), dplyr (Version 0.7.6; Wickham & Francois, 2016), ez (Version 4.4.0; Lawrence, 2016), ggplot2 (Version 2.2.1; Wickham, 2009), knitr (Version 1.20; Xie, 2015), lme4 (Version 1.1.15; Bates, Mächler, Bolker, & Walker, 2015), lsmeans (Version 2.27.61; Lenth, 2016), papaja (Version 0.1.0.9842; Aust & Barth, 2016), rmarkdown (Version 1.10; Allaire et al., 2017), shiny (Version 1.1.0; Chang, Cheng, Allaire, Xie, & McPherson, 2016), and wordcountaddin (Version 0.2.0; Marwick, n.d.). Icons are provide royalty


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##  ui       X11                         
##  language en_US:                      
##  collate  en_US.UTF-8                 
##  tz       Europe/Berlin               
##  date     2018-08-17
## Packages -----------------------------------------------------------------
##  package      * version    date       source                          
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##  colorspace     1.3-2      2016-12-14 CRAN (R 3.4.2)                  
##  compiler       3.4.4      2018-03-16 local                           
##  datasets     * 3.4.4      2018-03-16 local                           
##  devtools       1.13.5     2018-02-18 cran (@1.13.5)                  
##  DiagrammeR   * 0.9.2      2017-09-06 CRAN (R 3.4.2)                  
##  digest         0.6.15     2018-01-28 cran (@0.6.15)                  
##  downloader     0.4        2015-07-09 CRAN (R 3.4.2)                  
##  dplyr          0.7.6      2018-06-29 cran (@0.7.6)                   
##  evaluate       0.10.1     2017-06-24 CRAN (R 3.4.2)                  
##  ez           * 4.4-0      2016-11-02 CRAN (R 3.4.3)                  
##  ggplot2      * 2.2.1      2016-12-30 CRAN (R 3.4.2)                  
##  glue           1.2.0      2017-10-29 cran (@1.2.0)                   
##  graphics     * 3.4.4      2018-03-16 local                           
##  grDevices    * 3.4.4      2018-03-16 local                           
##  grid           3.4.4      2018-03-16 local                           
##  gridExtra      2.3        2017-09-09 CRAN (R 3.4.2)                  
##  gtable         0.2.0      2016-02-26 CRAN (R 3.4.2)                  
##  hms            0.3        2016-11-22 CRAN (R 3.4.2)                  
##  htmltools      0.3.6      2017-04-28 CRAN (R 3.4.2)                  
##  htmlwidgets    1.0        2018-01-20 cran (@1.0)                     
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##  influenceR     0.1.0      2015-09-03 CRAN (R 3.4.2)                  
##  jsonlite       1.5        2017-06-01 CRAN (R 3.4.2)                  
##  knitr          1.20       2018-02-20 cran (@1.20)                    
##  lattice        0.20-35    2017-03-25 CRAN (R 3.3.3)                  
##  lazyeval       0.2.0      2016-06-12 CRAN (R 3.4.2)                  
##  lme4           1.1-15     2017-12-21 cran (@1.1-15)                  
##  magrittr       1.5        2014-11-22 CRAN (R 3.4.2)                  
##  MASS           7.3-50     2018-04-30 CRAN (R 3.4.4)                  
##  Matrix         1.2-14     2018-04-09 CRAN (R 3.4.4)                  
##  MatrixModels   0.4-1      2015-08-22 CRAN (R 3.4.2)                  
##  memoise        1.1.0      2017-04-21 CRAN (R 3.4.2)                  
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##  nloptr         1.0.4      2017-08-22 CRAN (R 3.4.2)                  
##  nnet           7.3-12     2016-02-02 CRAN (R 3.4.0)                  
##  papaja       * 0.1.0.9842 2018-08-17 local (crsh/papaja@NA)          
##  parallel       3.4.4      2018-03-16 local                           
##  pbkrtest       0.4-7      2017-03-15 CRAN (R 3.4.2)                  
##  pillar         1.2.1      2018-02-27 cran (@1.2.1)                   
##  pkgconfig      2.0.1      2017-03-21 CRAN (R 3.4.2)                  
##  plyr           1.8.4      2016-06-08 CRAN (R 3.4.2)                  
##  purrr          0.2.5      2018-05-29 CRAN (R 3.4.4)                  
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##  stats        * 3.4.4      2018-03-16 local                           
##  stringi        1.2.4      2018-07-20 cran (@1.2.4)                   
##  stringr        1.3.1      2018-05-10 cran (@1.3.1)                   
##  tibble         1.4.2      2018-01-22 cran (@1.4.2)                   
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##  tidyselect     0.2.4      2018-02-26 cran (@0.2.4)                   
##  tools          3.4.4      2018-03-16 local                           
##  utils        * 3.4.4      2018-03-16 local                           
##  viridis        0.5.0      2018-02-02 cran (@0.5.0)                   
##  viridisLite    0.3.0      2018-02-01 cran (@0.3.0)                   
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##  withr          2.1.1      2017-12-19 cran (@2.1.1)                   
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##  yaml           2.2.0      2018-07-25 cran (@2.2.0)

