Documentation updates

7 files changed, 67 insertions, 46 deletions

diff --git a/man/coef.sparsestep.Rd b/man/coef.sparsestep.Rd
index 0505cbc..9c2afae 100644
--- a/man/coef.sparsestep.Rd
+++ b/man/coef.sparsestep.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/coef.sparsestep.R
 \name{coef.sparsestep}
-\alias{coef}
 \alias{coef.sparsestep}
+\alias{coef}
 \title{Get the coefficients of a fitted SparseStep model}
 \usage{
 \method{coef}{sparsestep}(object, ...)
@@ -27,14 +27,13 @@ fit <- sparsestep(x, y)
 coef(fit)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
  \emph{SparseStep: Approximating the Counting Norm for Sparse Regularization},
  arXiv preprint arXiv:1701.06967 [stat.ME]. 
  URL \url{https://arxiv.org/abs/1701.06967}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/path.sparsestep.Rd b/man/path.sparsestep.Rd
index 94dc4d4..6a57c75 100644
--- a/man/path.sparsestep.Rd
+++ b/man/path.sparsestep.Rd
@@ -4,10 +4,24 @@
 \alias{path.sparsestep}
 \title{Approximate path algorithm for the SparseStep model}
 \usage{
-path.sparsestep(x, y, max.depth = 10, gamma0 = 1000, gammastop = 1e-04,
-  IMsteps = 2, gammastep = 2, normalize = TRUE, intercept = TRUE,
-  force.zero = TRUE, threshold = 1e-07, XX = NULL, Xy = NULL,
-  use.XX = TRUE, use.Xy = TRUE, quiet = FALSE)
+path.sparsestep(
+  x,
+  y,
+  max.depth = 10,
+  gamma0 = 1000,
+  gammastop = 1e-04,
+  IMsteps = 2,
+  gammastep = 2,
+  normalize = TRUE,
+  intercept = TRUE,
+  force.zero = TRUE,
+  threshold = 1e-07,
+  XX = NULL,
+  Xy = NULL,
+  use.XX = TRUE,
+  use.Xy = TRUE,
+  quiet = FALSE
+)
 }
 \arguments{
 \item{x}{matrix of predictors}
@@ -91,10 +105,6 @@ y <- rnorm(100)
 pth <- path.sparsestep(x, y)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
  \emph{SparseStep: Approximating the Counting Norm for Sparse Regularization},
@@ -105,4 +115,7 @@ Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
 \code{\link{coef}}, \code{\link{print}}, \code{\link{predict}}, 
 \code{\link{plot}}, and \code{\link{sparsestep}}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/plot.sparsestep.Rd b/man/plot.sparsestep.Rd
index 0fd0171..b3d4ae1 100644
--- a/man/plot.sparsestep.Rd
+++ b/man/plot.sparsestep.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/plot.sparsestep.R
 \name{plot.sparsestep}
-\alias{plot}
 \alias{plot.sparsestep}
+\alias{plot}
 \title{Plot the SparseStep path}
 \usage{
 \method{plot}{sparsestep}(x, ...)
@@ -23,14 +23,13 @@ plot(fit)
 pth <- path.sparsestep(x, y)
 plot(pth)
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
  \emph{SparseStep: Approximating the Counting Norm for Sparse Regularization},
  arXiv preprint arXiv:1701.06967 [stat.ME]. 
  URL \url{https://arxiv.org/abs/1701.06967}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/predict.sparsestep.Rd b/man/predict.sparsestep.Rd
index d738e78..5707b5c 100644
--- a/man/predict.sparsestep.Rd
+++ b/man/predict.sparsestep.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/predict.sparsestep.R
 \name{predict.sparsestep}
-\alias{predict}
 \alias{predict.sparsestep}
+\alias{predict}
 \title{Make predictions from a SparseStep model}
 \usage{
 \method{predict}{sparsestep}(object, newx, ...)
@@ -29,14 +29,13 @@ fit <- sparsestep(x, y)
 yhat <- predict(fit, x)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
  \emph{SparseStep: Approximating the Counting Norm for Sparse Regularization},
  arXiv preprint arXiv:1701.06967 [stat.ME]. 
  URL \url{https://arxiv.org/abs/1701.06967}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/print.sparsestep.Rd b/man/print.sparsestep.Rd
index 3c436bb..b8a921e 100644
--- a/man/print.sparsestep.Rd
+++ b/man/print.sparsestep.Rd
@@ -21,14 +21,13 @@ fit <- sparsestep(x, y)
 print(fit)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
  \emph{SparseStep: Approximating the Counting Norm for Sparse Regularization},
  arXiv preprint arXiv:1701.06967 [stat.ME]. 
  URL \url{https://arxiv.org/abs/1701.06967}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/sparsestep-package.Rd b/man/sparsestep-package.Rd
index 9bf2144..99f3fd4 100644
--- a/man/sparsestep-package.Rd
+++ b/man/sparsestep-package.Rd
@@ -34,6 +34,7 @@ SparseStep}
 model}
 }
 }
+
 \examples{
 x <- matrix(rnorm(100*20), 100, 20)
 y <- rnorm(100)
@@ -45,14 +46,13 @@ x2 <- matrix(rnorm(50*20), 50, 20)
 y2 <- predict(fits, x2)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
  \emph{SparseStep: Approximating the Counting Norm for Sparse Regularization},
  arXiv preprint arXiv:1701.06967 [stat.ME]. 
  URL \url{https://arxiv.org/abs/1701.06967}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}
diff --git a/man/sparsestep.Rd b/man/sparsestep.Rd
index d00b47c..0fa9fd1 100644
--- a/man/sparsestep.Rd
+++ b/man/sparsestep.Rd
@@ -4,10 +4,23 @@
 \alias{sparsestep}
 \title{Fit the SparseStep model}
 \usage{
-sparsestep(x, y, lambda = c(0.1, 0.5, 1, 5, 10), gamma0 = 1000,
-  gammastop = 1e-04, IMsteps = 2, gammastep = 2, normalize = TRUE,
-  intercept = TRUE, force.zero = TRUE, threshold = 1e-07, XX = NULL,
-  Xy = NULL, use.XX = TRUE, use.Xy = TRUE)
+sparsestep(
+  x,
+  y,
+  lambda = c(0.1, 0.5, 1, 5, 10),
+  gamma0 = 1000,
+  gammastop = 1e-04,
+  IMsteps = 2,
+  gammastep = 2,
+  normalize = TRUE,
+  intercept = TRUE,
+  force.zero = TRUE,
+  threshold = 1e-07,
+  XX = NULL,
+  Xy = NULL,
+  use.XX = TRUE,
+  use.Xy = TRUE
+)
 }
 \arguments{
 \item{x}{matrix of predictors}
@@ -78,10 +91,6 @@ y <- rnorm(100)
 fit <- sparsestep(x, y)
 
 }
-\author{
-Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
-Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
-}
 \references{
 Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
  \emph{SparseStep: Approximating the Counting Norm for Sparse Regularization},
@@ -92,4 +101,7 @@ Van den Burg, G.J.J., Groenen, P.J.F. and Alfons, A. (2017).
 \code{\link{coef}}, \code{\link{print}}, \code{\link{predict}}, 
 \code{\link{plot}}, and \code{\link{path.sparsestep}}.
 }
-
+\author{
+Gerrit J.J. van den Burg, Patrick J.F. Groenen, Andreas Alfons\cr
+Maintainer: Gerrit J.J. van den Burg <gertjanvandenburg@gmail.com>
+}