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Assess replicate consistency and repeatability

Source: R/analysis.r
assess_replicates.Rd

Evaluates the statistical consistency and reliability of repeated thermal measurements. The function calculates the Intraclass Correlation Coefficient (ICC) and performs variance decomposition using Linear Mixed Models (LMM) to assess the proportion of variance attributable to between-subject differences versus measurement error.

Usage

assess_replicates(
  data,
  id_col,
  metrics,
  replicate_col = NULL,
  sort_cols = NULL,
  methods = "icc",
  return_models = FALSE,
  quiet = FALSE
)

Arguments

data

A data.frame containing the thermal metrics and identifier columns.

id_col

A single character string specifying the column name for subject IDs.

metrics

A character vector specifying the column names of the thermal metrics to be assessed.

replicate_col

A single character string specifying the column name for the replicate index. Default is NULL. If NULL, replicate indices are inferred from row order.

sort_cols

A character vector specifying the columns to sort the data by before inferring replicate indices. Default is NULL.

methods

A character vector specifying the statistical methods to apply. Valid options include "icc", "variance", and "lmm". Default is "icc".

return_models

Logical. If TRUE and "lmm" is in methods, the fitted linear mixed models are returned. Default is FALSE.

quiet

Logical. If TRUE, console messages are suppressed. Default is FALSE.

Value

An object of class BioThermR_replicate_assessment, which is a list containing:

settings

A list of the input parameters used for the assessment.

icc

A data.frame containing ICC results (if "icc" is selected).

variance

A data.frame containing variance decomposition results (if "variance" is selected).

lmm

A data.frame containing fixed effects and variance components from LMM (if "lmm" is selected).

models

A list of fitted lmer model objects (if return_models = TRUE).

Details

This function requires the psych package for ICC calculations and the lme4 package for variance decomposition and LMM fitting. Ensure these packages are installed before selecting the respective methods.

Examples

if (FALSE) { # \dontrun{
# Assuming df is a data.frame with columns: Sample, Rep, Mean
res <- assess_replicates(
  data = df,
  id_col = "Sample",
  metrics = "Mean",
  replicate_col = "Rep",
  methods = c("icc", "variance")
)
print(res$icc)
} # }