The files in this repository comprise the source code for creating Reproducible Research with R and RStudio.
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.
The book can be reproduced by using the R package knitr. To do this:
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Make sure you have R and LaTeX installed on your computer. If you will be using knitr version 1.4 or greater make sure to also install Andre Simon's highlighter utility.
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Place this repository in a file called
git_repositoriesin your root directory. -
Run the BookMake.R make file in R. Note: you must install the knitr R package before running this file.
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.
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. Also see the instructions for setting up the extrafont package (embedding the fonts is not strictly necessary however).
You will need to install the the R packages RCurl and XML seperately. See this post for more details.
The current version of the book manuscript was compiled with RStudio (v. 0.98.134 developer build) with the following R session:
## R version 3.0.1 (2013-05-16)
## Platform: x86_64-apple-darwin10.8.0 (64-bit)
##
## 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] tools grid splines stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] foreign_0.8-54 ZeligBayesian_0.1 MCMCpack_1.3-3
## [4] coda_0.16-1 Zelig_4.1-3 sandwich_2.2-10
## [7] boot_1.3-9 xtable_1.7-1 WDI_2.2
## [10] ROAuth_0.9.3 treebase_0.0-6 ape_3.0-8
## [13] texreg_1.25 tables_0.7 sqldf_0.4-6.4
## [16] RSQLite.extfuns_0.0.1 RSQLite_0.11.4 chron_2.3-43
## [19] gsubfn_0.6-5 proto_0.3-10 DBI_0.2-7
## [22] slidify_0.3.3 stargazer_3.0.1 RJSONIO_1.0-3
## [25] RCurl_1.95-4.1 bitops_1.0-5 reshape2_1.2.2
## [28] repmis_0.2.5.1 quantmod_0.4-0 TTR_0.22-0
## [31] xts_0.9-4 zoo_1.7-10 Defaults_1.1-1
## [34] plyr_1.8 openair_0.8-5 memisc_0.96-4
## [37] MASS_7.3-26 lattice_0.20-15 markdown_0.5.5
## [40] knitcitations_0.4-7 bibtex_0.3-5 Hmisc_3.10-1.1
## [43] survival_2.37-4 httr_0.2 googleVis_0.4.3
## [46] ggplot2_0.9.3.1 gdata_2.12.0.2 formatR_0.7
## [49] extrafont_0.14 estout_1.2 digest_0.6.3
## [52] devtools_1.2 data.table_1.8.8 countrycode_0.14
## [55] brew_1.0-6 apsrtable_0.8-8 animation_2.2
## [58] knitr_1.2
##
## loaded via a namespace (and not attached):
## [1] car_2.0-18 cluster_1.14.4 colorspace_1.2-2
## [4] dichromat_2.0-0 evaluate_0.4.3 gtable_0.1.2
## [7] gtools_2.7.1 labeling_0.1 latticeExtra_0.6-24
## [10] Matrix_1.0-12 memoise_0.1 mgcv_1.7-24
## [13] munsell_0.4 nlme_3.1-109 parallel_3.0.1
## [16] RColorBrewer_1.0-5 rjson_0.2.12 Rttf2pt1_1.2
## [19] scales_0.2.3 stringr_0.6.2 tcltk_3.0.1
## [22] twitteR_1.1.6 whisker_0.3-2 XML_3.95-0.2
## [25] yaml_2.1.7
© Christopher Gandrud (2014)