Source code files for the book Reproducible Research with R/RStudio
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CoverGraphics/2ndEditionCover_v1 cover 1st attempt Feb 16, 2015
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Source explain Rnw Mar 16, 2016
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README.md connect to 2nd edition images May 23, 2015

README.md

Reproducible Research with R and RStudio (Second Edition)

Christopher Gandrud

CRC Press/Chapman & Hall

The files in this repository comprise the source code for creating Reproducible Research with R and RStudio.

File Organization

The main files used to create the manuscript of the book are in the Source folder. This folder contains the parent knitr .Rnw file in the Source/Parent/ directory. Child documents for the book chapters are in the Source/Children/ directory and child files for the book's front matter are in the Source/FrontMatter/ directory.

Reproduce the Book

The book can be reproduced by using the R package knitr. To do this:

  1. Make sure you have R, LaTeX, and the knitr R package installed on your computer. Also install Andre Simon's highlighter utility.

  2. Download this repository and point the directories in the BookMake.R make file to where it is downloaded to.

  3. Run the BookMake.R make file in R.

Note: To install the R packages used to compile the book open the Source/Children/FrontMatter/Packages.Rnw. Find:

doInstall <- FALSE

in the code chunk labeled "FrontPackageCitations". Change the value FALSE to TRUE and run the code chunk.

Note: the LaTeX file will compile with errors and warnings. These are related to stylistic choices and should largely be ignored. But because of this you will need to compile the document a few times to get the full text with bibliography and index.

Reproducing the Book in Windows.

If you would like to reproduce the book and are using Windows you will need to install RTools. Please use the recommended installation to ensure that your system PATH is set up correctly. Otherwise your computer will not know where the tools are.

Reproducing this Book in Linux

You will need to install the R packages RCurl and XML separately. See this post for more details.

Session Info

The current version of the book manuscript was compiled with RStudio (v. 0.99.560 developer build) with the following R session:

## R version 3.2.0 (2015-04-16)
## Platform: x86_64-apple-darwin14.3.0 (64-bit)
## Running under: OS X 10.10.3 (Yosemite)
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ZeligBayesian_0.1   MCMCpack_1.3-3      coda_0.17-1        
##  [4] Zelig_4.2-1         sandwich_2.3-3      MASS_7.3-40        
##  [7] boot_1.3-16         xtable_1.7-4        WDI_2.4            
## [10] tidyr_0.2.0         texreg_1.35         survival_2.38-1    
## [13] stargazer_5.1       shiny_0.12.0        rvest_0.2.0        
## [16] RJSONIO_1.3-0       rmarkdown_0.6.1     repmis_0.4.2       
## [19] RCurl_1.95-4.6      bitops_1.0-6        quantmod_0.4-4     
## [22] TTR_0.22-0          xts_0.9-7           zoo_1.7-12         
## [25] packrat_0.4.3       openair_1.5         maps_2.3-9         
## [28] lazyeval_0.1.10     markdown_0.7.7      magrittr_1.5       
## [31] knitcitations_1.0.5 httr_0.6.1          htmlwidgets_0.4    
## [34] highlight_0.4.7     googleVis_0.5.8     ggplot2_1.0.1      
## [37] formatR_1.2         extrafont_0.17      dplyr_0.4.1        
## [40] digest_0.6.8        devtools_1.8.0      data.table_1.9.4   
## [43] countrycode_0.18    brew_1.0-6          animation_2.3      
## [46] knitr_1.10.5       
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-120        lubridate_1.3.3     bit64_0.9-4        
##  [4] RColorBrewer_1.1-2  R.cache_0.10.0      tools_3.2.0        
##  [7] R6_2.0.1            DBI_0.3.1           mgcv_1.8-6         
## [10] colorspace_1.2-6    bit_1.1-12          git2r_0.10.1       
## [13] chron_2.3-45        extrafontdb_1.0     labeling_0.3       
## [16] scales_0.2.4        hexbin_1.27.0       stringr_1.0.0      
## [19] R.utils_2.0.2       htmltools_0.2.6     bibtex_0.4.0       
## [22] highr_0.5           R.oo_1.19.0         Matrix_1.2-0       
## [25] Rcpp_0.11.6         munsell_0.4.2       proto_0.3-10       
## [28] RefManageR_0.8.45   R.methodsS3_1.7.0   stringi_0.4-1      
## [31] plyr_1.8.2          grid_3.2.0          parallel_3.2.0     
## [34] lattice_0.20-31     splines_3.2.0       mapproj_1.2-2      
## [37] rjson_0.2.15        reshape2_1.4.1      XML_3.98-1.1       
## [40] evaluate_0.7        latticeExtra_0.6-26 mapdata_2.2-3      
## [43] png_0.1-7           httpuv_1.3.2        RgoogleMaps_1.2.0.7
## [46] Rttf2pt1_1.3.3      twitteR_1.1.8       gtable_0.1.2       
## [49] assertthat_0.1      mime_0.3            memoise_0.2.1      
## [52] rversions_1.0.0     cluster_2.0.1

(c) Christopher Gandrud (2015)