====== Student BSc/MMath writeup ======

Some notes to help students write up. 

===== LaTeX =====

Use the prepared thesis format. You may prefer to tweak this to your satisfaction (e.g. you may prefer a report-style rather than a book-style). 

This documentclass uses the memoir package and you can look up the memoir documentation. 


===== Bibliographies =====

Best to use natbib in conjunction with bibtex. See the .bib file in thesis-template. Use Google Scholar to quickly obtain the metadata for bibtex. 

===== Illustrations  and images =====

Images take time to create! (At least) two choices: 

1. If you have nice handwriting, draw your images on paper and scan using an app like Camscanner. Produce .jpeg files of the images. This can look very nice (if you are meticulous), is a huge time saver, and can be used for prototyping for the final product. 

2. Use a vector graphics editor like Inkscape to create the images. 

If you want a truly professional format, use LaTeX overpic package to annotate the images. Again this takes time. 

===== Outputting images from Matlab =====

You may be using Matlab to create graphics. Some considerations: 

1. Save all data or all scripts. Get in the habit of save data as .mat files and scripts that will plot the data. This means if you ever need to regenerate pictures, you can do it very easily. 

2. Similar to above, you may want to save .fig files of the pictures. Again it allows fine-tuning. (In fact you can extract raw data from .fig files via scripts). 

3. Use export_fig packakge (Matlab file exchange) to export to pdf format. In general, output to PDF format unless the image is very detail-heavy (surface plots, contour plots, etc.). This ensures that the image is scalable and crisp. 

4. Use a similar startup.m script below to set figure defaults. This ensures that axis labels are appropriately sized. 

		% Example startup file 
		
		% This adds all paths recursively from the directory
		addpath(genpath('~/myfunctions'));
		% This adds a single path
		addpath ~/mysinglepath/
		
		% Set figure default to something more pragmatic
		
		colordef white
		set(0, 'Units', 'pixels');
		
		set(0, 'defaultaxesfontsize', 18, 'defaultaxeslinewidth', 1, ...
		        'defaultlinelinewidth', 1, 'defaultpatchlinewidth', .7, ...
		        'defaultAxesFontSize', 18);
		
		
		set(0,'DefaultFigureColor','w', ...
		      'DefaultAxesColor','w',...
		      'DefaultAxesXColor','k',...
		      'DefaultAxesYColor','k',...
		      'DefaultAxesZColor','k',...
		      'DefaultTextColor','k',...
		      'DefaultLineColor','k');
		
		clear
		close all
		
		% Add the starting path
		cd ~/mystartingpath/

===== Last minute checks =====

I usually give a checklist of things to check. 

  - Run your writing through a grammar and spelling checker. For example, you can install LanguageTool for your browser (if editing on Overleaf) or desktop. 
  - Check that all your figures are referenced within the text. The references should occur before the figure placement. 
  - Check that all your figure annotations are clear (they are often too small). If they are not clear, you can input them manually in the caption rather than re-generating the figure. 
  - Check that all your figure captions are self-sufficient. Parameter values should be stated, and generally anything that would require a reader to reproduce and immediately understand your image with minimal viewing of the rest of the document. 
  - Hardcore initials in the bibliography (e.g. Trinh, Philippe H becomes "Trinh, P. H.". This ensures that very bibliographic style will render the same style. 
  - Use a [[https://woodward.library.ubc.ca/woodward/research-help/journal-abbreviations/|Journal Abbreviations database]] to check journal abbreviations in your bibliography. 
  - Double check titles in your bibliography to ensure that the capitals are protected. So "Study of the Stokes phenomenon" should be "Study of the {S}tokes phenomenon".