From 9cefbce8432f95f7e1e70aac4ace106e27f8d797 Mon Sep 17 00:00:00 2001
From: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Date: Fri, 16 Aug 2024 13:01:45 +0200
Subject: [PATCH] fixed CRAN NOTE on documentation (issue #11)
---
DESCRIPTION | 2 +-
R/ridgeSIR.R | 14 +++++++-------
R/sparseSIR.R | 26 ++++++++++++++------------
man/SISIR.Rd | 10 +++++-----
man/ridgeSIR.Rd | 14 +++++++-------
man/sparseSIR.Rd | 16 +++++++++-------
6 files changed, 43 insertions(+), 39 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index e141054..4a99111 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -41,6 +41,6 @@ Imports:
Suggests:
testthat
License: GPL (>= 2)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
Encoding: UTF-8
Repository: CRAN
diff --git a/R/ridgeSIR.R b/R/ridgeSIR.R
index 27b0ace..a0b3acc 100644
--- a/R/ridgeSIR.R
+++ b/R/ridgeSIR.R
@@ -26,13 +26,13 @@
#' @param mu2 ridge regularization parameter (numeric, positive)
#' @param d number of dimensions to be kept
#'
-#' @author {Victor Picheny, \email{victor.picheny@inrae.fr}\cr
+#' @author Victor Picheny, \email{victor.picheny@inrae.fr}\cr
#' Remi Servien, \email{remi.servien@inrae.fr}\cr
-#' Nathalie Vialaneix, \email{nathalie.vialaneix@inrae.fr}}
+#' Nathalie Vialaneix, \email{nathalie.vialaneix@inrae.fr}
#'
-#' @references {Picheny, V., Servien, R. and Villa-Vialaneix, N. (2019)
+#' @references Picheny, V., Servien, R. and Villa-Vialaneix, N. (2019)
#' Interpretable sparse SIR for digitized functional data.
-#' \emph{Statistics and Computing}, \strong{29}(2), 255--267.}
+#' \emph{Statistics and Computing}, \strong{29}(2), 255--267.
#'
#' @seealso \code{\link{sparseSIR}}, \code{\link{SISIR}},
#' \code{\link{tune.ridgeSIR}}
@@ -49,20 +49,20 @@
#' \dontrun{print(res_ridge)}
#'
#' @return S3 object of class \code{ridgeRes}: a list consisting of
-#' \itemize{
+#' \describe{
#' \item{\code{EDR}}{ the estimated EDR space (a p x d matrix)}
#' \item{\code{condC}}{ the estimated slice projection on EDR (a d x H
#' matrix)}
#' \item{\code{eigenvalues}}{ the eigenvalues obtained during the generalized
#' eigendecomposition performed by SIR}
#' \item{\code{parameters}}{ a list of hyper-parameters for the method:
-#' \itemize{
+#' \describe{
#' \item{\code{H}}{ number of slices}
#' \item{\code{d}}{ dimension of the EDR space}
#' \item{\code{mu2}}{ regularization parameter for the ridge penalty}
#' }}
#' \item{\code{utils}}{ useful outputs for further computations:
-#' \itemize{
+#' \describe{
#' \item{\code{Sigma}}{ covariance matrix for x}
#' \item{\code{slices}}{ slice number for all observations}
#' \item{\code{invsqrtS}}{ value of the inverse square root of the
diff --git a/R/sparseSIR.R b/R/sparseSIR.R
index 646a9a1..7eb9bf7 100644
--- a/R/sparseSIR.R
+++ b/R/sparseSIR.R
@@ -50,29 +50,31 @@
#' res_sparse <- sparseSIR(res_ridge, rep(10, 20))
#'
#' @return S3 object of class \code{sparseRes}: a list consisting of
-#' \itemize{
+#' \describe{
#' \item{\code{sEDR}}{ the estimated EDR space (a p x d matrix)}
#' \item{\code{alpha}}{ the estimated shrinkage coefficients (a vector having
#' a length similar to \code{inter_len})}
#' \item{\code{quality}}{ a vector with various qualities for the model (see
#' Details)}
#' \item{\code{adapt_res}}{ if \code{adaptive = TRUE}, a list of two vectors:
-#' \itemize{
+#' \describe{
#' \item{\code{nonzeros}}{ indexes of variables that are strong non zeros}
