Commit 34c07c89 authored by Tom Reynkens's avatar Tom Reynkens

Link to documentation of glmsmurf-class

parent 816b942b
Type: Package
Package: smurf
Title: Sparse Multi-Type Regularized Feature Modeling
Version: 0.3.0.9024
Version: 0.3.0.9025
Date: 2018-09-21
Authors@R: c(
person("Tom", "Reynkens", email = "tomreynkens@hotmail.com", role = c("aut", "cre"),
......
......@@ -10,12 +10,12 @@
#' @description Function to extract the coefficients of the estimated model.
#' \code{coefficients} is an \emph{alias} for it.
#'
#' @param object An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param object An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param ... Additional arguments which are currently ignored.
#'
#' @return A vector containing the coefficients of the estimated model in \code{object}.
#'
#' @seealso \code{\link{coef_reest}}, \code{\link[stats]{coef}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}
#' @seealso \code{\link{coef_reest}}, \code{\link[stats]{coef}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples \dontrun{
#'
......@@ -47,13 +47,13 @@ coefficients.glmsmurf <- coef.glmsmurf
#' \code{coefficients_reest} is an \emph{alias} for it.
#'
#' @param object An object for which the extraction of model coefficients is meaningful.
#' E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @inheritParams coef.glmsmurf
#'
#' @return A vector containing the coefficients of the re-estimated model in \code{object},
#' when they are available, or, otherwise, the coefficients of the estimated model in \code{object} with a warning.
#'
#' @seealso \code{\link{coef.glmsmurf}}, \code{\link[stats]{coef}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}
#' @seealso \code{\link{coef.glmsmurf}}, \code{\link[stats]{coef}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples \dontrun{
#'
......
......@@ -10,13 +10,13 @@
#'
#' @description Function to extract the deviance of the estimated model.
#'
#' @param object An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param object An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param ... Additional arguments which are currently ignored.
#'
#' @return The deviance of the estimated model in \code{object}.
#'
#' @seealso \code{\link{deviance_reest}}, \code{\link[stats]{deviance}}, \code{\link{summary.glmsmurf}},
#' \code{\link{glmsmurf}}
#' \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples \dontrun{
#'
......@@ -42,14 +42,14 @@ deviance.glmsmurf <- function(object, ...) {
#' @description Function to extract the deviance of the re-estimated model.
#'
#' @param object An object for which the extraction of the deviance is meaningful.
#' E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @inheritParams deviance.glmsmurf
#'
#' @return The deviance of the re-estimated model in \code{object},
#' when it is available or, otherwise, the deviance of the estimated model in \code{object} with a warning.
#'
#' @seealso \code{\link{deviance.glmsmurf}}, \code{\link[stats]{deviance}}, \code{\link{summary.glmsmurf}},
#' \code{\link{glmsmurf}}
#' \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples \dontrun{
#'
......
......@@ -10,12 +10,12 @@
#'
#' @description Function to extract the fitted values of the estimated model.
#'
#' @param object An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param object An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param ... Additional arguments which are currently ignored.
#'
#' @return A vector containing the fitted values of the estimated model in \code{object}.
#'
#' @seealso \code{\link{fitted_reest}}, \code{\link[stats]{fitted.values}}, \code{\link{glmsmurf}}
#' @seealso \code{\link{fitted_reest}}, \code{\link[stats:fitted.values]{fitted}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples \dontrun{
#'
......@@ -41,12 +41,14 @@ fitted.glmsmurf <- function(object, ...) {
#' @description Function to extract the fitted values of the re-estimated model.
#'
#' @param object An object for which the extraction of fitted values is meaningful.
#' E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @inheritParams deviance.glmsmurf
#' E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @inheritParams fitted.glmsmurf
#'
#' @return A vector containing the fitted values of the re-estimated model in \code{object},
#' when they are available or, otherwise, the fitted values of the estimated model in \code{object} with a warning.
#'
#'
#' @seealso \code{\link{fitted.glmsmurf}}, \code{\link[stats:fitted.values]{fitted}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#
#' @examples \dontrun{
#'
#' # See example(glmsmurf) on how to obtain
......
