R: Fitting Order-Restricted Generalized Linear Models

orglm.fit {mcprofile}

R Documentation

Fitting Order-Restricted Generalized Linear Models

Description

orglm.fit is used to fit generalized linear models with restrictions on the parameters, specified by giving a description of the linear predictor, a description of the error distribution, and a description of a matrix with linear constraints. The quadprog package is used to apply linear constraints on the parameter vector.

Usage

orglm.fit(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL,
  mustart = NULL, offset = rep(0, nobs), family = gaussian(),
  control = list(), intercept = TRUE, constr, rhs, nec)

Arguments

`x`	is a design matrix of dimension `n * p`
`y`	is a vector of observations of length `n`
`weights`	an optional vector of ‘prior weights’ to be used in the fitting process. Should be `NULL` or a numeric vector.
`start`	starting values for the parameters in the linear predictor.
`etastart`	starting values for the linear predictor.
`mustart`	starting values for the vector of means.
`offset`	this can be used to specify an a priori known component to be included in the linear predictor during fitting. This should be `NULL` or a numeric vector of length equal to the number of cases. One or more `offset` terms can be included in the formula instead or as well, and if more than one is specified their sum is used. See `model.offset`.
`family`	a description of the error distribution and link function to be used in the model. This can be a character string naming a family function, a family function or the result of a call to a family function. (See `family` for details of family functions.)
`control`	a list of parameters for controlling the fitting process. For `orglm.fit` this is passed to `glm.control`.
`intercept`	logical. Should an intercept be included in the null model?
`constr`	a matrix with linear constraints. The columns of this matrix should correspond to the columns of the design matrix.
`rhs`	right hand side of the linear constraint formulation. A numeric vector with a length corresponding to the rows of `constr`.
`nec`	Number of equality constrints. The first `nec` constraints defined in `constr` are treated as equality constraints; the remaining ones are inequality constraints.

Details

Non-NULL weights can be used to indicate that different observations have different dispersions (with the values in weights being inversely proportional to the dispersions); or equivalently, when the elements of weights are positive integers w_i, that each response y_i is the mean of w_i unit-weight observations. For a binomial GLM prior weights are used to give the number of trials when the response is the proportion of successes: they would rarely be used for a Poisson GLM. If more than one of etastart, start and mustart is specified, the first in the list will be used. It is often advisable to supply starting values for a quasi family, and also for families with unusual links such as gaussian("log"). For the background to warning messages about ‘fitted probabilities numerically 0 or 1 occurred’ for binomial GLMs, see Venables & Ripley (2002, pp. 197–8).

Value

An object of class "glm" is a list containing at least the following components:

coefficients: a named vector of coefficients
residuals: the working residuals, that is the residuals in the final iteration of the IWLS fit. Since cases with zero weights are omitted, their working residuals are NA.
fitted.values: the fitted mean values, obtained by transforming the linear predictors by the inverse of the link function.
rank: the numeric rank of the fitted linear model.
family: the family object used.
linear.predictors: the linear fit on link scale.
deviance: up to a constant, minus twice the maximized log-likelihood. Where sensible, the constant is chosen so that a saturated model has deviance zero.
null.deviance: The deviance for the null model, comparable with deviance. The null model will include the offset, and an intercept if there is one in the model. Note that this will be incorrect if the link function depends on the data other than through the fitted mean: specify a zero offset to force a correct calculation.
iter: the number of iterations of IWLS used.
weights: the working weights, that is the weights in the final iteration of the IWLS fit.
prior.weights: the weights initially supplied, a vector of 1s if none were.
df.residual: the residual degrees of freedom of the unconstrained model.
df.null: the residual degrees of freedom for the null model.
y: if requested (the default) the y vector used. (It is a vector even for a binomial model.)
converged: logical. Was the IWLS algorithm judged to have converged?
boundary: logical. Is the fitted value on the boundary of the attainable values?

Author(s)

Modification of the original glm.fit by Daniel Gerhard. The original R implementation of glm was written by Simon Davies working for Ross Ihaka at the University of Auckland, but has since been extensively re-written by members of the R Core team. The design was inspired by the S function of the same name described in Hastie & Pregibon (1992).

References

Dobson, A. J. (1990) An Introduction to Generalized Linear Models. London: Chapman and Hall.
Hastie, T. J. and Pregibon, D. (1992) Generalized linear models. Chapter 6 of Statistical Models in S eds J. M. Chambers and T. J. Hastie, Wadsworth & Brooks/Cole.
McCullagh P. and Nelder, J. A. (1989) Generalized Linear Models. London: Chapman and Hall.
Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics with S. New York: Springer.