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:
-
Make sure you have R, LaTeX, and the knitr R package installed on your computer. Also install Andre Simon's highlighter utility.
-
Download this repository and point the directories in the BookMake.R make file to where it is downloaded to.
-
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.
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.
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. 0.98.880 developer build) with the following R session:
## R version 3.1.0 (2014-04-10)
## Platform: x86_64-apple-darwin13.2.0 (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 splines grid stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] ZeligBayesian_0.1 MCMCpack_1.3-3 coda_0.16-1
## [4] Zelig_4.2-1 sandwich_2.3-0 boot_1.3-11
## [7] xtable_1.7-3 WDI_2.4 ROAuth_0.9.3
## [10] treebase_0.0-7.1 ape_3.1-2 texreg_1.32
## [13] tables_0.7.64 sqldf_0.4-7.1 RSQLite.extfuns_0.0.1
## [16] RSQLite_0.11.4 DBI_0.2-7 gsubfn_0.6-5
## [19] proto_0.3-10 slidify_0.4 stargazer_5.1
## [22] RJSONIO_1.2-0.2 RCurl_1.95-4.1 bitops_1.0-6
## [25] reshape2_1.4 repmis_0.2.10 quantmod_0.4-0
## [28] TTR_0.22-0 xts_0.9-7 zoo_1.7-11
## [31] Defaults_1.1-1 plyr_1.8.1 openair_0.9-2
## [34] memisc_0.96-9 MASS_7.3-33 markdown_0.7
## [37] knitcitations_0.6-2 RefManageR_0.8.1 bibtex_0.3-6
## [40] Hmisc_3.14-4 Formula_1.1-1 survival_2.37-7
## [43] lattice_0.20-29 httr_0.3 googleVis_0.5.2
## [46] ggplot2_1.0.0 gdata_2.13.3 formatR_0.10
## [49] extrafont_0.16 estout_1.2 dplyr_0.2
## [52] digest_0.6.4 devtools_1.5 data.table_1.9.2
## [55] countrycode_0.16 brew_1.0-6 apsrtable_0.8-8
## [58] animation_2.2 knitr_1.6
##
## loaded via a namespace (and not attached):
## [1] assertthat_0.1 car_2.0-20 chron_2.3-45
## [4] cluster_1.15.2 colorspace_1.2-4 evaluate_0.5.5
## [7] extrafontdb_1.0 gtable_0.1.2 gtools_3.4.1
## [10] highr_0.3.1 labeling_0.2 latticeExtra_0.6-26
## [13] lubridate_1.3.3 Matrix_1.1-3 memoise_0.2.1
## [16] mgcv_1.7-29 munsell_0.4.2 nlme_3.1-117
## [19] nnet_7.3-8 parallel_3.1.0 R.cache_0.9.0
## [22] R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.32.4
## [25] RColorBrewer_1.0-5 Rcpp_0.11.1 rJava_0.9-6
## [28] rjson_0.2.13 Rttf2pt1_1.3 scales_0.2.4
## [31] stringr_0.6.2 tcltk_3.1.0 twitteR_1.1.7
## [34] whisker_0.3-2 xlsx_0.5.5 xlsxjars_0.6.0
## [37] XML_3.98-1.1 yaml_2.1.11
(c) Christopher Gandrud (2014)