In opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils

r variable$name

hasCategories <- (length(variable$categories) > 0)
hasAttributes <- (length(variable$attributes) > 0)
hasNonMissingCategory <- FALSE
if (hasCategories) {
  for (category in variable$categories) {
    if (!category$isMissing) {
      hasNonMissingCategory <- TRUE      
      break;
    }
  }
}
isCategorical <- (hasCategories & hasNonMissingCategory) | variable$valueType == 'boolean'
isNumerical <- (variable$valueType == 'integer' | variable$valueType == 'decimal') & !isCategorical
allIsNA <- TRUE
if (withStatistics) {
  allIsNA <- opal.execute(o, paste0("all(is.na(D$", variable$name, "))"))
}

Properties

Property | Value
---------------- | ---------------- Entity type | r variable$entityType Value type | r variable$valueType Unit | r variable$unit Mime Type | r variable$mimeType Repeatable | r variable$isRepeatable Occurrence Group | r variable$occurrenceGroup

cat("#### Attributes\n")

cat("Name | Value\n")
cat("---------------- | ----------------\n")
added <- c()
for (attribute in variable$attributes) {
  name <- attribute$name
  if (length(attribute$namespace) > 0) {
    name <- paste0("[", attribute$namespace, "] ", name)
  }
  if (length(grep(paste0("^", name, "$"), added)) == 0) {
    values <- opal.attribute_values(variable$attributes, namespace=attribute$namespace, name=attribute$name)
    cat(paste0(name, " | ", paste(values, collapse="<br/>"), "\n"))
    added <- append(added, name)
  }
}

cat("#### Categories\n")

cat("Name | Label | Missing\n")
cat("---------------- | ---------------- | ----------------\n")
for (category in variable$categories) {
  labels <- paste(opal.attribute_values(category$attributes, name="label"), collapse="<br/>")
  row <- paste0(category$name, " | ", gsub("\\|","/", labels) ," | ")
  if (category$isMissing) {
    row <- paste0(row, "<span class='glyphicon glyphicon-ok'></span>")
  }
  cat(paste0(row, "\n"))
}

outsummary <- knit_child('opal-variable-categorical.Rmd')

outsummary <- knit_child('opal-variable-continuous.Rmd')

r if(withStatistics & (isNumerical | isCategorical)) paste(outsummary, collapse='\n')

opalr documentation built on Sept. 18, 2024, 9:11 a.m.