The design matrix and the hypotheses matrices must be entered in RGLM specific format. For the design matrix, the first line must be one or more astericks (*), the second line must be n p and the following lines are the augmented design matrix and response vector.

A hypothesis matrix does not have to be entered, but if it is, then the first line is one or more astericks, second line is number of hypotheis matrices and the third line is one or more astericks. The following lines are the hypotheses matrices. Each hypothesis matrix must be separated by a line of astericks. The first line of each hypothesis matrix must be q p g, where the size of the hypothesis matrix is qxp and g is the constraint indicator, followed by the rows of the hypothesis matrix.

The RGLM.IN file indicates the type of analysis performed by rglm. If it is not provided, then the default is run, with the default being the Wilcoxon scores and the intercept estimated by median of the residuals.