Function for Medical Decision Analysis. Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value.
Usage
decision(
data,
gold,
goldPositive,
newtest,
testPositive,
pp = FALSE,
pprob = 0.3,
od = FALSE,
fnote = FALSE,
ci = FALSE,
fagan = FALSE,
showNaturalLanguage = TRUE,
showClinicalInterpretation = TRUE,
showReportTemplate = FALSE,
showAboutAnalysis = FALSE
)Arguments
- data
The data as a data frame. The data frame should contain the variables specified in the 'variables' option.
- gold
The gold standard reference variable representing true disease status.
- goldPositive
The level indicating presence of disease in the gold standard variable.
- newtest
The diagnostic test variable being evaluated for performance.
- testPositive
The level representing a positive result for the test under evaluation.
- pp
Boolean selection whether to use known population prevalence instead of study prevalence.
- pprob
Population disease prevalence as a proportion between 0.001 and 0.999.
- od
Boolean selection whether to show original data frequency tables.
- fnote
Boolean selection whether to show detailed explanatory footnotes.
- ci
Boolean selection whether to calculate and display 95\ confidence intervals.
- fagan
Boolean selection whether to generate a Fagan nomogram plot.
- showNaturalLanguage
Boolean selection whether to show the natural language clinical summary.
- showClinicalInterpretation
Boolean selection whether to show the clinical interpretation guide.
- showReportTemplate
Boolean selection whether to show the copy-ready report template.
- showAboutAnalysis
Boolean selection whether to show the about analysis section.
Value
A results object containing:
results$rawContingency | a table | ||||
results$rawCounts | a table | ||||
results$cTable | a table | ||||
results$nTable | a table | ||||
results$ratioTable | a table | ||||
results$missingDataSummary | a html | ||||
results$epirTable_ratio | a table | ||||
results$epirTable_number | a table | ||||
results$plot1 | an image | ||||
results$naturalLanguageSummary | a html | ||||
results$clinicalInterpretation | a html | ||||
results$reportTemplate | a html | ||||
results$aboutAnalysis | a html |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$rawContingency$asDF
as.data.frame(results$rawContingency)