Digital Pathology Validation

Digital Pathology Validation

Usage

digitalvalidation(
  data,
  reference,
  test,
  platform_var,
  validation_type = "both",
  acceptance_criteria = "fda_standard",
  custom_correlation_threshold = 0.9,
  custom_icc_threshold = 0.75,
  bias_assessment = TRUE,
  decision_threshold1 = 0,
  decision_threshold2 = 0,
  decision_threshold3 = 0,
  bootstrap_ci = TRUE,
  bootstrap_n = 1000,
  show_validation_plots = TRUE,
  generate_report = TRUE
)

Arguments

data

the data as a data frame

reference

reference/gold standard measurements

test

test method measurements to be validated

platform_var

platform or batch identifier for stratified analysis

validation_type

type of validation analysis to perform

acceptance_criteria

regulatory acceptance criteria for validation

custom_correlation_threshold

minimum acceptable correlation coefficient

custom_icc_threshold

minimum acceptable ICC value

bias_assessment

perform systematic and proportional bias assessment

decision_threshold1

first clinical threshold for decision impact analysis

decision_threshold2

second clinical threshold for decision impact analysis

decision_threshold3

third clinical threshold for decision impact analysis

bootstrap_ci

use bootstrap method for robust confidence intervals

bootstrap_n

number of bootstrap replicates

show_validation_plots

display validation and residual plots

generate_report

generate comprehensive validation report

Value

A results object containing:

results$interpretation					a html
results$performancetable					Comprehensive validation performance metrics
results$biastable					Systematic and proportional bias analysis
results$agreementtable					ICC, CCC, and correlation measures
results$thresholdtable					Impact at different clinical thresholds
results$validationplot					Scatter plot with regression and agreement lines
results$blandaltmanplot					Agreement analysis with limits of agreement
results$residualplot					Residual patterns for bias detection
results$validationreport					Complete validation report with regulatory framework
results$acceptancesummary					Pass/fail status for regulatory criteria

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$performancetable$asDF

as.data.frame(results$performancetable)