ECVP 2019

Getting ready to take off for ECVP in Leuven. I have a poster to present that includes some of the last work Christie Haskell Marsh did before she completed her PhD (she now works as senior data scientists with Johnson & Johnson in their Baby Products Division). In addition to Christie's data, there is data collected using virtually the same data collected as a replication. I recorded in the readme for the repo of my Haskell parsing code of all the pain I caused myself, but rarely is the easy way the fun way, or the interesting way, or the educational way or the "moral" way. So, I am back on another painful path trying to make a scientific poster that is reproducible. This isn't about replicability as in "crisis", this is about making a scientific document that clearly documents what you did and how you did it, and that allows others to repeat your analyses exactly as you did them to produce the poster, manuscript, or blog. Unfortunately, the tools that you need to do this require you to work at it and makes it less likely people will do it. If you like making your poster or figures in powerpoint or illustrator I do not know how you will be able to do this. But if you are willing to spend some time, have some patience, and are willing to compromise a bit on your aesthetic vision, it is not too hard to achieve this goal right now. For the poster in Leuven I wrote the poster as an Rnw file. This is a combination of R and nowebformat that allows using R to conduct the analyses and generate the figures while subsequently allowing me to subsequently use LaTeX tools to produce the document I will display. I have done other posters starting with an org file and using org-babel for including the code, but if you are going to have to write a bunch of LaTeX and R anyway the convenience of orgmode is largely absent. Here in short is the basic production line. Do whatever you want to do in RStudio or elsewhere until you have a pretty good idea of the workflow that the poster will need (you can actually include code blocks form other documents, but I did not do that here). Then get to writing your Rnw file. When ready you move over to R and library(knitr) then knit("yourFileName.Rnw"). My current draft of this file is here. The result of this will be a file: yourFileName.tex. You can change that output if you want, but tex is the default. Then you LaTex the file as many times as you need to, with the tools you have set up to get a pdf version. The benefit of this approach is that if you have my data (and I will be posting this some where publically soon) you can start with my raw file and reconstruct the poster. Don't like my analysis? Do your own. You will have the exact code I used available to change. So, this doesn't sound so hard. What is the problem? Well, getting your tools set up. And then there is the fact that if you want to deviate from the established templates or default mode there can be a lot of time on stackoverflow trying to get the tweaks just so. But, it is the right way. Our analyses and our choices should be transparent. Throw away your programs of oppression and free yourself to code your posters. Reproducible scientists of the world unite!

Date: 2019-08-16 Fri 00:00

Author: Britt Anderson

Created: 2024-05-18 Sat 11:05