Tech review vignette updates

[madison-feshuk]

Creating a catch all ticket for vignette updates needed based on tech reviewer comments:

• Remove api key and server parameters from bioactivity requests https://cran.r-project.org/web/packages/ccdR/vignettes/Bioactivity.html (Code was code from API markdown where parameters were needed to access staging)
• Remove head() if data is not being displayed

[madison-feshuk]

Tech review comments from John:

The R package “ccdR” represents the culmination of more than a decade of effort by the CompTox center to make chemical risk assessment information easily accessible for informatics researchers. The vignettes reviewed here provide example computer instructions and background on how to use ccdR to obtain chemical information. Although I was familiar with the CompTox Chemicals Dashboard (CCD), I had never previously used ccdR. The information provided in the vignettes was clear, helpful, and sufficient to new users of the ccdR package. I have only minor suggestions:

• I really like that you start off with how to use the CCD and batch search. That is very valuable in itself. • Maybe list some papers that reference using the CCD? Or how many times Williams et al. has been cited? • Maybe mention explicitly that the CCD provides a “graphical user interface” aimed at a useful human -driven experience? • You should probably define “landing page”. • Similarly, I am not sure that “endpoints” as a term will be familiar to everyone. • This may just be a me thing, but when I cut-and-paste from the PDF in Adobe Acrobat into another program (including the R terminal, Rstudio, and the Text App) I get weird line breaks around the parentheses. This prevents me from copying code as is into a script or session. • For example: This stores the key in the current session register_ccdr(key = '') Turns into: This stores the key in the current session register_ccdr ( key = '' ) I get an error message because the open parenthesis is on the second line. This would work if at least that first parenthesis was on line 1.

• I love that units are included in get_chem_info. That’s really helpful! • The chemical_starts_with command is currently returning a “Bad Request” message. res_dt<- chemical_starts_with( word = 'DTXSID70201' )

However, this works: res_dt<- chemical_starts_with( word = 'bisphenol'

[madison-feshuk]

For the CCD reference, consider adding link to About page https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard-about (incudes link to CCD paper)

[madison-feshuk]

This link https://api-ccte.epa.gov/docs/ will soon be deprecated. For help documentation, we should direct to this EPA web page https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-data-apis (to be updated)

[madison-feshuk]

Update any reference to "CCTE APIs" as "Computational Toxicology and Exposure (CTX) APIs"

[madison-feshuk]

“CTX APIs” can stay plural, but the individual data domain API in text should be singular