---
title:     Computational Documents
date:   Wed Mar 20 13:19:19 2019 
---

This document gathers most references mentioned in the videos. This is a
rather crude
list.

# Table of Contents <span class="tag" data-tag-name="TOC"><span class="smallcaps">TOC</span></span>

  - [M2-S0: Computational Documents](#m2-s0-computational-documents)
  - [M2-S1: A few Recent Controversial
    Studies](#m2-s1-a-few-recent-controversial-studies)
      - [Economy: Austerity in Fiscal
        Policy](#economy-austerity-in-fiscal-policy)
      - [Functional MRI](#functional-mri)
      - [Incorrect Protein Structures](#incorrect-protein-structures)
      - [Other domains](#other-domains)
  - [M2-S2: Why is This so Difficult?](#m2-s2-why-is-this-so-difficult)
      - [Mistakes](#mistakes)
      - [Going Public?](#going-public)
  - [M2-S3: Computational Documents:
    Principles](#m2-s3-computational-documents-principles)
  - [M2-S5: Collaborating](#m2-s5-collaborating)
      - [Preparing a Document for a Journal or a
        Conference](#preparing-a-document-for-a-journal-or-a-conference)
  - [M2-S6: Comparative Study](#m2-s6-comparative-study)
      - [Exemples of Org-Mode
        documents](#exemples-of-org-mode-documents)

# M2-S0: Computational Documents

# M2-S1: A few Recent Controversial Studies

## Economy: Austerity in Fiscal Policy

  - [Reinhart et
    Rogoff](https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt):
    *Growth in a Time of Debt*
  - Herndon, Ash et Pollin
  - Wray: combining data across centuries, exchange rate regimes,

## Functional MRI

  - 2010: [Bennett et al. and the dead
    salmon](https://www.researchgate.net/publication/255651552_Neural_correlates_of_interspecies_perspective_taking_in_the_post-mortem_Atlantic_Salmon_an_argument_for_multiple_comparisons_correction)
    ☺
  - 2016: [Eklund, Nichols, and
    Knutsson](http://www.pnas.org/content/113/28/7900.abstract). [A bug
    in fmri software could invalidate 15 years of brain
    research](http://www.sciencealert.com/a-bug-in-fmri-software-could-invalidate-decades-of-brain-research-scientists-discover)
    (*40 000 articles*)
  - 2016: But it's [more subtle than it looks
    like](https://www.cogneurosociety.org/debunking-the-myth-that-fmri-studies-are-invalid/).
    [Nichols](http://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/).
    *≈ 3 600 impacted studies*

## Incorrect Protein Structures

[A "buggy
software"](https://people.ligo-wa.caltech.edu/~michael.landry/calibration/S5/getsignright.pdf).

## Other domains

  - [Oncology](http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true):
    "*half of published studies, even in prestigious journals, can't be
    reproduced in industrial
    labs*"
  - [Psychology](http://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596):
    "*attempting to reproduce 100 previously published findings*, *only
    one-third of published psychology research was found to be
    reliable*"

# M2-S2: Why is This so Difficult?

## Mistakes

  - [Computers broke
    science](http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938)
  - [Programming and data manipulation mistakes in
    Genomics](https://qz.com/768334/years-of-genomics-research-is-riddled-with-errors-thanks-to-a-bunch-of-botched-excel-spreadsheets/)

## Going Public?

  - Someone may [benefit from my hard
    work](http://www.nature.com/news/the-top-100-papers-1.16224)

# M2-S3: Computational Documents: Principles

# M2-S5: Collaborating

## Preparing a Document for a Journal or a Conference

Requirements for producing a **pdf**:

  - Internally, *pandoc*, *knitr* or *emacs/org-mode*

  - *LaTeX* should be installed
    
      - <http://blog.juliusschulz.de/blog/ultimate-ipython-notebook>
          - <https://github.com/kirbs-/hide_code> is a
        must-have
      - <http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/>
      - <https://github.com/balouf/Kleinberg/blob/master/KleinbergsGridSimulator.ipynb>

# M2-S6: Comparative Study

## [Exemples of Org-Mode documents](../ressources/orgmode_examples/README.org)