amended bibliography & re-run

MTUS-W6-adult-episodes-data-processing.Rmd

 ---
 title: "MTUS World 6 Data Processing"
-author: "Ben Anderson"
-date: "(b.anderson@soton.ac.uk, @dataknut)"
+author: "Ben Anderson (b.anderson@soton.ac.uk/@dataknut)"
+date: 'Last run at: `r Sys.time()`'
 output:
   pdf_document:
     toc: yes
@@ -13,6 +13,7 @@ output:
     theme: journal
     toc: yes
     toc_depth: 3
+bibliography: ~/bibliography.bib
 ---
 
 ```{r setupKnitr, include=FALSE}
@@ -24,20 +25,25 @@ knitr::opts_chunk$set(fig_caption = TRUE)
 knitr::opts_chunk$set(tidy = TRUE)
 ```
 
-# About this document
+# Introduction
 
-Document last refreshed: `r Sys.time()`
+Purpose:
 
-This document was created using [knitr](https://cran.r-project.org/package=knitr) in [RStudio](http://www.rstudio.com). Knitr supports the embedding of R statistical analysis code within markdown text documents allowing them to be updated and re-run. Things to note:
+* To process the MTUS World 6 episode data
+* To save a processed & gzipped .csv file containing data for just the UK.
+
+Data:
 
-* Depending on the options set Knitr will display warnings (but not errors) from R. The warnings may or may not be important to the interpretation of the results;
-* Knitr is very clever but it does not always support pretty tables.
+* MTUS [World 6](http://www.timeuse.org/mtus) - episodes file
 
 This work was funded by RCUK through the End User Energy Demand Centres Programme via the "DEMAND: Dynamics of Energy, Mobility and Demand" Centre:
 
  * http://www.demand.ac.uk 
  * http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=EP/K011723/1
 
+Code:
+ * https://github.com/dataknut/MTUS
+ 
 `License:`
 
 `The R code embedded in this document is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License (http://choosealicense.com/licenses/gpl-2.0/), or (at your option) any later version.`
@@ -46,8 +52,16 @@ This work was funded by RCUK through the End User Energy Demand Centres Programm
     
 >YMMV - http://en.wiktionary.org/wiki/YMMV
 
-***
+# Set up R environment
 
+Key packages used:
+
+ * base R - for the basics [@baseR]
+ * foreign - for loading SPSS data [@foreign]
+ * data.table - for fast (big) data handling [@data.table]
+ * knitr - to create this document [@knitr]
+ * dplyr & dtplyr - for data manipulation [@dplyr][@dtplyr]
+ 
 ````{r houseKeeping}
 # Clear out all old objects etc ----
 # to avoid confusion
@@ -57,15 +71,12 @@ rm(list = ls())
 starttime <- Sys.time()
 
 # Load required packages ----
-packs <- c("ggplot2", # slick & easy graphs
-       "foreign", # loading SPSS/STATA
+packs <- c("foreign", # loading SPSS/STATA
        "data.table", # fast data manipulation
-       "gmodels", # for table proportions
-       "knitr", # for kable
-       "profvis", # profiling code visualisations
-       "dplyr" # data transformation
+       "dplyr", # data manipulation
+       "dtplyr", # data table & dplyr code
+       "knitr" # for kable
        )
-# xtable - not useful: outputs latex only ----
 
 # do this to install them if needed
 # install.packages(x)
@@ -84,16 +95,6 @@ episodesFile <- "MTUS-adult-episode.sav"
 efile <- paste0(mtusPath, episodesFile)
 ````
 
-# Introduction
-Purpose:
-
-* To process the MTUS World 6 episode data (`r episodesFile`)
-* To save a processed & gzipped .csv file containing data for just the UK.
-
-Data:
-
-* MTUS [World 6](http://www.timeuse.org/mtus) - episodes file
-
 # Load and process episodes file
 Loading and processing `r efile`.
 
@@ -840,5 +841,4 @@ kable(
 __Meta:__
 Analysis completed in: `r round(Sys.time() - starttime, 3)` seconds using [knitr](https://cran.r-project.org/package=knitr) in [RStudio](http://www.rstudio.com).
 
-***
-__Footnotes:__
+# References