Widget updates

[jwildfire]

Overview

• Adds init function for aeTimelines giving support for custom Severity and Seriousness mappings. Fix Update htmlwidgets to use latest releases #71.
• Updates hep-explorer widget from v1.3.1 to version 1.4.2. All release notes are here, but the main additions are the nRatio should be available as an option on the x-axis and pAlt should be calculated for all participants by default (see arrows in screenshot below). Fix AESER is an undocumented requirement for safetyTimeline widget #88.

This should wrap up the updates for v0.3! Once this is merged I'll work on getting this to CRAN and then try to finalize safetyGraphics v2.1.

Test Notes

• For hep-explorer, confirm functionality listed above is present and no other obvious bugs are found.
• Test code for aeTimeline:

#Confirm that new metadata mappings for severity and seriousness work as expected in aetimelines

customSevSer <- safetyData::adam_adae %>%
rename(sev=AESEV) %>%
rename(ser=AESER) 

safetyGraphicsApp(
    domainData = list(aes=customSevSer),
    mapping=list(aes=list(severity_col="sev", serious_col="ser"))
)

# Extra color added when new category added. Not 100% ideal, but ok. 
customSevSer <- safetyData::adam_adae %>%
rename(sev=AESEV) %>%
rename(ser=AESER) %>%
mutate(sev = if_else(sev=="MILD","WILD!",sev))


safetyGraphicsApp(
    domainData = list(aes=customSevSer),
    mapping=list(aes=list(severity_col="sev", serious_col="ser"))
)

[xni7]

Looks great @jwildfire ! a couple of minor comments

• hepExplorer

  • nR and Palt work well! I like having the Palt reference!
  • suggest adding reference to R and nR ratio somewhere (ideally in the widget), e.g.
    • https://www.gastrojournal.org/article/S0016-5085(14)01484-X/fulltext
    • or this paper
  • baseline and analysis mapping in hepExplorer() do not match hepexplorer.js parameterization
    

    safetyCharts/R/hepExplorer.R

    Lines 53 to 56 in 4652165

    	baseline_flag_col = "",
    	baseline_flag_values = "",
    	analysis_flag_col = "",
    	analysis_flag_values = "",

    
    expecting baseline as a list
    

    safetyCharts/inst/htmlwidgets/lib/hep-explorer-1.4.2/hepexplorer.js

    Lines 255 to 258 in 4652165

    	baseline: {
    	value_col: null, //synced with studyday_col in syncsettings()
    	values: [0]
    	},

    
    mDish is working with the following code.

   # enable mDish plot example
   mapping_baseline <- list(
       measure_col = "PARAM",
       measure_values = list(
           ALT = "Alanine Aminotransferase (U/L)",
           AST = "Aspartate Aminotransferase (U/L)",
           TB = "Bilirubin (umol/L)",
           ALP = "Alkaline Phosphatase (U/L)"
       ),
       ## mDish does not work with this mapping
       # baseline_flag_col = "ABLFL",
       # baseline_flag_values = "Y",
       ## mDish works with a baseline list, 
       baseline = list(
           value_col = "ABLFL",
           values = "Y"
       ),
       analysis_flag_col = "",
       analysis_flag_values = "",
       id_col = "USUBJID",
       value_col = "AVAL",
       normal_col_low = "A1LO",
       normal_col_high = "A1HI",
       studyday_col = "ADY",
       visit_col = "VISIT",
       visitn_col = "VISITNUM",
       unit_col = ""
   )
   
   hepExplorer(df = safetyData::adam_adlbc, mapping = mapping_baseline)

• aeTimelines. Looks great! Only comment is the ASTDY has huge negative values in safetyData::adam_adae. Perhaps can filter out in vignette for better viewing experience.

  # Extra color added when new category added. Not 100% ideal, but ok.
  customSevSer <- safetyData::adam_adae %>%
      filter(ASTDY > -50) %>% # add a filter to make the timeline more viewable
      rename(sev = AESEV) %>%
      rename(ser = AESER) %>%
      mutate(sev = if_else(sev == "MILD", "WILD!", sev))
  
  
  safetyGraphicsApp(
      domainData = list(aes = customSevSer),
      mapping = list(aes = list(severity_col = "sev", serious_col = "ser"))
  )

[jwildfire]

suggest adding reference to R and nR ratio somewhere (ideally in the widget), e.g.

• https://www.gastrojournal.org/article/S0016-5085(14)01484-X/fulltext
• or this paper

Good idea - filed SafetyGraphics/hep-explorer#335

[jwildfire]

• baseline and analysis mapping in hepExplorer() do not match hepexplorer.js parameterization

I updated the docs a bit in #104 on Friday and cleaned this up.

FWIW, the default mapping was pasted from the safetyGraphicsApp() export which includes baseline_flag_X and analysis_flag_X. As you noted, they're not currently used in hepExplorer though. Should probably write a little hepexplorer_init to set them up in the safetyGraphics app. That actually obfuscates the new the hepExplorer function a bit though, so maybe we should just delete those non-standard mappings. Not sure ... Will file an issue and leave it for a future release.

[jwildfire]

Actually going to just delete those options. See #105.

[jwildfire]

• Only comment is the ASTDY has huge negative values in safetyData::adam_adae. Perhaps can filter out in vignette for better viewing experience.

Yeah, I've been meaning to do this in the hosted example. Added a comment here as a reminder.