Documentation updates

24 files changed, 106 insertions, 130 deletions

diff --git a/man/coef.gensvm.Rd b/man/coef.gensvm.Rd
index 0132ab9..9f08ecc 100644
--- a/man/coef.gensvm.Rd
+++ b/man/coef.gensvm.Rd
@@ -30,10 +30,6 @@ fit <- gensvm(x, y)
 V <- coef(fit)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -43,4 +39,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{gensvm}}, \code{\link{plot.gensvm}}, 
 \code{\link{predict.gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/coef.gensvm.grid.Rd b/man/coef.gensvm.grid.Rd
index 5e84db1..744809f 100644
--- a/man/coef.gensvm.grid.Rd
+++ b/man/coef.gensvm.grid.Rd
@@ -25,10 +25,6 @@ grid <- gensvm.grid(x, y)
 pg <- coef(grid)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -37,4 +33,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \seealso{
 \code{\link{gensvm.grid}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/fitted.gensvm.Rd b/man/fitted.gensvm.Rd
index 148b233..b242eb8 100644
--- a/man/fitted.gensvm.Rd
+++ b/man/fitted.gensvm.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/fitted.gensvm.R
 \name{fitted.gensvm}
-\alias{fitted}
 \alias{fitted.gensvm}
+\alias{fitted}
 \title{Show fitted labels for the GenSVM model}
 \usage{
 \method{fitted}{gensvm}(fit, ...)
@@ -32,10 +32,6 @@ yhat <- fitted(fit)
 gensvm.accuracy(y, yhat)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -45,4 +41,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{plot.gensvm}}, \code{\link{predict.gensvm.grid}}, 
 \code{\link{gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/fitted.gensvm.grid.Rd b/man/fitted.gensvm.grid.Rd
index 49ebb70..1e2f697 100644
--- a/man/fitted.gensvm.grid.Rd
+++ b/man/fitted.gensvm.grid.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/fitted.gensvm.grid.R
 \name{fitted.gensvm.grid}
-\alias{fitted}
 \alias{fitted.gensvm.grid}
+\alias{fitted}
 \title{Fitted labels for the GenSVMGrid class}
 \usage{
 \method{fitted}{gensvm.grid}(grid, ...)
@@ -32,10 +32,6 @@ yhat <- fitted(fit)
 gensvm.accuracy(y, yhat)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -45,4 +41,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{plot.gensvm}}, \code{\link{predict.gensvm.grid}}, 
 \code{\link{gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm-package.Rd b/man/gensvm-package.Rd
index 7c4e2a5..479648f 100644
--- a/man/gensvm-package.Rd
+++ b/man/gensvm-package.Rd
@@ -99,10 +99,7 @@ The following nonlinear kernels are implemented in the GenSVM package:
  }
  }
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
+
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -111,4 +108,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \seealso{
 \code{\link{gensvm}}, \code{\link{gensvm.grid}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.Rd b/man/gensvm.Rd
index e48444f..b6c9bf0 100644
--- a/man/gensvm.Rd
+++ b/man/gensvm.Rd
@@ -11,8 +11,8 @@ gensvm(x, y, p = 1, lambda = 1e-08, kappa = 0, epsilon = 1e-06,
 }
 \arguments{
 \item{x}{data matrix with the predictors. \cr\cr
-Note that for SVMs categorical features should be converted to binary dummy 
-features. This can be done with using the \code{\link{model.matrix}} 
+Note that for SVMs categorical features should be converted to binary dummy
+features. This can be done with using the \code{\link{model.matrix}}
 function (i.e. \code{model.matrix( ~ var - 1)}).}
 
 \item{y}{class labels}
@@ -21,15 +21,15 @@ function (i.e. \code{model.matrix( ~ var - 1)}).}
 
 \item{lambda}{regularization parameter for the loss function (lambda > 0)}
 
-\item{kappa}{parameter for the hinge function in the loss function (kappa > 
+\item{kappa}{parameter for the hinge function in the loss function (kappa >
 -1.0)}
 
-\item{weights}{type or vector of instance weights to use. Options are 'unit' 
-for unit weights and 'group' for group size correction weights (eq. 4 in the 
+\item{weights}{type or vector of instance weights to use. Options are 'unit'
+for unit weights and 'group' for group size correction weights (eq. 4 in the
 paper). Alternatively, a vector of weights can be provided.}
 
