Audits the completeness of structured / synoptic pathology reports: the proportion of required data elements present per report, per required element, and by subspecialty or reporting pathologist, with an optional completeness trend over time.
Usage
synopticcompleteness(
data,
items,
presenceRule = "nonmissing",
presentValue = "",
group = NULL,
timeVar = NULL,
completeThreshold = 100,
showOverall = TRUE,
showPerItem = TRUE,
showByGroup = TRUE,
showTrend = TRUE,
showPlot = TRUE,
showSummary = TRUE,
showExplanation = FALSE
)Arguments
- data
.
- items
The required synoptic data elements. Each is counted as present for a report when it is non-missing (and, for text, not blank or an explicit absence marker).
- presenceRule
How each element is judged present.
- presentValue
When the rule is "specified value", the value that marks an element present.
- group
Optional grouping for stratified completeness (e.g. subspecialty or reporting pathologist).
- timeVar
Optional ordered time/period variable for a completeness trend.
- completeThreshold
A report counts as complete when at least this percentage of elements are present.
- showOverall
.
- showPerItem
.
- showByGroup
.
- showTrend
.
- showPlot
.
- showSummary
.
- showExplanation
.
Value
A results object containing:
results$todo | a html | ||||
results$overallTable | a table | ||||
results$perItemTable | a table | ||||
results$byGroupTable | a table | ||||
results$trendTable | a table | ||||
results$plot | an image | ||||
results$addCompletenessToData | an output | ||||
results$summary | a html | ||||
results$explanation | a html |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$overallTable$asDF
as.data.frame(results$overallTable)