#' @title Class of Multi-Type Regularized GLMs Fitted Using the SMuRF Algorithm
#'
#' @description The functions \code{\link{glmsmurf}} and \code{\link{glmsmurf.fit}} return objects of the S3 class "\code{glmsmurf}"
#' which partially inherits from the "\code{glm}" and "\code{lm}" classes.
#' @description The functions \code{\link{glmsmurf}} and \code{\link{glmsmurf.fit}} return objects of the S3 class '\code{glmsmurf}'
#' which partially inherits from the '\code{glm}' and '\code{lm}' classes.
#'
#' @return An object of class "\code{glmsmurf}" is a list with at least following components:
#' @return An object of class '\code{glmsmurf}' is a list with at least following components:
#' \item{coefficients}{Coefficients of the estimated model.}
#' \item{residuals}{Working residuals of the estimated model, see \code{\link[stats]{glm}}: \eqn{((y_1-\mu_1)/(d\mu/d\eta(\eta_1)), \ldots, (y_n-\mu_n)/(d\mu/d\eta(\eta_n)))}.}
#' \item{fitted.values}{Fitted mean values of the estimated model \eqn{(\mu_1, \ldots, \mu_n)=(g^{-1}(\eta_1), \ldots, g^{-1}(\eta_n))} with \eqn{g^{-1}} the inverse link function.}
......
......@@ -61,7 +61,7 @@
#' @param y.return Logical indicating if the used response vector should be returned in the output object, default is \code{TRUE}.
#' @param pen.weights.return Logical indicating if the list of the used penalty weight vector per predictor should be returned in the output object, default is \code{FALSE}.
#' @param control A list of parameters used in the fitting process. This is passed to \code{\link{glmsmurf.control}}.
#' @return An object of class \code{"glmsmurf"} is returned. See \code{\link{glmsmurf-class}} for more details about this class and its generic functions.
#' @return An object of class '\code{glmsmurf}' is returned. See \code{\link{glmsmurf-class}} for more details about this class and its generic functions.
#'
#' @details See the package vignette for more details and a complete description of a use case.
#'
......
......@@ -11,7 +11,7 @@
#'
#' @description Function to plot the coefficients of the estimated model.
#'
#' @param x An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param x An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param xlab Label for the x-axis, default is \code{"Index"}.
#' @param ylab Label for the y-axis, default is \code{"Estimated coefficients"}.
#' @param basic Logical indicating if the basic lay-out is used for the plot, default is \code{FALSE}.
......@@ -20,7 +20,7 @@
#' @details When \code{basic=FALSE}, the improved lay-out for the plot is used. Per predictor, groups of unique coefficients are indicated
#' in the same color (up to 8 colors), and zero coefficients are indicated by grey squares.
#'
#' @seealso \code{\link{plot_reest}}, \code{\link{coef.glmsmurf}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}
#' @seealso \code{\link{plot_reest}}, \code{\link{coef.glmsmurf}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples ## See example(glmsmurf) for examples
plot.glmsmurf <- function(x, xlab = "Index", ylab = "Estimated coefficients", basic = FALSE, ...) {
......@@ -36,7 +36,7 @@ plot.glmsmurf <- function(x, xlab = "Index", ylab = "Estimated coefficients", ba
#' @description Function to plot the coefficients of the re-estimated model.
#'
#' @param x An object for which the extraction of model coefficients is meaningful.
#' E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param ylab Label for the y-axis, default is \code{"Re-estimated coefficients"}.
#' @inheritParams plot.glmsmurf
#'
......@@ -45,7 +45,7 @@ plot.glmsmurf <- function(x, xlab = "Index", ylab = "Estimated coefficients", ba
#'
#' See \code{\link{plot.glmsmurf}} for more details.
#'
#' @seealso \code{\link{plot.glmsmurf}}, \code{\link{coef_reest}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}
#' @seealso \code{\link{plot.glmsmurf}}, \code{\link{coef_reest}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples ## See example(glmsmurf) for examples
plot_reest <- function(x, ...) UseMethod("plot_reest", x)
......