-\item{kernel}{the kernel type to use in the classifier. It must be one of 
-'linear', 'poly', 'rbf', or 'sigmoid'. See the section "Kernels in GenSVM" 
+\item{kernel}{the kernel type to use in the classifier. It must be one of
+'linear', 'poly', 'rbf', or 'sigmoid'. See the section "Kernels in GenSVM"
 in \code{\link{gensvm-package}} for more info.}
 
 \item{gamma}{kernel parameter for the rbf, polynomial, and sigmoid kernel.
@@ -39,24 +39,24 @@ If gamma is 'auto', then 1/n_features will be used.}
 
 \item{degree}{parameter for the polynomial kernel}
 
-\item{kernel.eigen.cutoff}{Cutoff point for the reduced eigendecomposition 
-used with kernel-GenSVM. Eigenvectors for which the ratio between their 
-corresponding eigenvalue and the largest eigenvalue is smaller than this 
+\item{kernel.eigen.cutoff}{Cutoff point for the reduced eigendecomposition
+used with kernel-GenSVM. Eigenvectors for which the ratio between their
+corresponding eigenvalue and the largest eigenvalue is smaller than this
 cutoff value will be dropped.}
 
 \item{verbose}{Turn on verbose output and fit progress}
 
-\item{random.seed}{Seed for the random number generator (useful for 
+\item{random.seed}{Seed for the random number generator (useful for
 reproducible output)}
 
 \item{max.iter}{Maximum number of iterations of the optimization algorithm.}
 
-\item{seed.V}{Matrix to warm-start the optimization algorithm. This is 
-typically the output of \code{coef(fit)}. Note that this function will 
+\item{seed.V}{Matrix to warm-start the optimization algorithm. This is
+typically the output of \code{coef(fit)}. Note that this function will
 silently drop seed.V if the dimensions don't match the provided data.}
 }
 \value{
-A "gensvm" S3 object is returned for which the print, predict, coef, 
+A "gensvm" S3 object is returned for which the print, predict, coef,
 and plot methods are available. It has the following items:
 \item{call}{The call that was used to construct the model.}
 \item{p}{The value of the lp norm in the loss function}
@@ -68,7 +68,7 @@ and plot methods are available. It has the following items:
 \item{gamma}{The value of the gamma parameter of the kernel, if applicable}
 \item{coef}{The value of the coef parameter of the kernel, if applicable}
 \item{degree}{The degree of the kernel, if applicable}
-\item{kernel.eigen.cutoff}{The cutoff value of the reduced 
+\item{kernel.eigen.cutoff}{The cutoff value of the reduced
 eigendecomposition of the kernel matrix.}
 \item{verbose}{Whether or not the model was fitted with progress output}
 \item{random.seed}{The random seed used to seed the model.}
@@ -83,12 +83,12 @@ eigendecomposition of the kernel matrix.}
 \item{training.time}{Total training time}
 }
 \description{
-Fits the Generalized Multiclass Support Vector Machine model 
-with the given parameters. See the package documentation 
+Fits the Generalized Multiclass Support Vector Machine model
+with the given parameters. See the package documentation
 (\code{\link{gensvm-package}}) for more general information about GenSVM.
 }
 \note{
-This function returns partial results when the computation is interrupted by 
+This function returns partial results when the computation is interrupted by
 the user.
 }
 \examples{
@@ -121,17 +121,16 @@ all.equal(coef(fit), coef(fit2))
 
