Merge branch 'master' of https://github.com/phuse-org/phuse-scripts

Author: DanteDT

Diff for: CSS_2016.md

@@ -0,0 +1,51 @@
+## CSS 2016 Task List
+
+In preparation for [CSS 2016](http://www.phuse.eu/annual-conference.aspx), **Working Group 5, Standard Analyses**, highlight a few tasks that we will initiate or complete during our annual symposium.
+
+Our two main subteams are: 
+  1. White Papers (define analyses), and 
+  2. Standard Scripts (implement analyses)
+
+#### Standard Analyses (White Papers)
+
+Please see this [status of current white papers](https://github.com/phuse-org/phuse-scripts/blob/master/TODO.md#white-papers-project-08). We will focus on:
+  1. Reviewing any proposed updates and revisions to 4 previously published papers
+    + including [queries raised while implementing Central Tendency analyses](https://github.com/phuse-org/phuse-scripts/blob/master/TODO.md#wg5-principles-and-conventions)
+  2. Discussing the 3 papers in active development
+
+#### Standard Scripts
+
+We have 2 main sources for standard scripts:
+  1. Scripts from the FDA's JumpStart workflow
+  2. Implementations of Standard Analyses from PhUSE CS White Papers, above
+
+###### FDA JumpStart Scripts
+
+We will present recent developments during CSS 2016. **If you want to get involved immediately** in reviewing and testing these scripts, please contact Hanming Tu (see the [PhUSE Wiki](http://www.phusewiki.org/wiki/index.php?title=Standard_Scripts) for email address).
+
+###### Standard PhUSE CS Analyses (White Paper implementation)
+
+There is still much to do to deliver the analyses in the White Paper on Central Tendency (**WPCT**). For full details, see our [WPCT Task List](https://github.com/phuse-org/phuse-scripts/blob/master/whitepapers/WPCT/TODO.md). From that list, we highlight a few specific tasks, to illustrate the range of ways that you can contribute your expertise. In increasing complexity:
+
+  * Learn about the WPCT package from
+    * [Our PhUSE wiki page](http://www.phusewiki.org/wiki/index.php?title=WG5_Project_02)
+    * [Our GitHub WPCT User & Contributor Guide](https://github.com/phuse-org/phuse-scripts/blob/master/whitepapers/CentralTendency-UserGuide.md)
+  * Test a Standard Script
+    * R: Using our test data or your own ADaM data, produce Fig 7.1 and Fig 7.2 using the corresponding [R script](https://github.com/phuse-org/phuse-scripts/tree/master/whitepapers/WPCT)
+    * SAS: Using our test data or your own ADaM data, produce Fig 7.1, 7.2, 7.3, 7.6, 7.7 and 7.8 using the corresponding [SAS script](https://github.com/phuse-org/phuse-scripts/tree/master/whitepapers/WPCT)
+    * **Give us feedback** on usability, documentation, design, etc. Help improve the approach and scripts.
+  * Enhance a SAS or R script
+    * Current R and SAS scripts are coded for 1 data domain, such as labs or vitals signs.
+    * Analyse and document domain difference. ADaM expertise is highly valuable.
+    * Propose an approach or mechanism for handling all intended domains: labs, vital signs, ECG.
+  * Qualification criteria
+    * Outline qualification requirements for each WPCT Figure. What should we test, to confirm the scripts work as expected? What would convince you that they are accurate and robust?
+    * References: 
+      * [White Paper on Central Tendency](http://www.phusewiki.org/wiki/images/4/48/CSS_WhitePaper_CentralTendency_v1.0.pdf)
+      * [Specifications for the WPCT standard analyses](https://github.com/phuse-org/phuse-scripts/tree/master/whitepapers/specification), 
+  * Test the [SAS macros behind the standard SAS scripts](https://github.com/phuse-org/phuse-scripts/wiki/Utility-Macro-Index-(SAS)).
+    * That [SAS Macro Index page](https://github.com/phuse-org/phuse-scripts/wiki/Utility-Macro-Index-(SAS)) shows what has been done ("qualified"), and what remains ("implemented").
+    * Define and implement the tests for one of the remaining SAS macros
+  * Test automation
+    * Industry code should behave as expected for different users, in different environments
+    * Design and propose a test-automation solution for the repository and code that we have

Diff for: docs/guides/Git_workflow_exercises.md

@@ -33,7 +33,7 @@ Relevant roles for phuse-org/phuse-scripts?
     2. modify file
     3. "pull request" ... screenshots
   * Substantial change (takes some time)
-    1. ? Create a branch
+    1. ? Create a fork (is branching only for members with "write" access??)
     2. develop modules
     3. "pull" changes from master branch
     4. resolve any conflicts

Diff for: whitepapers/README.md

@@ -30,4 +30,3 @@ A brief description of each folder at this level:
 * [**images**](https://github.com/phuse-org/phuse-scripts/tree/master/whitepapers/images)
   * Images to support our github documentation. See for example our [WPCT to-do list](https://github.com/phuse-org/phuse-scripts/blob/master/whitepapers/WPCT/TODO.md)
 
-**Note**: Code on this site is by definition 'under development'.

Diff for: whitepapers/WPCT/TODO.md

@@ -1,7 +1,11 @@
-### WPCT Task List
+### White Paper on Central Tendency Task List
 
 The Repository Content team aim to deliver a package of robust, easy to use and understand SAS and R scripts that create the WPCT standard analyses and displays. For further details, see [the README file in this folder](./README.md).
 
+**Contents:**
+ 1. [To-do list to complete the WPCT package](https://github.com/phuse-org/phuse-scripts/blob/master/whitepapers/WPCT/TODO.md#to-complete-the-wpct-package)
+ 2. [Table: Implementation Status of WPCT Figures](https://github.com/phuse-org/phuse-scripts/blob/master/whitepapers/WPCT/TODO.md#wpct-figures--scripts-with-qualification-details)
+
 **But feel free to be creative** when considering the expertise that you can contribute:
 * Do you have Spotfire expertise, and time to create templates for these analyses?
 * Do you have RStudio Shiny expertise, and time to create a web interface to our R scripts?