Monthly Archives: February 2016

How we can assign multiple selections to variables when mapping data for SmartVA-Analyze 1.1

Dear ,

Thank you for your interest in this work. I have an easy answer for your second question: for anything that is a “select multiple” question (see the “type” column of the “survey” sheet in the xls form), you can encode multiple selections as a space-separated list, i.e “1 2” for cigarettes and pipe.

Here is where to look to find out if a question is a “select multiple” in PHMRC_Shortened_Instrument_8_20_2015.xls for when this comes up with other questions:

(This already came up with a different group mapping injuries, see here if you want to know more: )

In order to answer your first question, I think I need more information. Can you give me an example of what you are trying to do? It also be helpful if you can try it, and let me know what goes wrong if it does not work.


Comments Off on How we can assign multiple selections to variables when mapping data for SmartVA-Analyze 1.1

Filed under software engineering

agedays column in SmartVA data

Here is another little detail for the detail-oriented mapper who is trying to get data into SmartVA-Analyze: agedays.

In the tutorial, I mentioned that there are handful of additional columns that are not in the Guide, because they are created automatically by the ODK form.

The one called agedays is a bit important, because it gets used to determine if the age of the deceased is above or below a threshold. So set it! The important things currently are if it is more or less than 300 and if it is more or less than 3.

Comments Off on agedays column in SmartVA data

Filed under software engineering

Cool example of reproducible research

—–Original Message—–
From: Ben Marwick
Sent: Monday, January 11, 2016 4:06 PM
To: escience_reproducibility
Subject: [Reproducible] New paper on reproducible research in archaeology

Hi everyone,

You might be interested to know of a peer-reviewed paper on reproducible research in archaeology that I’ve just had published.

The paper owes a big debt to the UW eScience Institute, especially the Reproducibility and Open Science Working Group. So this paper is a kind of tribute to all of you in that group who have helped me make sense of reproducibility, thanks!

Here’s the citation and a link to the PDF:

Marwick, B. (2016). Computational reproducibility in archaeological
research: Basic principles and a case study of their implementation.
Journal of Archaeological Method and Theory, 1-27. doi:

All the gory details of the case study paper are here: so you can give it a try. It works on my machine 😉

Happy reading!


Comments Off on Cool example of reproducible research

Filed under science policy

Satire is funny

Satirical paper puts evidence-based medicine in the spotlight

Best reference (fictitious, I think): Rawlings, F. & Wilson, B. R. (1999) Inducing minor traumatic injuries in toddlers for the purpose of conducting randomised controlled trials. Techniques in Evidence-Based Medicine (Canada), 2 (5), 328–386.

Comments Off on Satire is funny

Filed under health communication

Git says this is binary and it is not

I had an annoying little issue, where git was saying my file was binary. What do I care what git thinks? Well, I care if it refuses to show me my diff:

[abie@cluster-dev TICS]$ git diff
diff --git a/ b/
index 3b5b4ca..2cb591e 100644
Binary files a/ and b/ differ

Google and Stack Overflow usually solve any problem I have like this, but today they under-delivered. They gave me a good hint, there must be some funny character in my .py file. That can happen when a 1.5 year old is helping with the typing.

Here is a quick fix, in case I (or you) ever find ourselves in this situation again:

import unidecode
f = file('').read()
with file('', 'w') as f2:

All better. Thanks again unidecode.

Comments Off on Git says this is binary and it is not

Filed under software engineering