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
-Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
-Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
+Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized
+Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 17(225):1--42. URL \url{http://jmlr.org/papers/v17/14-526.html}.
 }
 \seealso{
-\code{\link{coef}}, \code{\link{print}}, \code{\link{predict}}, 
+\code{\link{coef}}, \code{\link{print}}, \code{\link{predict}},
 \code{\link{plot}}, \code{\link{gensvm.grid}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.accuracy.Rd b/man/gensvm.accuracy.Rd
index 7d07167..9463fa5 100644
--- a/man/gensvm.accuracy.Rd
+++ b/man/gensvm.accuracy.Rd
@@ -19,10 +19,6 @@ fit <- gensvm(x, y)
 gensvm.accuracy(predict(fit, x), y)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -32,4 +28,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{predict.gensvm.grid}}, \code{\link{predict.gensvm}}, 
 \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.generate.cv.idx.Rd b/man/gensvm.generate.cv.idx.Rd
index 34f4f64..38d8829 100644
--- a/man/gensvm.generate.cv.idx.Rd
+++ b/man/gensvm.generate.cv.idx.Rd
@@ -10,4 +10,3 @@ gensvm.generate.cv.idx(n, folds)
 This function generates a vector of length \code{n} with values from 0 to 
 \code{folds-1} to mark train and test splits.
 }
-
diff --git a/man/gensvm.grid.Rd b/man/gensvm.grid.Rd
index b365e10..11dc892 100644
--- a/man/gensvm.grid.Rd
+++ b/man/gensvm.grid.Rd
@@ -126,6 +126,7 @@ Note that this function reorders the parameter grid to make the warm starts
 as efficient as possible, which is why the param.grid in the result will not 
 be the same as the param.grid in the input.
 }
+
 \examples{
 x <- iris[, -5]
 y <- iris[, 5]
@@ -150,10 +151,6 @@ pg <- expand.grid(kernel=c('rbf'), gamma=c(1e-2, 1e-1, 1, 1e1, 1e2),
 grid <- gensvm.grid(x, y, param.grid=pg, verbose=2)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -164,4 +161,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{plot.gensvm.grid}}, \code{\link{gensvm}}, 
 \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.load.full.grid.Rd b/man/gensvm.load.full.grid.Rd
index d754831..18c7095 100644
--- a/man/gensvm.load.full.grid.Rd
+++ b/man/gensvm.load.full.grid.Rd
@@ -16,10 +16,6 @@ combinations of the following parameter sets:
 \code{kappa = c(-0.9, 0.5, 5.0)}
 \code{weights = c('unit', 'group')}
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -29,4 +25,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{gensvm.grid}}, \code{\link{gensvm.load.tiny.grid}}, 
 \code{\link{gensvm.load.full.grid}}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.load.small.grid.Rd b/man/gensvm.load.small.grid.Rd
index 218dac3..ac82084 100644
--- a/man/gensvm.load.small.grid.Rd
+++ b/man/gensvm.load.small.grid.Rd
@@ -16,10 +16,6 @@ parameter sets:
 \code{kappa = c(-0.9, 0.5, 5.0)}
 \code{weights= c('unit', 'group')}
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -29,4 +25,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{gensvm.grid}}, \code{\link{gensvm.load.tiny.grid}}, 
 \code{\link{gensvm.load.small.grid}}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.load.tiny.grid.Rd b/man/gensvm.load.tiny.grid.Rd
index 9ef0694..1b20151 100644
--- a/man/gensvm.load.tiny.grid.Rd
+++ b/man/gensvm.load.tiny.grid.Rd
@@ -17,10 +17,6 @@ performance on most datasets.
 Note that this grid is only tested to work well in combination with the 
 linear kernel.
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -30,4 +26,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{gensvm.grid}}, \code{\link{gensvm.load.small.grid}}, 
 \code{\link{gensvm.load.full.grid}}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.maxabs.scale.Rd b/man/gensvm.maxabs.scale.Rd
index 7b96a37..cbbfd29 100644
--- a/man/gensvm.maxabs.scale.Rd
+++ b/man/gensvm.maxabs.scale.Rd
@@ -51,10 +51,6 @@ x.train.scl <- scaled$x
 x.test.scl <- scaled$x.test
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -64,4 +60,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{gensvm}}, \code{\link{gensvm.grid}}, 
 \code{\link{gensvm.train.test.split}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.rank.score.Rd b/man/gensvm.rank.score.Rd
index 3c1549d..a92d4be 100644
--- a/man/gensvm.rank.score.Rd
+++ b/man/gensvm.rank.score.Rd
@@ -14,4 +14,3 @@ This function computes the ranks for the values in an array. The highest
 value gets the smallest rank. Ties are broken by assigning the smallest 
 value.
 }
-
diff --git a/man/gensvm.refit.Rd b/man/gensvm.refit.Rd
index d57189f..8a711bc 100644
--- a/man/gensvm.refit.Rd
+++ b/man/gensvm.refit.Rd
@@ -45,10 +45,6 @@ fit1 <- gensvm(x1, y1)
 fit2 <- gensvm.refit(fit1, x2, y2)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -57,4 +53,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \seealso{
 \code{\link{gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.train.test.split.Rd b/man/gensvm.train.test.split.Rd
index 6d23964..fe2b1fb 100644
--- a/man/gensvm.train.test.split.Rd
+++ b/man/gensvm.train.test.split.Rd
@@ -50,10 +50,6 @@ fit <- gensvm(x.train, y.train)
 gensvm.accuracy(y.test, predict(fit, x.test))
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -62,4 +58,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \seealso{
 \code{\link{gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/gensvm.validate.param.grid.Rd b/man/gensvm.validate.param.grid.Rd
index 5528f16..69882fe 100644
--- a/man/gensvm.validate.param.grid.Rd
+++ b/man/gensvm.validate.param.grid.Rd
@@ -7,4 +7,3 @@
 gensvm.validate.param.grid(df)
 }
 \keyword{internal}
-
diff --git a/man/gensvm.validate.params.Rd b/man/gensvm.validate.params.Rd
index 1d249a9..8e50137 100644
--- a/man/gensvm.validate.params.Rd
+++ b/man/gensvm.validate.params.Rd
@@ -8,4 +8,3 @@ gensvm.validate.params(p = NULL, kappa = NULL, lambda = NULL,
   epsilon = NULL, gamma = NULL, weights = NULL, kernel = NULL, ...)
 }
 \keyword{internal}
-
diff --git a/man/plot.gensvm.Rd b/man/plot.gensvm.Rd
index 9c15bea..d99c2a0 100644
--- a/man/plot.gensvm.Rd
+++ b/man/plot.gensvm.Rd
@@ -63,10 +63,6 @@ plot(fit, x.test=x.mis)
 plot(fit, y.mis.true, x.test=x.mis)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -76,4 +72,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{plot.gensvm.grid}}, \code{\link{predict.gensvm}}, 
 \code{\link{gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/plot.gensvm.grid.Rd b/man/plot.gensvm.grid.Rd
index 3e5ef39..44c599e 100644
--- a/man/plot.gensvm.grid.Rd
+++ b/man/plot.gensvm.grid.Rd
@@ -10,8 +10,6 @@
 \item{grid}{A \code{gensvm.grid} object trained with refit=TRUE}
 
