Oct 12, 2017 Meeting Notes

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Sep 28, 2017

Present First Name Last Name Affiliation
Yes Kevin Snyder FDA
Elaine Thompson FDA
Kevin Cahill EPL
Bill Varady Boehringer-Ingelheim
Bob Dorsam FDA
Yes Bob Friedman Xybion
Chris Eley Pfizer
Stephen MacMannis Pfizer
Fred Mura PDS
Anthony Fata PDS
Hanming Tu Accenture
Yes Bill Houser Bristol-Myers Squibb
Carol Gleason Bristol-Myers Squibb
Yes Atul Mishra Pfizer
Peter Scaefer Validated Cloud Applications
Mark Pinches Lhasa

Notes from Aug 31:

  • Stephen is trying again to get permission to share. He is working on a script to anonymize data. Over the next few months he hops to adapt the BW script for use with other SEND data such as PC, LB, or the future IS domain.
  • Kevin started preparing a box-plot of data. Maybe it will be ready for our next meeting
  • Hanming is preparing an improved index to the phuse github repository which he is building as an R-Shiny app. This will enable the index to be updated automatically when the script authors supply the appropriate metada with their contribution. In the process he is becoming familiar with roxygen2, a tool to help create R packages.
  • Bill mentioned that he contacted Gábor Csárdi <csardi.gabor@gmail.com>, the maintainer of parsedate, with our ISO 8601 duration function. Gábor's response was enthusiastic, but to contribute we need to create documentation with roxygen2 and tests using testthat and a more readable regular expression using named and non-capturing groups.
  • Bob Friedman volunteered to gain familiarity with roxygen2 and testthat and share what he learns.
  • Kevin also demonstrated the user interface he is building for a network diagram of correlated MI findings using Rgraphviz package from bioconductor (https://bioconductor.org/packages/release/bioc/html/Rgraphviz.html). He is building this for the Histopath visualization group in PhUSE and intends to place this in github. He built it because he often finds when looking at an incidence table if the 4 out of 10 animals with one finding are the same 4 animals with a different finding.

Topics for Sep 28

  • SHARE API 2.0 https://wiki.cdisc.org/display/PUB/SHARE+API+2.0+Public+Input
  • SAS XPT files are predominantly ASCII and can be successfully searched and (with caution) edited using text manipulation tools such as notepad++.
  • Most of the meeting was Bob showing what he had learned about Roxygen2 and adding some documentation to the dur-to-seconds function.

File:Parsedate-master Sep 2017.pdf

File:ROxygen - Phuse Nonclinical Scripts.zip

File:Parsedate-package R file working.zip

Meeting Oct 12, 2017:

  • Good R tutorial found by Kevin and added to the bottom of our project's wiki page: http://www.phusewiki.org/wiki/index.php?title=Oct_12,_2017_Meeting_Notes&action=edit&redlink=1
    • the edit function to make interactive changes to values in an array.
    • explains the reasons for factors and how to use them
    • differences between matricies and arrays
    • explained the plotting function
    • explains how to use statistics functions
    • explains each of the data types
    • chapter 8 is helpful when working with SEND. To compute averages on selected records aggregate() may be helpful
    • Chapter 11 describes advanced features like creating an expression in a string variable and then evaluating it.
  • Bob shared how to use ROxygen2 to create documentation as is done in the parsedate package.