Update documentation

R/bru.inference.R

@@ -17,46 +17,59 @@ generate = function(object, ...){ UseMethod("generate") }
 
 #' @title Convenient model fitting using (iterated) INLA
 #'
-#' @description This method is a wrapper for \link[INLA]{inla} and provides multiple enhancements. 
-#' 
-#' \itemize{
-#' \item{Easy usage of spatial covariates and automatic construction of inla projection matrices for (spatial) SPDE models. 
-#'       This feature is accessible via the \code{components} parameter.
-#'       Practical examples on how to use spatial data by means of the components parameter can also be found by looking at the \link{lgcp}
-#'       function's documentation.}
-#' \item{Constructing multiple likelihoods is straight forward. See \link{like} for more information on how to provide additional
-#'       likelihoods to \code{bru} using the ... parameter list.}
-#' \item{Support for non-linear predictors. See example below.}
-#' \item{Log Gaussian Cox process (LGCP) inference is available by using the \code{cp} family or (even easier) by using the 
-#'       \link{lgcp} function.}
-#' }
+#' @description This method is a wrapper for \link[INLA]{inla} and provides
+#'   multiple enhancements.
+#'
+#'   \itemize{
+#'     \item
+#'       Easy usage of spatial covariates and automatic construction
+#'       of inla projection matrices for (spatial) SPDE models. This feature is
+#'       accessible via the \code{components} parameter. Practical examples on how
+#'       to use spatial data by means of the components parameter can also be found
+#'       by looking at the \link{lgcp} function's documentation.
+#'     \item
+#'       Constructing multiple likelihoods is straight forward. See \link{like} for more
+#'       information on how to provide additional likelihoods to \code{bru} using
+#'       the \code{...} parameter list.
+#'     \item
+#'       Support for non-linear predictors. See example below.
+#'     \item
+#'       Log Gaussian Cox process (LGCP) inference is
+#'       available by using the \code{cp} family or (even easier) by using the
+#'       \link{lgcp} function.
+#'   }
 #' @aliases bru
 #' @export
-#' 
+#'
 #' @author Fabian E. Bachl <\email{bachlfab@@gmail.com}>
-#' 
-#' @param components a \link{formula} describing the latent components. See \link{bru.components} for details.
-#' @param family A string indicating the likelihood family. The default is \code{gaussian} with 
-#'               identity link. In addition to the likelihoods provided by inla 
-#'               (see \code{inla.models()$likelihood}) inlabru supports fitting Cox processes 
-#'               via \code{family = "cp"}. The latter requires contructing a likelihood using the \link{like}
-#'               function and providing it via the ... parameter list. As an alternative to bru, the \link{lgcp} 
-#'               function provides a convenient interface to fitting Cox processes. See details.
+#'
+#' @param components a \link{formula} describing the latent components. See
+#'   \link{bru.components} for details.
+#' @param family A string indicating the likelihood family. The default is
+#'   \code{gaussian} with identity link. In addition to the likelihoods provided
+#'   by inla (see \code{inla.models()$likelihood}) inlabru supports fitting Cox
+#'   processes via \code{family = "cp"}. The latter requires contructing a
+#'   likelihood using the \link{like} function and providing it via the ...
+#'   parameter list. As an alternative to bru, the \link{lgcp} function provides
+#'   a convenient interface to fitting Cox processes. See details.
 #' @param data A data.frame or SpatialPoints[DataFrame] object. See details.
-#' @param ... Additional likelihoods, each constructed by a calling \link{like}. See details.
-#' @param options A list of name and value pairs that are either interpretable by \link{bru.options} 
-#'                or valid inla parameters. 
-#'                
-#' @details family and ... must either be parameters to \link{like}, or \code{lhood} objects constructed by \link{like}.
-#'          \code{data} must either be an \code{lhood} object, a data container, or \code{NULL}. If \code{NULL},
-#'          data must be supplied through direct calls to \link{like}.
-#' 
-#' @return bru returns an object of class "bru". A \code{bru} object inherits from \link[INLA]{inla} 
-#'         (see the inla documentation for its properties) and adds additional information stored 
-#'         in the \code{sppa} field.
-#' 
+#' @param ... Additional likelihoods, each constructed by a calling \link{like}.
+#'   See details.
+#' @param options A list of name and value pairs that are either interpretable
+#'   by \link{bru.options} or valid inla parameters. See \link{bru.options} for
+#'   caveats about some of the \code{control.*} inla options.
+#'
+#' @details family and ... must either be parameters to \link{like}, or
+#'   \code{lhood} objects constructed by \link{like}. \code{data} must either be
+#'   an \code{lhood} object, a data container, or \code{NULL}. If \code{NULL},
+#'   data must be supplied through direct calls to \link{like}.
+#'
+#' @return bru returns an object of class "bru". A \code{bru} object inherits
+#'   from \link[INLA]{inla} (see the inla documentation for its properties) and
+#'   adds additional information stored in the \code{sppa} field.
+#'
 #' @example inst/examples/bru.R
-#' 
+#'   
 
 bru = function(components = y ~ Intercept,
                family = NULL,