 \item{...}{further arguments are passed to the plot function}
-
-\item{x}{the dataset to plot}
 }
 \value{
 returns the object passed as input
@@ -29,10 +27,6 @@ grid <- gensvm.grid(x, y)
 plot(grid, x)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -42,4 +36,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{plot.gensvm}}, \code{\link{gensvm.grid}}, 
 \code{\link{predict.gensvm.grid}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/predict.gensvm.Rd b/man/predict.gensvm.Rd
index 0b82662..52c2395 100644
--- a/man/predict.gensvm.Rd
+++ b/man/predict.gensvm.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/predict.gensvm.R
 \name{predict.gensvm}
-\alias{predict}
 \alias{predict.gensvm}
+\alias{predict}
 \title{Predict class labels with the GenSVM model}
 \usage{
 \method{predict}{gensvm}(fit, newdata, add.rownames = FALSE, ...)
@@ -40,10 +40,6 @@ y.test.pred <- predict(fit, x.test)
 gensvm.accuracy(y.test, y.test.pred)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -53,4 +49,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{plot.gensvm}}, \code{\link{predict.gensvm.grid}}, 
 \code{\link{gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/predict.gensvm.grid.Rd b/man/predict.gensvm.grid.Rd
index 194700e..01bf610 100644
--- a/man/predict.gensvm.grid.Rd
+++ b/man/predict.gensvm.grid.Rd
@@ -37,10 +37,6 @@ grid <- gensvm.grid(x, y)
 y.hat <- predict(grid, x)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -50,4 +46,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{gensvm}}, \code{\link{predict.gensvm.grid}}, 
 \code{\link{plot.gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/print.gensvm.Rd b/man/print.gensvm.Rd
index f85db96..e3367fa 100644
--- a/man/print.gensvm.Rd
+++ b/man/print.gensvm.Rd
@@ -31,10 +31,6 @@ fit <- gensvm(x, y)
 predict(print(fit), x)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -44,4 +40,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{gensvm}}, \code{\link{predict.gensvm}}, 
 \code{\link{plot.gensvm}}, \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/print.gensvm.grid.Rd b/man/print.gensvm.grid.Rd
index cf4c257..3b603c1 100644
--- a/man/print.gensvm.grid.Rd
+++ b/man/print.gensvm.grid.Rd
@@ -26,10 +26,6 @@ grid <- gensvm.grid(x, y)
 print(grid)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J. and Groenen, P.J.F. (2016). \emph{GenSVM: A Generalized 
 Multiclass Support Vector Machine}, Journal of Machine Learning Research, 
@@ -40,4 +36,7 @@ Multiclass Support Vector Machine}, Journal of Machine Learning Research,
 \code{\link{plot.gensvm.grid}}, \code{\link{gensvm.grid}}, 
 \code{\link{gensvm-package}}
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen \cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}