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misc:why_wiki:start

Why Wiki?

Why do I use wiki for research?

Motivation

  • Multiple projects
    • Involve with many research projects concurrently.
    • It's hard to manage research activities across different projects.
  • Time issue
    • Research takes time.
    • Clients often visit my office after many months of inactivity. This means:
      • I may not remember what I did 3 months ago on a particular project.
      • "What did I do before?" "How was this variable defined?"

What I used to do

  • Create an analytic summary before presenting to clients in a meeting.
  • Tables prepared in Excel. Plots in a graphical format. Combine them & write analysis descriptions in Word.
    • When on a tight deadline, even used raw computer output.

Problems?

  • You end up with too many summary files:
    • e.g., Analysis 03122019 v3.docx; Logistic model adj Kcal sleep 12022018.xlsx
    • Can you tell what analysis was done in which file?
  • Keep sending files to others via email – Recipe for disaster!
Did you receive this?
No I didn't. Send it again
Sorry I forgot to attach this file!
See this file for this analysis & see that file for that analysis.
I'm on zoom. What table are you looking at now?
Can you include this variable to this table & send me again today?
See attached. This is version 3 of today's summary!
  • Imagine you have to dig through these emails, looking for results that were revised multiple times after many months. :-\
  • Or maybe you end up with a pile of printouts, hopelessly looking for the "right" table. :-\
  • Need a better way to present results to others!
  • Need a better way to organize research activities!!

Wiki comes in & saves my life

  • No more searching for files and output. No more sending them to others.
    • Everything is in one place
      • "See my wiki page online. I just added more results a few minutes ago."
  • Easy to create a page and post results there.
    • Include tables & figures. Can post as files or graphics.
      • "The table is posted in my wiki. You can download it in an Excel file if you want."
      • "Journal is asking graphs in a vector file? Just get the PDF file from my wiki."
  • Hyperlinks
    • Found a relevant paper that you want to share with others? Need to include it in references later? Just insert a link.
    • Cross-reference between wiki pages.
  • Collaborative editing
    • Most of research require collaborative efforts. You don't know the whole aspect of a research project.
      • You need someone else to provide some specific information on a research.
      • "Can you fill in this information in my wiki, please?"
    • Get feedback.
      • Your collaborators can insert comments and add discussions.

What I do with wiki

Must assume that the future you won't remember anything about the project!

Describe what I was given

  • Study design
  • Subjects
    • Recruitment, inclusion/exclusion criteria
  • Datasets:
    • How many data files are involved?
    • When data files were received? When data files were updated?
    • Outcomes, variables, the number of obs

Describe what I did in every phase of analysis

  • Data integrity
    • Error checking and validation
  • Data management
    • How multiple datasets were merged?
    • How many subjects were eventually used?
    • Derived variables and how they were defined
      • If necessary, include your code/syntax in wiki
      • Can include equations using LaTeX notations, like $L(\boldsymbol{\theta})= \prod_{i=1}^n f(y_i|\boldsymbol{\theta})$
  • Demographic tables, descriptive statistics
  • Descriptions of statistical models
  • Model building/specification, model diagnostics
  • Supplementary analyses

Provide results, tables, and figures

  • Include lots of figures
    • Figures are extremely useful especially during data checking and exploratory phases.
    • Most of these figures won't be used in a paper, but that's okay.
    • Embed figures in wiki pages. Need to post graphic files first.
  • Tables
    • Most of the time I simply copy and paste computer output, with minimal editing
      • This makes it easy to revise tables upon request (which happens always)
      • But do add titles, superscripts and footnotes to make them self-explanatory
    • For large tables, create in Excel and post the file
  • Results
    • Write brief interpretations of results
    • Comment on results that you find interesting or unexpected
    • Detailed output can be included, but hidden in a page (folding/unfolding texts)
  • Update results as needed
    • Can always revert back to previous edits
    • If necessary, keep old results in a separate wiki page and create a link to it
  • Present results in a logical order
    • Do NOT present results by date

Keep meeting logs

  • There will be many meetings during a project. Keep meeting logs.
    • Do this by date, the latest date on top of the list
  • Meeting logs may include:
    • Attendants
    • To do list and reminders
    • Change of plan
    • Next meeting date
  • Keep the log to CYA in case something goes wrong

Other benefits

Accessibility

  • Can check/edit wiki pages anytime, anywhere
  • Analysis on the go using R and RStudio in a USB drive

Content management

  • Nested hierarchy of contents
    • One front page for each research project
    • Can create multiple wiki pages branching from there
    • Not so easy in Google Docs
  • A wiki page has different levels of headlines
    • TOC automatically generated on a page based on headlines
  • Forces to think a logical way to present results
  • Preserve page history
    • Can revert back to old revisions if necessary

Reproducibility

  • Reproduciable research: Make your analysis more transparent
    • If necessary, copy & paste code/syntax used for analysis

Security issues

  • For security purposes, may need to prepare a user account for every collaborator.
    • Requires a password
    • Only authorized users can view/edit certain wiki pages.
  • DokuWiki has an easy way to manage user groups and access control.
    • I usually create a user group when a new project starts.

  • Can post results, but do NOT post data files.
    • Electric data should be securely stored in relational databases, such as a SQL server.
    • Users should access data directly from a SQL server or other secure data storages with password protection.
    • Avoid file transfer between users as much as possible. It is the weakest link in data security.
misc/why_wiki/start.txt · Last modified: 2020/01/27 04:33 by koda