References

Xie, Y. (2015). Dynamic documents with R and knitr (2nd ed.). Boca Raton, Florida: Chapman; Hall/CRC. Retrieved from http://yihui.name/knitr/

Gandrud, C. (2013). Reproducible Research with R and Rstudio (Auflage: New.). Boca Raton: Crc Pr Inc.

Stodden, V., Leisch, F., & Peng, R. D. (2014). Implementing Reproducible Research. Boca Raton: Chapman and Hall/CRC. Retrieved from https://osf.io/s9tya/

R Core Team. (2016). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from https://www.R-project.org/

Singmann, H., Bolker, B., Westfall, J., & Aust, F. (2016). Afex: Analysis of factorial experiments. Retrieved from https://CRAN.R-project.org/package=afex

Müller, K. (2017). Bindrcpp: An ’rcpp’ interface to active bindings. Retrieved from https://CRAN.R-project.org/package=bindrcpp

Fox, J., & Weisberg, S. (2011). An R companion to applied regression (Second.). Thousand Oaks CA: Sage. Retrieved from http://socserv.socsci.mcmaster.ca/jfox/Books/Companion

Aust, F. (2016). Citr: ’RStudio’ add-in to insert markdown citations. Retrieved from https://CRAN.R-project.org/package=citr

Sveidqvist, K., Bostock, M., Pettitt, C., Daines, M., Kashcha, A., & Iannone, R. (2016). DiagrammeR: Create graph diagrams and flowcharts using r. Retrieved from https://CRAN.R-project.org/package=DiagrammeR

Wickham, H., & Francois, R. (2016). Dplyr: A grammar of data manipulation. Retrieved from https://CRAN.R-project.org/package=dplyr

Lawrence, M. A. (2016). Ez: Easy analysis and visualization of factorial experiments. Retrieved from https://CRAN.R-project.org/package=ez

Wickham, H. (2009). Ggplot2: Elegant graphics for data analysis. Springer-Verlag New York. Retrieved from http://ggplot2.org

Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67(1), 1–48. doi:10.18637/jss.v067.i01

Lenth, R. V. (2016). Least-squares means: The R package lsmeans. Journal of Statistical Software, 69(1), 1–33. doi:10.18637/jss.v069.i01

Aust, F., & Barth, M. (2016). Papaja: Create apa manuscripts with rmarkdown. Retrieved from https://github.com/crsh/papaja

Allaire, J., Xie, Y., McPherson, J., Luraschi, J., Ushey, K., Atkins, A., … Chang, W. (2017). Rmarkdown: Dynamic documents for r. Retrieved from https://CRAN.R-project.org/package=rmarkdown

Chang, W., Cheng, J., Allaire, J., Xie, Y., & McPherson, J. (2016). Shiny: Web application framework for r. Retrieved from http://shiny.rstudio.com

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