R/imports.R

In DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models

#### Package car ####

# this is copied from car, to avoid dependencies / S3 clashes when importing car together with lme4

leveneTest <- function (y, ...) {
  UseMethod("leveneTest") 
}

leveneTest.default <- function (y, group, center=median, ...) { # original levene.test
  if (!is.numeric(y)) 
    stop(deparse(substitute(y)), " is not a numeric variable")
  if (!is.factor(group)) {
    warning(deparse(substitute(group)), " coerced to factor.")
    group <- as.factor(group)
  }
  valid <- complete.cases(y, group)
  meds <- tapply(y[valid], group[valid], center, ...)
  resp <- abs(y - meds[group])
  table <- anova(lm(resp ~ group))[, c(1, 4, 5)]
  rownames(table)[2] <- " "
  dots <- deparse(substitute(...))
  attr(table, "heading") <- paste("Levene's Test for Homogeneity of Variance (center = ", 
                                  deparse(substitute(center)), if(!(dots == "NULL")) paste(":", dots),  ")", sep="")
  table
}


leveneTest.formula <- function(y, data, ...) {
  form <- y
  mf <- if (missing(data)) model.frame(form) else model.frame(form, data)
  if (any(sapply(2:dim(mf)[2], function(j) is.numeric(mf[[j]])))) 
    stop("Levene's test is not appropriate with quantitative explanatory variables.")
  y <- mf[,1]
  if(dim(mf)[2]==2) group <- mf[,2]
  else {
    if (length(grep("\\+ | \\| | \\^ | \\:",form))>0) stop("Model must be completely crossed formula only.")
    group <- interaction(mf[,2:dim(mf)[2]])
  }
  leveneTest.default(y=y, group=group, ...)
}


leveneTest.lm <- function(y, ...) {
  m <- model.frame(y)
  m$..y <- model.response(m)
  f <- formula(y)
  f[2] <- expression(..y)
  leveneTest.formula(f, data=m, ...)
}