v2 Alpha Testing - Round 2

[jwildfire]

Summary

The goal of this thread is to facilitate a second round of alpha testing on the v2.0 release of the safetyGraphics app. This builds upon the first round of alpha testing discussed here. Alpha testers are being asked to complete 2 tasks:

1. Provide feedback on the updated functionality in the default app.
2. Provide feedback on the new safetyGraphicsInit().

See the following sections for more details.

Part 1 - Provide feedback on the updates in the default app

Access the app with this link or install the package using the instructions below and then initialize the default app by calling safetyGraphicsApp(). Any feedback is welcome, but place a special emphasis on reviewing the updated chart export process and settings tab, which have both been updated since the first Alpha testing.

Part 2 - Try the new app initialization workflow.

Install the package using the instructions below and then load the chart initialization app by calling safetyGraphicsInit(). Try loading data for multiple domains using the UI, selecting a custom set of charts and then running the app.

Installation Instructions

Insure that your are using R version 4 or higher, and then run the following code to install the app:

install.packages("devtools")
library("devtools")
devtools::install_github("safetyGraphics/safetyGraphics", ref="v2.0.0-alpha2") 
library(safetyGraphics)
devtools::install_github("safetyGraphics/safetyCharts", ref="v1.0.0-alpha2") 
library(safetyCharts)

devtools will likely prompt you to install/update some packages, say yes!

[jwildfire]

@samussiah @xni7 @elimillera @JimBuchanan @mli1 - I think we're ready for a quick second round of alpha testing! Just let me know if you have any questions and we can discuss here!

[JimBuchanan]

Here are my findings so far. Because I took some screenshots, I've attached a Word document with my collective observations.

Alpha testing - Jim.docx

[jwildfire]

Thanks for the nice write-up, @JimBuchanan! Will reply in more detail later, but first a quick question - How were you using the app? Default or custom data? Did you use the init workflow here? Most of the comments are expected, but I'm a bit confused about why the paneled outlier explorer isn't running properly ...

[jwildfire]

This error makes me think you've got some non-numeric data in your visit number column (which could be causing the issues in outlier explorer and paneled outlier explorer)

[JimBuchanan]

It looks like the VISITNUM column has text formatted as "General". It contains terms such as "Day 1", "Week 01", "Week 02", etc.

[JimBuchanan]

Hi Jeremy, I ran the default code in RStudio and then ran safetyGraphicsInit(). From there I loaded two sets of lab data. One was a set designed for the hepatic explorer. The second was a set I used for the laboratory analysis exercise I did for Abbvie. It contains a broader range of lab analytes which I ran with the (previous) outlier explorer. I’ve attached the dataset if that helps. Thanks, Jim

[JimBuchanan]

In the Hepatic Explorer, the R and nR values over time are displayed along with the ALT, AST, total bilirubin and alkaline phosphatase value in the section Standardized Lab Values by Study Day. Previously, the R ratio over time was displayed in the section R Ratio by Study Day. That section no longer has a display (because it's not needed now), but the section heading still remains. We can remove the R Ratio by Study Day section heading.