# Keiji Wiki

### Site Tools

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 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!
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."
• 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.

## 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.