clinDataReview

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examples

Running examples in ‘clinDataReview-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sunburstClinData
> ### Title: Sunburst interactive plot.
> ### Aliases: sunburstClinData
> 
> ### ** Examples
> 
> library(clinUtils)
> 
> data(dataADaMCDISCP01)
> labelVars <- attr(dataADaMCDISCP01, "labelVars")
> 
> dataAE <- dataADaMCDISCP01$ADAE
> dataDM <- dataADaMCDISCP01$ADSL
> 
> ## example of basic sunburst:
> 
> # sunburst takes as input table with counts
> if (requireNamespace("inTextSummaryTable", quietly = TRUE)) {
+ 
+ # total counts: Safety Analysis Set (patients with start date for the first treatment)
+ dataTotal <- subset(dataDM, RFSTDTC != "")
+ 
+ # compute adverse event table
+ tableAE <- inTextSummaryTable::getSummaryStatisticsTable(
+ 		
+ 	data = dataAE,
+ 	rowVar = c("AESOC", "AEDECOD"),
+ 	dataTotal = dataTotal,
+ 	rowOrder = "total",
+ 	labelVars = labelVars,
+ 	stats = inTextSummaryTable::getStats("count"),
+ 	
+ 	# plotly treemap requires records (rows) for each group
+ 	rowVarTotalInclude = "AEDECOD",
+ 	outputType = "data.frame-base"
+ 
+ )
+ 
+ dataSunburst <- tableAE
+ 
+ dataSunburst$n <- as.numeric(dataSunburst$n)
+ 
+ # create plot
+ sunburstClinData(
+ 	data = dataSunburst,
+ 	vars = c("AESOC", "AEDECOD"),
+ 	valueVar = "n",
+     valueLab = "Number of patients with adverse events"
+ )
+ 
+ ## example where sum(counts) of child = counts of parent
+ 
+ # counts of patients per arm/site
+ tableDM <- inTextSummaryTable::getSummaryStatisticsTable(
+ 	data = dataDM,
+ 	rowVar = c("ARM", "SITEID"),
+ 	labelVars = labelVars,
+ 	# plotly treemap requires records (rows) for each group
+ 	rowVarTotalInclude = "SITEID",
+ 	rowTotalInclude = TRUE,
+ 	outputType = "data.frame-base"
+ )
+ tableDM$statN <- as.numeric(tableDM$statN)
+ 
+ # create the plot
+ sunburstClinData(
+ 	data = tableDM,
+ 	vars = c("ARM", "SITEID"),
+ 	valueVar = "statN", valueLab = "Counts of patients",
+ 	valueType = "total",
+ 	caption = "The sectors are colored by category.",
+ 	subtitle = "Group: treatment and site"
+ )
+ 
+ }
Error in basename(x) : a character vector argument expected
Calls: <Anonymous> ... file_ext -> ifelse -> grepl -> is.factor -> basename
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
scatterplotClinData 7.551  0.224   9.944

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installed package size

  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb

installed package size

  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb

installed package size

  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb

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