WG5 P02 Script header - SAS

From PHUSE Wiki
Revision as of 22:56, 2 May 2015 by DanteDT (talk | contribs)
Jump to: navigation, search

Script headers use YAML to describe scripts and declare a TO-DO list. The following references provide YAML details:

Elements of the HEADER

  • SOURCE - Name of white paper describing the target of this script
  • DISPLAY - Title of the target, taken from white paper
  • SPECS - Link to specifications document in PhUSE/CSS repository
  • TO-DO - List of outstanding development tasks, transferred to PhUSE/CSS Trello board by self-assigned developer

Elements of the TO-DO list
  • task: brief statement of the task
  • desc: sufficient detail for a developer to commence
  • detail: guidance on implementation, to assist new developer

The following SAS header template for PhUSE/CSS scripts is based on

Template for SAS Script Headers


   White paper: Central Tendencies
   Display:     Figure 7.1 Box plot - Measurements by Analysis Timepoint, Visit and Planned Treatment
   page:  http://www.phusewiki.org/wiki/index.php?title=Scriptathon2014_targets
   image: http://www.phusewiki.org/wiki/index.php?title=File:CSS_WhitePaper_CentralTendency_f7_1.jpg
   Specs:       https://github.com/phuse-org/phuse-scripts/blob/master/whitepapers/specification/WPCT-F.07.01_specs.yml
   Notes:       • Program box plots all visits, ordered by AVISITN, with maximum of 20 boxes on a page (default)
                  + see user option MAX_BOXES_PER_PAGE, below, to change 20 per page
                • Program separately plots all parameters in PARAMCD
                • Measurements within each PARAMCD and ATPTN determine precision of stats
                  + MEAN gets 1 extra decimal, STD DEV gets 2 extra decimals
                  + see macro UTIL_VALUE_FORMAT to adjust this behavior
                • If your treatment names are too long for the summary table,
                  Change TRTP in the input data, and add a footnote that explains your short Tx codes
   TO DO:
     • Complete and confirm specifications (see Outliers & Reference limit discussions, below)
     • Set uniform y-axis scale for all pages of a plot, based on MAX measured value for PARAMCD and ATPTN
     • RED color for values outside pre-defined reference limits
         - See discussion in section 7.1
         - See Figure 6.1 Explanation of Box Plot, from SAS/STAT user guide
         - Symbol for IQR outliers
         - Apply RED color for values outside pre-defined reference limits
         - EG, include ANRLO and ANRHI in dependencies and program logic
     • Confirm meaning of "N" in summary table
         - Population size?
         - Sample size?
         - Should display distinguish between "N" (pop), "n" (samples), and pop with NO measures?
     • Reference limit lines. Provide options for several scenarios (see explanation in White Paper):
         - NONE:    DEFAULT. no reference lines
         - UNIFORM: reference limits are uniform for entire population
                    only display uniform ref lines, to match outlier logic, otherwise no lines
                    NB: preferred alternative to default (NONE)
         - NARROW:  reference limits vary across selected population (e.g., based on some demographic or lab)
                    display reference lines for the narrowest interval
                    EG: highest of the low limits, lowest of the high limits
                    NB: discourage, since creates confusion for reviewers
         - ALL:     reference limits vary across selected population (e.g., based on some demographic or lab)
                    display all reference lines, pairing low/high limits by color and line type
                    NB: discourage, since creates confusion for reviewers

end HEADER ***/