R/my_verify.R

In nclSLR: The nclSLR package.

my_verify <-
  function(x, y, qualitative=FALSE, na.rm=na.rm)
  {
    # x: matrix or data frame with explanatory variables
    # y: vector or factor with group memberships
    # qualitative: logical indicating verification for disqual
    # na.rm: logical indicating missing values in x

    # x matrix or data.frame
    if (is.null(dim(x)))
      stop("\n'variables' is not a matrix or data.frame")
    # no missing values allowed when na.rm=FALSE
    if (!na.rm) {
      if (length(complete.cases(x)) != nrow(x))
        stop("\nSorry, no missing values allowed in 'variables'")
    }
    # check lengths of x and y
    if (nrow(x) != length(y))
      stop("\n'variables' and 'group' have different lengths")
    # y vector or factor
    if (!is.vector(y) && !is.factor(y))
      stop("\n'group' must be a factor")
    # make sure y is a factor
    if (!is.factor(y)) y = as.factor(y)
    # no missing values in y
    if (any(!is.finite(y)))
      stop("\nNo missing values allowed in 'group'")
    # quantitative or qualitative variables?
    if (!qualitative)
    { # quantitative data
      # make sure is matrix
      if (!is.matrix(x)) x <- as.matrix(x)
      # only numeric values
      if (!is.numeric(x))
        stop("\n'variables' must contain only numeric values")
    } else { # data frame with qualitative data
      # variables as data frame with factors
      fac_check = sapply(x, class)
      if (!is.data.frame(x) && any(fac_check != "factor"))
        stop("\nA data frame with factors was expected")
    }

    # verified inputs
    if (is.null(colnames(x)))
      colnames(x) = paste(rep("X", ncol(x)), seq_len(ncol(x)), sep='')
    if (is.null(rownames(x)))
      rownames(x) = 1L:nrow(x)
    list(X=x, y=y)
  }