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## Makefile to build PhD thesis | |
###-------------------------------------------------- | |
### T. Ravalde ([email protected]) | |
### Last edited: 2016/05/31 | |
### Adapted from Keiran Healy (https://github.com/kjhealy/workflow-paper/blob/master/Makefile) | |
###-------------------------------------------------- | |
## Put this Makefile in your project directory | |
## - Change/add the paths to at the top of the file as needed (e.g. line 37) |
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#!/bin/bash | |
###-------------------------------------------------- | |
### T. Ravalde | |
### Last edited: 2016/05/17 | |
###-------------------------------------------------- | |
# Command line thesaurus based on code from http://www.linuxhowtos.org/Tips%20and%20Tricks/cmdline_thesaurus.htm | |
###-------------------------------------------------- |
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# Example of using the ReporteRs package to convert R plots to editable figures in PowerPoint | |
## Based on article at http://www.sthda.com/english/wiki/create-an-editable-graph-from-r-software | |
## Data | |
### (Data from searching Scopus for 'open data' or 'open-data') | |
year <- c(1995:2014) | |
number <- c(5, 14, 5, 3, 4, 7, 15, 16, 13, 18, 19, 28, 29, 43, 69, 148, 230, 424, 618, 759) | |
open_data <- data.frame(year, number) |
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sh vc # Create the version control data | |
Rscript knit.R # Knit the file (details below) | |
if [ `hostname` = "cv-tr608-01" ] # Determine which computer is being used | |
then | |
pandoc --latex-engine=xelatex --template=/home/tr608/.pandoc/templates/tom.xelatex --natbib --bibliography=/home/tr608/ImpCol/PhD/my-refs.bib -o paper.tex paper.md # Generate *.tex filer using templates and bibioligraphic data | |
else | |
pandoc --latex-engine=xelatex --template=default.latex --include-in-header=custom-local.sty --natbib -o paper.tex paper.md | |
fi | |
xelatex paper # Build PDF from *.tex source | |
bibtex paper |
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# Gantt chart based on my PhD completion timetable. | |
## Below is a copy of gantt.csv (built initially in a spreadsheet) | |
#Task,Start,End,Chapter | |
#"Metabolic efficiency reading (3)",2014/08/01,2014/11/30,3 | |
#"Metabolic efficiency data analysis (3)",2014/11/01,2015/02/28,3 | |
#"Model development (4)",2014/08/01,2014/10/30,4 | |
#"Shann Gu case study (5)",2014/08/01,2014/10/30,5 | |
#"Metabolic pathway database construction (6)",2014/08/01,2015/04/30,6 | |
#"Metabolic pathaway analysis (6)",2015/03/01,2015/06/30,6 |
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xrdb -merge ~/.Xresources | |
# Source: http://askubuntu.com/questions/302736/solarized-color-name-not-defined |
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source("http://www.bioconductor.org/biocLite.R") | |
biocLite("Rgraphviz") | |
library("Rgraphviz") |
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function parse_git_branch () { | |
git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/ (\1)/' | |
} | |
PS1="\u@\h \w\[\033[01;36m\] \W\[\033[0;33m\]\$(parse_git_branch)\[\033[0m\]\$ " |
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\documentclass{article} | |
\usepackage{booktabs} | |
\usepackage{geometry} | |
\usepackage{tabularx} | |
\geometry{lmargin=72pt,tmargin=72pt,textwidth=350pt,marginparwidth=144pt} | |
\usepackage{tufte-sidenotes} | |
\begin{document} | |
Here is demo of the \verb#tufte-sidenotes# style. |