R/r2lme.R

In jbirstler/biostatrpts: Functions for UW-Biostatistics Report Creation

#' Calculates R-squared for lme model
#'
#' Calculates R-squared for lme model
#'
#' implements R2 from Edwards, Muller, Wolfinger, Qaqish and Schabenberger,
#' 2008.  need the aod package for wald.test function
#'
#' @param obj lme object
#' @return R-square value
#' @export
#' @importFrom aod wald.test
#' @importFrom nlme fixef

r2lme <- function(obj) {
  # implements R2 from Edwards, Muller, Wolfinger, Qaqish and Schabenberger, 2008.
  if (class(obj) != "lme") {
    stop("lme object expected")
  }
  n <- obj$dims[["N"]] # the number of observations
  p <- ncol(coef(obj)) # number of parameters
  df.error <- n - p
  wald.obj <- wald.test(b = fixef(obj), Sigma = vcov(obj), df = df.error, Terms = 2:p)
  wald.F <- as.numeric(wald.obj$result$Ftest[1])
  ((p - 1) * 1 / df.error * wald.F) / (1 + (p - 1) * 1 / df.error * wald.F)
}