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I'm currently writing a thesis. Just the introduction is 25 pages/8000 words. The whole document will probably be 70 pages or so. With a document this large, and on such a complex topic, it can be quite hard to keep track of what's going on where.

I'm looking for ways to summarise the document structure, that might make it easier to figure out what needs changing. Things like lists of topic sentences and signposts (possibly marked as such in the code); word, paragraph, and image counts per chapter/section/subsection; visualisations of flow; plots of keyword densities and readability; and so forth.

What types of tools are there (aside from the ones I mentioned), and what software implementations are available (including for the tools I mentioned)? Answers that deal with non-computer based visualisations (e.g. sketches) are also welcome.

(Note: I asked this on Tex.SE, but I think that the question is too specific for that site.)

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I think it would help to know what field you are writing your thesis in. – Kit Z. Fox Jul 27 '12 at 13:16
Hi @kitfox: I'm in climate science/statistics, but I'd prefer it if answers weren't field-specific, so others could benefit from them. – naught101 Jul 28 '12 at 1:33
edited question to make it clearer that non-software visualisations are also welcome. – naught101 Oct 1 '12 at 4:15

I'm willing to bet Scrivener can handle a lot of what you're looking for. I will cheerfully admit I haven't even read the documentation (I'm a Mac user... we don'need no steenken manuals) so it's got powerful tools I don't even know much about.

You can separate your work into individual documents (section, subsection) which can then be put into folders and dragged around on a virtual corkboard, and compiled into a single document for reading over. You can add keywords, highlight chunks of text in multiple colors, create internal hyperlinks, and do word counts and word frequency counts. I have no idea what "visualization of flow" means, so I can't advise you there.

You can download it and try it for free for a month, and export everything to Word or text so it's not held proprietarily hostage.

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I added a link to what I meant by "visualisations of flow" (those are just some good examples, I don't need exactly that). Another good example is this awesome xkcd cartoon – naught101 Jul 28 '12 at 1:37
::jawdrop:: Wow. Okay, you need a graphics program for that. But you can then import the graphic into Scrivener for reference. – Lauren Ipsum Jul 28 '12 at 13:07

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