......@@ -12,7 +12,7 @@
#' as a function of lambda when lambda is selected in-sample, out-of-sample or using cross-validation.
#'
#' @param x An object for which the extraction of goodness-of-fit statistics or information criteria is meaningful.
#' E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param xlab Label for the x-axis. The default value is \code{NULL} which means that \code{substitute(log(lambda))} is used when \code{log.lambda=TRUE}
#' and \code{substitute(lambda)} when \code{log.lambda=FALSE}.
#' @param ylab Label for the y-axis. The default value is \code{NULL} which means that the y-axis label is
......@@ -27,7 +27,7 @@
#' @details This plot can only be made when lambda is selected in-sample, out-of-sample or using cross-validation,
#' see the \code{lambda} argument of \code{\link{glmsmurf}}.
#'
#' @seealso \code{\link{glmsmurf}}
#' @seealso \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @example /inst/Rent_example2.R
plot_lambda <- function(x, ...) UseMethod("plot_lambda", x)
......
......@@ -10,7 +10,7 @@
#'
#' @description Function to obtain predictions using the estimated model.
#'
#' @param object An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param object An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param newdata Optionally, a data frame containing the predictors used in the prediction.
#' This can only be used when \code{object} contains a formula.
#' When \code{newdata} is omitted, the predictions are based on the data used to fit the model in \code{object}.
......@@ -24,7 +24,7 @@
#' @return A vector containing the predicted values using the estimated model in \code{object}.
#'
#' @seealso \code{\link{predict_reest}}, \code{\link[stats]{predict.glm}}, \code{\link[stats]{predict}},
#' \code{\link{glmsmurf}}
#' \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples \dontrun{
#'
......@@ -49,14 +49,14 @@ predict.glmsmurf <- function(object, newdata = NULL, newoffset = NULL, type = c(
#' @description Function to obtain predictions using the re-estimated model.
#'
#' @param object An object for which predictions are meaningful.
#' E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @inheritParams predict.glmsmurf
#'
#' @return A vector containing the predicted values using the re-estimated model in \code{object},
#' when this is available, or the predicted values using the estimated model otherwise.
#'
#' @seealso \code{\link{predict.glmsmurf}}, \code{\link[stats]{predict.glm}}, \code{\link[stats]{predict}},
#' \code{\link{glmsmurf}}
#' \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @examples \dontrun{
#'
......
......@@ -11,7 +11,7 @@
#' @description Function to extract the residuals of the estimated model.
#' \code{resid} is an \emph{alias} for it.
#'
#' @param object An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param object An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param type Type of residuals that should be returned. One of \code{"deviance"} (default),
#' \code{"pearson"}, \code{"working"}, \code{"response"} or \code{"partial"}.
#' @param ... Additional arguments which are currently ignored.
......@@ -52,7 +52,7 @@ resid.glmsmurf <- residuals.glmsmurf
#' \code{resid_reest} is an \emph{alias} for it.
#'
#' @param object An object for which the extraction of model residuals is meaningful.
#' E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @inheritParams residuals.glmsmurf
#'
#' @return A vector containing the residuals of the re-estimated model in \code{object}
......
......@@ -20,11 +20,11 @@ print.glmsmurf <- function(x, ...) {
#'
#' @description Function to print a summary of a \code{glmsmurf} object.
#'
#' @param object An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param object An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.
#' @param digits The number of significant digits used when printing, default is 3.
#' @param ... Additional arguments which are currently ignored.
#'
#' @seealso \code{\link[stats]{summary.glm}}, \code{\link{glmsmurf}}
#' @seealso \code{\link[stats]{summary.glm}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
#'
#' @method summary glmsmurf
#'
......
......@@ -10,7 +10,7 @@
\method{coefficients}{glmsmurf}(object, ...)
}
\arguments{
\item{object}{An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{object}{An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments which are currently ignored.}
}
......@@ -36,5 +36,5 @@ coef_reest(munich.fit)
}
\seealso{
\code{\link{coef_reest}}, \code{\link[stats]{coef}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}
\code{\link{coef_reest}}, \code{\link[stats]{coef}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -17,7 +17,7 @@ coefficients_reest(object, ...)
