Sun 09 November 2014

Filed under nerdvana

Tags R reproducibleResearch

Here is my custom build system for compiling rmarkdown files in sublime-text 3 on Linux.

"cmd": ["R", "-e", "library(knitr);rmarkdown::render(input = '$file',output_file = '$file_base_name.pdf')"],
    "selector": "text.html.markdown",
    "path": "/home/steve/.cabal/bin/:/home/steve/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games"
}

Obviously you will have to replace the /home/steve parts with your own path which has to include your pandoc installation path, otherwise pandoc will fail when you call it from Sublime Text. Took me a while to figure that out.

Bottom line: now I can write a markdown file in sublime which includes some knitr R chunks, and run it from sublime, without having to switch to rstudio. Very useful.

Comment

Sat 01 November 2014

Filed under mAndE

Tags research evaluation

Assumptions and context

Assumptions

A potential assumption in a logic model is a variable A, not under our control, e.g. tomorrow's weather in our town, (and a designated value or set of values d of that variable, e.g. fair weather with no heavy rain or storms) which ...

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Fri 03 October 2014

Filed under nerdvana

Tags reproducibleResearch opensource zotero

The problem

Every student, researcher and scientist has to read and make notes and highlight or scribble on texts. In long-gone days I spent ages working on Uni literature and making summary charts of what I read, and I really wish I still had some of those notes at my ...

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Fri 03 October 2014

Filed under nerdvana

Tags reproducibleResearch opensource zotero

The problem

Zotero is a really great tool for organising your scientific and professional documents and their citations, and keeping documents and citations together.

Now usually we want to store documents in some kind of hierarchical or tagged structure. Up to now it has been possible to do that either ...

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Wed 10 September 2014

Filed under nerdvana

Tags reproducibleResearch opensource

Wordpress is a great blogging engine. But I spend almost all my time with plaintext files in markdown. Whatever I am working on, from my CV to statistical reports, I have it here on my hard disk and I can compile it as pdf or Word or whatever I feel ...

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Sun 10 August 2014

Filed under resilience

Tags evaluation development

This article is work in progress! Feel free to add a comment. There should be a pdf at this link.

Background and motivation…

Why should we care about resilience?

Self-healing systems - This is what we want!

After the terrible earthquake in Haiti in 2010, billions of dollars of aid money ...

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Wed 11 June 2014

Filed under odds and ends

Tags ggplot R reproducibleResearch

Bar charts and histograms are easily to understand. I often write for non-specialist audiences so I tend to use them a lot. People like percentages too, so a bar chart with counts on the y axis but percentage labels is a useful thing to be able to produce.

But how ...

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Tue 10 June 2014

Filed under nerdvana

Tags opensource tech ubuntu

I quite often get asked (and ask myself) what is the best GANTT software for basic use.

Recently we have been comparing a few solutions so here are a couple of quick tips.

If you have a license for Microsoft Project I would use that, though it is a bit ...

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Mon 28 April 2014

Filed under nerdvana

Tags R reproducibleResearch

Screenshot from 2014-04-28 09:13:14

If you love knitr and rstudio and use them to produce long reports, you probably know that you can produce a table of contents in your html (and pdf) documents. In the newer rstudio (Version 0.98.801 or later) you do it by requesting a toc in the doc ...

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Thu 06 March 2014

Filed under total_speculation

Tags future psychology socialCapital society

Is the free-text search box the defining invention of the last twenty years? I think it probably is. Now more than half the entire Western world (and a lot of the rest of it) can find the answer to more or less any text-based question that occurs to them within ...

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Thu 12 December 2013

Filed under nerdvana

Tags reproducibleResearch zotero

Well, for now I have regretfully given up on docear for writing papers - although it fantastic to be able to mindmap your ideas and citations, it still leads you into a dead-end when you want to actually get your paper finished - sadly, the export functions are not very pretty and ...

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Tue 10 December 2013

Filed under odds and ends

Tags Bosnia-Herzegovina ptsd

10yearsAfter

Rita Rosner presented our 10 years after study in Boston at ISTSS this summer.

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