Pathology Composition Analysis

Semi-quantitative analysis of histologic components and their association with clinical outcomes. Based on advanced pathology research methodologies, particularly gastric cancer composition analysis. Performs component risk assessment, composition pattern analysis, and optimal threshold identification.

Usage

pathologycomposition(
  data,
  outcome_variable,
  component1,
  component2,
  component3,
  component4,
  composition_analysis = TRUE,
  optimal_composition = TRUE,
  trend_test = TRUE,
  confidence_level = 0.95,
  low_risk_threshold = 0.05,
  high_risk_threshold = 0.2,
  min_group_size = 10,
  quantitative_categories = "gastric_cancer",
  composition_plot = TRUE
)

Arguments

data

the data as a data frame

outcome_variable

Clinical outcome variable for composition analysis

component1

First histologic component (proportion or category)

component2

Second histologic component (proportion or category)

component3

Third histologic component (proportion or category)

component4

Fourth histologic component (proportion or category)

composition_analysis

Analyze risk based on component composition patterns

optimal_composition

Identify optimal low-risk and high-risk composition patterns

trend_test

Perform trend tests for dose-response relationships

confidence_level

Confidence level for risk estimates and intervals

low_risk_threshold

Maximum risk probability for low-risk classification (5 percent = 0.05)

high_risk_threshold

Minimum risk probability for high-risk classification (20 percent = 0.20)

min_group_size

Minimum number of cases required for composition pattern analysis

quantitative_categories

Semi-quantitative categorization system for components

composition_plot

Generate scatter plot of component composition vs risk

Value

A results object containing:

results$instructions					a html
results$componentanalysis					a table
results$compositionrisk					a table
results$optimalcompositions					a table
results$compositionplot					an image
results$interpretation					a html

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

results$componentanalysis$asDF

as.data.frame(results$componentanalysis)

Examples

# \donttest{
data('pathology_data')
#> Warning: data set ‘pathology_data’ not found

pathologycomposition(data = pathology_data,
                    outcome_variable = lymph_node_metastasis,
                    component1 = signet_ring_cells,
                    component2 = poorly_differentiated,
                    composition_analysis = TRUE)
#> Error in pathologycomposition(data = pathology_data, outcome_variable = lymph_node_metastasis,     component1 = signet_ring_cells, component2 = poorly_differentiated,     composition_analysis = TRUE): argument "component3" is missing, with no default
# }