}
\arguments{
\item{object}{An object for which the extraction of model coefficients is meaningful.
E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments which are currently ignored.}
}
......@@ -44,5 +44,5 @@ coef_reest(munich.fit)
}
\seealso{
\code{\link{coef.glmsmurf}}, \code{\link[stats]{coef}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}
\code{\link{coef.glmsmurf}}, \code{\link[stats]{coef}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -7,7 +7,7 @@
\method{deviance}{glmsmurf}(object, ...)
}
\arguments{
\item{object}{An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{object}{An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments which are currently ignored.}
}
......@@ -33,5 +33,5 @@ deviance_reest(munich.fit)
}
\seealso{
\code{\link{deviance_reest}}, \code{\link[stats]{deviance}}, \code{\link{summary.glmsmurf}},
\code{\link{glmsmurf}}
\code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -11,7 +11,7 @@ deviance_reest(object, ...)
}
\arguments{
\item{object}{An object for which the extraction of the deviance is meaningful.
E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments which are currently ignored.}
}
......@@ -38,5 +38,5 @@ deviance_reest(munich.fit)
}
\seealso{
\code{\link{deviance.glmsmurf}}, \code{\link[stats]{deviance}}, \code{\link{summary.glmsmurf}},
\code{\link{glmsmurf}}
\code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -7,7 +7,7 @@
\method{fitted}{glmsmurf}(object, ...)
}
\arguments{
\item{object}{An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{object}{An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments which are currently ignored.}
}
......@@ -32,5 +32,5 @@ fitted_reest(munich.fit)
}
\seealso{
\code{\link{fitted_reest}}, \code{\link[stats]{fitted.values}}, \code{\link{glmsmurf}}
\code{\link{fitted_reest}}, \code{\link[stats:fitted.values]{fitted}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -11,7 +11,7 @@ fitted_reest(object, ...)
}
\arguments{
\item{object}{An object for which the extraction of fitted values is meaningful.
E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments which are currently ignored.}
}
......@@ -36,3 +36,6 @@ fitted_reest(munich.fit)
}
}
\seealso{
\code{\link{fitted.glmsmurf}}, \code{\link[stats:fitted.values]{fitted}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -5,7 +5,7 @@
\alias{glmsmurf-class}
\title{Class of Multi-Type Regularized GLMs Fitted Using the SMuRF Algorithm}
\value{
An object of class "\code{glmsmurf}" is a list with at least following components:
An object of class '\code{glmsmurf}' is a list with at least following components:
\item{coefficients}{Coefficients of the estimated model.}
\item{residuals}{Working residuals of the estimated model, see \code{\link[stats]{glm}}: \eqn{((y_1-\mu_1)/(d\mu/d\eta(\eta_1)), \ldots, (y_n-\mu_n)/(d\mu/d\eta(\eta_n)))}.}
\item{fitted.values}{Fitted mean values of the estimated model \eqn{(\mu_1, \ldots, \mu_n)=(g^{-1}(\eta_1), \ldots, g^{-1}(\eta_n))} with \eqn{g^{-1}} the inverse link function.}
......@@ -79,8 +79,8 @@ When the object is output from \code{\link{glmsmurf}}, following elements are al
\item{xlevels}{The levels of the factors used in fitting (when relevant).}
}
\description{
The functions \code{\link{glmsmurf}} and \code{\link{glmsmurf.fit}} return objects of the S3 class "\code{glmsmurf}"
which partially inherits from the "\code{glm}" and "\code{lm}" classes.
The functions \code{\link{glmsmurf}} and \code{\link{glmsmurf.fit}} return objects of the S3 class '\code{glmsmurf}'
which partially inherits from the '\code{glm}' and '\code{lm}' classes.
}
\section{S3 generics}{
......
......@@ -103,7 +103,7 @@ When the predictor is not a factor or no reference category is present, it is eq
when a reference category is present.}
}
\value{
An object of class \code{"glmsmurf"} is returned. See \code{\link{glmsmurf-class}} for more details about this class and its generic functions.
An object of class '\code{glmsmurf}' is returned. See \code{\link{glmsmurf-class}} for more details about this class and its generic functions.
