PhUSE Wiki

• Add a Help File to guide users on how to work with the Wikis and code depositories
• For new Wikis have generic template text prefilled to guide user where to add what content
• uploading images to Wikis (e.g. graph examples)
• change "Metatags" into "Search Terms" and have separate Metadata entry, which can be used as config file of code 
• Include a "Sandbox" area that helps new users get used to the wiki and its features. In addition to highlights of the wiki features, this could include a simple example of a tool that is registered into the wiki.
• Once a Wiki is set up, there needs to be the possibility to add additional headers, change header titles and change the name of the Wiki as well. At the moment there doesn't seem to be an intuitive solution for this.
• Once a Wiki is opened, navigation to other Wikis or sections (i.e. Good Programming Practice, Derivation Standards and Output Templates) is not directly possible. One first has to click the left hand "PhUSE Wiki" link again to see the structure
  • This should be resolved as of 18. October 2010
• It would be nice to hyperlink to specific code included in the Documents Tab.
• Is there any way to contact a contributor while their content is pending approval? Email addresses don't appear to be available- would be nice to have that visible, at least to the moderators.

• Including more information for a tool entered. Please see below for an example of a trimmed mean. Ideally, these would be sections to be filled out when creating a new tool. Note that some of the information provided below is already captured in the current platform.

Tool Name: trimmed.mean
Tool Description: This calculates a trimmed mean of a numeric vector
Engine Type: R
Engine Version: R v10.1
Operating Environment: tested only on Windows XP
Author Name and Email: Mat Soukup (Mat.Soukup@fda.hhs.gov)
Create Date: 10/14/2010
Last Modified Date: currently no modifications exist
Latest Version: 1.0
Required Arguments: 
            x                a numeric vector 
            trim            percentage (value between 0 and 0.5) of x to trim from the calculation
Optional Arguments:
          na.rm           exclude missing values in x; default is FALSE
Output / Value Returned:      The numeric value trimmed mean of x
Error Return Codes: None currently; simple code to not do this
Example Data Source: None
Protocol/Trial Source: For illustrative purposes
File/URL/UUID Paths: This would be the path where the code is stored and from which could be sourced within the engine for which the code is written
Method Details: More details on what the code does; could include mathematical representations if needed. Not provided in the current example
Example(s):
set.seed(123)
x <- rnorm(100)
trimmed.mean(x, trim=0.1)
References: R base package for mean
See Also: mean function in R
 

• In addition to listing tools by category, it would be helpful to have one big library of code which would be listed alphabetically.
• Is there the ability to read in the code?
  • Not quite sure what is meant by that.
  • For example, if we wanted to read in a function on the wiki from R, I would use: source("www.phuse.eu/path/fcnname"). Ideally, this would also allow one to read in a specific version of fcnname. I'm sure SAS users would do something similar though my SAS skills are a bit novice at the time.
    

 

• I recently used a TiddyWiki interface to enter content into a Wiki. TiddlyWiki seems to be an open source application that can be reused for non-profit purposes. I especially like the editing tools that cover a lot of the change requests for this Wiki. Would it be possible to incorporate these tools for our use?  
  
   

When creating a new wiki topic, there is no way to back out if you change your mind other than exiting the web page. it would be nice to have an exit button.

Suggestion:   Normally in a search field pressing the “Enter” key will be accepted as the “Go” command.  But for the PhUSE page search box (and other boxes like password), one has to press the “>” icon.  This is nonstandard behavior and confusing.   I suggest these fields should accept the “Enter” as same as hitting “>”.

 

The proposal is to have Wiki admins assigned to sections of the platform, i.e. have dedicated admins coordinating content for Good Programming Practice (GPP), Derivation Standards and Output Templates.

For GPP we do already have two admins, who have taken responsibility for the main GPP Wiki. Applying this governance model to the other sections as well could help bringing in consistency into the content rather than having too many cooks working on the same soup.

Are the admins the people who have the right to "Approve" content submitted by others? If so, a nightly email to these admins about recent content submitted/edited/etc. would be helpful.

It is not easy to comment on the PhUSE Wiki because, as stated in the very first paragraph of this page (“… add a help file …”), it does not really become clear how the intended use of the PhUSE wiki is. I guess that it is intended as a library of code and of best practices and it is obvious that this could be a really helpful tool for PhUSE members and for every statistical programmer. I have two comments, one about guidance and one about usability.

My experience with closed wikis in my company as well as with a public wiki shows me that a strong guidance for contributors is necessary. If you leave everything to contributors, the wiki will not unfold its value and in the worst case nothing will happen. Guidance applies to 

• technical things as how the wiki can be used to enter and change information,
• basic things about content structure as how information should be organized in pages (or "wikis" as they are called here), how large a page should be, how to use links and categories and so on. 
• the goals of the wiki, which should be stated clearly. 
• the presence of a moderator who feels responsible for the wiki and who takes the time to promote the wiki, to find new contributors, to communicate the goals to potential contributors, to guide contributors, and to look after the wiki at least some hours per week.
• promotion of the wiki whenever there is an opportunity, at least on every PhUSE conference and on the SDEs. New articles can be introduced and stories of successful adoption of wiki content can be told.

I think that there is valuable information in the wiki pages here. But it is to some extent assembled into huge articles, where best practices and code snippets have been put together. The idea of a wiki, as I understand it, is to have straightforward items of information which are linked together and structured by categories, so information emerges into knowledge, if this is possible at all in an IT system. Everything can be changed by everybody at any time very easily, also links and categories, and every change can be tracked and undone, if necessary. Maybe I do not understand how to use this wiki, but it seems to be rather rigid. Isn’t it possible to add a new section to a page? The golden standard for a wiki software (there are hundreds of it, please excuse that I am biased) is the MediaWiki software also used by Wikipedia. It is very robust, easy to use (for the IT people setting it up, for administrators, contributors and readers) and, best of all, everybody knows it at least as a reader, many even as contributors.
 
Just one example: One of the most basic and also important things in a wiki is to link to another page in the same wiki (a "wiki" in this respect is a collection of wiki pages, not a single page so the whole PhUSE wiki would be a "wiki").
In order to insert a link to a page section in the PhUSE wiki, I have to go to the page to link to, click on the TOC in order to get the address of the section, copy the address out of the address field of my browser, go to the page where I want to add the link and use the "create link" tool to insert it.
In the MediaWiki software, this is done by just writing the name of the linked page in square brackets. That’s all, a link is inserted into the page and if the page linked to does not yet exist, a click on the link creates the page and gives you the opportunity to edit it. If you have this possibility to create pages rather flexibly and to link them up easily, you can create one page per best practice, per code snippet, per “tool”, per contributor, per Document and so on and link them together in order to form structured articles or to create portal pages where everything about a certain topic can be linked.