![11 org mode
Example objective function
min
x
z =
n
i=1
x4
i + x3
i − 2x2
i
x ∈ [a, b] ∩ Rn](https://image.slidesharecdn.com/talk-181104162453/85/Literate-programming-and-reproducible-research-11-320.jpg)
![13 org mode
Tangling
Create an octave file with the objective function using tangling:
function [ z g ] = f ( x )
z = sum( x .^4 + x .^3 − 2∗x . ^ 2 ) ;
g = 0; % unconstrained
endfunction](https://image.slidesharecdn.com/talk-181104162453/85/Literate-programming-and-reproducible-research-13-320.jpg)
![15 org mode
Bringing bits together
The code to include the problem setup directly and solve the
problem:
clear
format short
n = 2;
x0 = rand (n , 1 ) ;
a = −2∗ones (n , 1 ) ;
b = 2∗ones (n , 1 ) ;
[ x y ] = strawberry ( x0 , a , b , @f , 10 , 10);
[ x ; y ] ’](https://image.slidesharecdn.com/talk-181104162453/85/Literate-programming-and-reproducible-research-15-320.jpg)
![20 org mode
Project management
Support for tasks, scheduling, appointments:
[3/4] prepare and give presentation on literate programming
collect images
write slides
book hotel
give presentation](https://image.slidesharecdn.com/talk-181104162453/85/Literate-programming-and-reproducible-research-20-320.jpg)
Literate programming and reproducible research
- 1. Literate programming and reproducible research Professor Eric S Fraga, UCL 6 June 2018 EGL2018, Essex v1.33 4th June 2018
- 2. 2 Outline Introduction The aim & challenge Literate programming Emacs org mode Programming Writing Conclusions Summary
- 3. 3 Introduction Reproducible research To ensure that our research is reproducible both by ourselves and by others.
- 4. 4 Introduction Coding, processing, writing In doing research, 1 we all write programs . . . 2 which generate results . . . 3 which need to be processed . . . 4 and which should be disseminated. Currently, we use different tools for each step.
- 5. 5 Introduction Tools Workflow: coding IDE, MATLAB editor, vi, notepad, . . . results .txt, .xls, .dat processing spreadsheet, R dissemination Word, PowerPoint, LATEX, beamer project management ? leading to constant transfer of data from one place to another.
- 6. 6 Introduction Definition Literate programming is a programming paradigm intro- duced by Donald Knuth in which a program is given as an explanation of the program logic in a natural language, such as English, interspersed with snippets of macros and traditional source code, from which a compilable source code can be generated. https://en.wikipedia.org/wiki/Literate_programming
- 7. 7 Introduction Code and documentation Source
- 8. 8 Introduction Example: the Strawberry algorithm https://www.ucl.ac.uk/~ucecesf/strawberry.html
- 9. 9 Introduction Editor originally written in 1976 content aware editing fully extensible in Emacs LISP self-documenting with comprehensive help system large eco-system of packages https://www.gnu.org/software/emacs/
- 10. 10 Introduction org mode Text (it’s all text) based mode for writing & dissemination project management literate programming https://orgmode.org/
- 11. 11 org mode Example objective function min x z = n i=1 x4 i + x3 i − 2x2 i x ∈ [a, b] ∩ Rn
- 12. 12 org mode Plot of objective function
- 13. 13 org mode Tangling Create an octave file with the objective function using tangling: function [ z g ] = f ( x ) z = sum( x .^4 + x .^3 − 2∗x . ^ 2 ) ; g = 0; % unconstrained endfunction
- 14. 14 org mode Code segments Specify the parameters for the optimisation problem: n = 2; x0 = rand (n , 1 ) ; a = −2∗ones (n , 1 ) ; b = 2∗ones (n , 1 ) ;
- 15. 15 org mode Bringing bits together The code to include the problem setup directly and solve the problem: clear format short n = 2; x0 = rand (n , 1 ) ; a = −2∗ones (n , 1 ) ; b = 2∗ones (n , 1 ) ; [ x y ] = strawberry ( x0 , a , b , @f , 10 , 10); [ x ; y ] ’
- 16. 16 org mode Plotting results Using data in table of results on previous slide:
- 17. 17 org mode Processing results Statistical analysis of results obtained above: Statistic Value Best -5.666 Average -5.582 Worst -5.255 Standard deviation 0.094
- 18. 18 org mode Outlines Example (a recent paper): Can show, hide, and move individual sub-trees.
- 19. 19 org mode Publishable output org will export to LATEX (and hence to PDF) or ODT (MS Word compatible).
- 20. 20 org mode Project management Support for tasks, scheduling, appointments: [3/4] prepare and give presentation on literate programming collect images write slides book hotel give presentation
- 21. 21 org mode Revision control A research project is a long term activity comprised of many individual tasks. Revision control should (must) be an integral element of project management. Think track changes but on steroids and which works for data as well. Excellent tools exist: git, mercurial, subversion, . . .
- 22. 22 org mode Example of revision control
- 23. 23 Conclusions Emacs & org Single tool for writing, coding, data manipulation, data provenance, dissemination, and project management.
- 24. 24 Conclusions Testimonial I By the age of 35 you should have realized that Emacs is the One True Editor and should have embraced it. If that’s not the case - your life so far has been completely wasted. @bbatsov, 04:02 pm May 20, 2018
- 25. 25 Conclusions Testimonial II The advantages of plain text are hard to overstate, as is the advantage of having everything from plot notes to research material in a single (large) file under version control. And building up a novel from an outline is a natural process with org-mode. Bob Newell, emacs.help newsgroup, 2018-05-30.
- 26. 26 Conclusions Links Emacs https://www.gnu.org/software/emacs/ Complete computing environment http://doc.rix.si/cce/cce.html org mode https://orgmode.org/ reproducible research https://reproducibleresearch.net/links/ blog reproducible research for management