Hi DaSHers,
Today we had a wide ranging discussion which meandered around two main themes: colour blind friendly figures; and good practice programming.
Colour blind friendly figures
Over the last few weeks, Tom has been investigating how to simplify making figures colourblind friendly. He brought a few simple solutions. Although it is very easy to chose and set colour blind friendly colours/palettes, knowing how and where to find them is tricky depending on the platform/program you are in. So here is a rainbow range:
| hexcode | normalname | designername |
|---|---|---|
| #000000 | colourblindblack | black |
| #999999 | colourblindgrey | dustygrey |
| #0072B2 | colourblinddarkblue | deepcerulean |
| #56B4E9 | colourblindlightblue | pictonblue |
| #009E73 | colourblindgreen | greenhaze |
| #F0E442 | colourblindyellow | starship |
| #E69F00 | colourblindorange | orangepeel |
| #D55E00 | colourblindred | tenn |
| #CC79A7 | colourblindpink | hopbush |
One of the biggest challenges was finding a way to check how an entire image looked with a particular kind of colour blindness. The app ‘Color Oracle’ (http://colororacle.org/) provided a free, simple, easy, rapid, cross platform solution. It just changes the screen colour palette temporaily, allowing a quick check (if your using R, Paul Murrel from R-core recommends the ‘dichromat’ package ). Here are three different checks of the original image.
Normal vision
Deuteranopia
Protanopia
Tritanopia
Good Practice Programming
A number of issues were discussed around good practice programming including: script design; including tests; memory management; efficiency testing and overall profiling of code performance, debugging. Mike and Damien provided links to various resources throughout the discussion to help support the discussion. These are:
Colour issues
- End the rainbow: http://www.climate-lab-book.ac.uk/2014/end-of-the-rainbow/
- https://www.stat.auckland.ac.nz/~ihaka/downloads/DSC-Color.pdf
R weirdness
- https://ironholds.org/projects/rbitrary/
Speed issues
- The R Inferno http://www.burns-stat.com/documents/books/the-r-inferno/
Testing
-
Software Carpentry lesson on testing http://katyhuff.github.io/python-testing/
-
testthat https://cran.r-project.org/web/packages/testthat/index.html
Building a package with devtools
- adding functions
- documenting with roxygen2
- use_test()
- Ctrl-SHIFT-B / T / E
- use_readme_rmd()
Errors and debugging
- debugger in RStudio https://support.rstudio.com/hc/en-us/articles/205612627-Debugging-with-RStudio
- http://software-carpentry.org/blog/2011/03/using-a-debugger.html
Functions in R
- http://adv-r.had.co.nz/Functions.html
R’s copy semantics and memory
- http://adv-r.had.co.nz/memory.html
Profiling R code:
- https://github.com/rstudio/profvis
Next week (29 Apri)
Intro to GIS concepts (with Manifold and QGIS)
Coming up
- Software package management
- Speeding up R
- Form mastery
When: Friday 22 April 2016, 0915hrs - 1015hrs
Where: the ground floor Flex Room at IMAS / ACE CRC Salamanca (‘the Waterfront’).