}
\description{
SMuRF algorithm to fit a generalized linear model (GLM) via regularized maximum likelihood with a multi-type Lasso penalty.
......
......@@ -8,7 +8,7 @@
ylab = "Estimated coefficients", basic = FALSE, ...)
}
\arguments{
\item{x}{An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{x}{An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{xlab}{Label for the x-axis, default is \code{"Index"}.}
......@@ -29,5 +29,5 @@ in the same color (up to 8 colors), and zero coefficients are indicated by grey
## See example(glmsmurf) for examples
}
\seealso{
\code{\link{plot_reest}}, \code{\link{coef.glmsmurf}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}
\code{\link{plot_reest}}, \code{\link{coef.glmsmurf}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -12,7 +12,7 @@ plot_lambda(x, ...)
}
\arguments{
\item{x}{An object for which the extraction of goodness-of-fit statistics or information criteria is meaningful.
E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments for the \code{\link[graphics]{plot}} function.}
......@@ -110,5 +110,5 @@ plot_lambda(munich.fit.cv, xlim = c(-8, -4), ylim = c(1550, 1750))
}
}
\seealso{
\code{\link{glmsmurf}}
\code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -12,7 +12,7 @@ plot_reest(x, ...)
}
\arguments{
\item{x}{An object for which the extraction of model coefficients is meaningful.
E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments for the \code{\link[graphics]{plot}} function.}
......@@ -35,5 +35,5 @@ When the re-estimated model is not included in \code{x},
## See example(glmsmurf) for examples
}
\seealso{
\code{\link{plot.glmsmurf}}, \code{\link{coef_reest}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}
\code{\link{plot.glmsmurf}}, \code{\link{coef_reest}}, \code{\link{summary.glmsmurf}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -8,7 +8,7 @@
type = c("link", "response", "terms"), ...)
}
\arguments{
\item{object}{An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{object}{An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{newdata}{Optionally, a data frame containing the predictors used in the prediction.
This can only be used when \code{object} contains a formula.
......@@ -45,5 +45,5 @@ predict_reest(munich.fit, type = "link")
}
\seealso{
\code{\link{predict_reest}}, \code{\link[stats]{predict.glm}}, \code{\link[stats]{predict}},
\code{\link{glmsmurf}}
\code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -12,7 +12,7 @@ predict_reest(object, ...)
}
\arguments{
\item{object}{An object for which predictions are meaningful.
E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments which are currently ignored.}
......@@ -50,5 +50,5 @@ predict_reest(munich.fit, type = "link")
}
\seealso{
\code{\link{predict.glmsmurf}}, \code{\link[stats]{predict.glm}}, \code{\link[stats]{predict}},
\code{\link{glmsmurf}}
\code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
......@@ -12,7 +12,7 @@
"working", "response", "partial"), ...)
}
\arguments{
\item{object}{An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{object}{An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{type}{Type of residuals that should be returned. One of \code{"deviance"} (default),
\code{"pearson"}, \code{"working"}, \code{"response"} or \code{"partial"}.}
......
......@@ -19,7 +19,7 @@ resid_reest(object, ...)
}
\arguments{
\item{object}{An object for which the extraction of model residuals is meaningful.
E.g. an object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
E.g. an object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{...}{Additional arguments which are currently ignored.}
......
......@@ -7,7 +7,7 @@
\method{summary}{glmsmurf}(object, digits = 3L, ...)
}
\arguments{
\item{object}{An object of class "glmsmurf", typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{object}{An object of class '\code{\link[=glmsmurf-class]{glmsmurf}}', typically the result of a call to \code{\link{glmsmurf}} or \code{\link{glmsmurf.fit}}.}
\item{digits}{The number of significant digits used when printing, default is 3.}
......@@ -20,5 +20,5 @@ Function to print a summary of a \code{glmsmurf} object.
## See example(glmsmurf) for examples
}
\seealso{
\code{\link[stats]{summary.glm}}, \code{\link{glmsmurf}}
\code{\link[stats]{summary.glm}}, \code{\link{glmsmurf}}, \code{\link{glmsmurf-class}}
}
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