#' \item{\code{zeros}}{ indexes of variables that are strong zeros}
#' }}
#' \item{\code{parameters}}{ a list of hyper-parameters for the method:
-#' \itemize{
+#' \describe{
#' \item{\code{inter_len}}{ lengths of intervals}
#' \item{\code{sel_prop}}{ if \code{adaptive = TRUE}, fraction of the
#' coefficients which are considered as strong zeros or strong non zeros}
#' }}
#' \item{\code{rSIR}}{ same as the input \code{object}}
#' \item{\code{fit}}{ a list for LASSO fit with:
-#' \itemize{
-#' \item{\code{glmnet}} result of the \code{\link[glmnet]{glmnet}} function
-#' \item{\code{lambda}} value of the best Lasso parameter by CV
-#' \item{\code{x}} exploratory variable values as passed to fit the model
+#' \describe{
+#' \item{\code{glmnet}}{ result of the \code{\link[glmnet]{glmnet}}
+#' function}
+#' \item{\code{lambda}}{ value of the best Lasso parameter by CV}
+#' \item{\code{x}}{ exploratory variable values as passed to fit the
+#' model}
#' }}
#' }
#'
@@ -310,13 +312,13 @@ project <- function(object) {
#' number of parameters is either the number of non null intervals or the
#' number of non null parameters with respect to the original variables
#'
-#' @author {Victor Picheny, \email{victor.picheny@inrae.fr}\cr
+#' @author Victor Picheny, \email{victor.picheny@inrae.fr}\cr
#' Remi Servien, \email{remi.servien@inrae.fr}\cr
-#' Nathalie Vialaneix, \email{nathalie.vialaneix@inrae.fr}}
+#' Nathalie Vialaneix, \email{nathalie.vialaneix@inrae.fr}
#'
-#' @references {Picheny, V., Servien, R. and Villa-Vialaneix, N. (2016)
+#' @references Picheny, V., Servien, R. and Villa-Vialaneix, N. (2016)
#' Interpretable sparse SIR for digitized functional data.
-#' \emph{Statistics and Computing}, \strong{29}(2), 255--267.}
+#' \emph{Statistics and Computing}, \strong{29}(2), 255--267.
#'
#' @seealso \code{\link{ridgeSIR}}, \code{\link{sparseSIR}}
#'
@@ -335,7 +337,7 @@ project <- function(object) {
#' \dontrun{res_fused <- SISIR(res_ridge, rep(1, ncol(x)))}
#'
#' @return S3 object of class \code{SISIR}: a list consisting of
-#' \itemize{
+#' \describe{
#' \item{\code{sEDR}}{ the estimated EDR spaces (a list of p x d matrices)}
#' \item{\code{alpha}}{ the estimated shrinkage coefficients (a list of
#' vectors)}
diff --git a/man/SISIR.Rd b/man/SISIR.Rd
index ffa47d2..42f3234 100644
--- a/man/SISIR.Rd
+++ b/man/SISIR.Rd
@@ -37,7 +37,7 @@ NULL, all available cores minus one are used}
}
\value{
S3 object of class \code{SISIR}: a list consisting of
-\itemize{
+\describe{
\item{\code{sEDR}}{ the estimated EDR spaces (a list of p x d matrices)}
\item{\code{alpha}}{ the estimated shrinkage coefficients (a list of
vectors)}
@@ -78,15 +78,15 @@ res_ridge <- ridgeSIR(x, y, H = 10, d = 2, mu2 = 10^8)
}
\references{
-{Picheny, V., Servien, R. and Villa-Vialaneix, N. (2016)
+Picheny, V., Servien, R. and Villa-Vialaneix, N. (2016)
Interpretable sparse SIR for digitized functional data.
-\emph{Statistics and Computing}, \strong{29}(2), 255--267.}
+\emph{Statistics and Computing}, \strong{29}(2), 255--267.
}
\seealso{
\code{\link{ridgeSIR}}, \code{\link{sparseSIR}}
}
\author{
-{Victor Picheny, \email{victor.picheny@inrae.fr}\cr
+Victor Picheny, \email{victor.picheny@inrae.fr}\cr
Remi Servien, \email{remi.servien@inrae.fr}\cr
-Nathalie Vialaneix, \email{nathalie.vialaneix@inrae.fr}}
+Nathalie Vialaneix, \email{nathalie.vialaneix@inrae.fr}
}
diff --git a/man/ridgeSIR.Rd b/man/ridgeSIR.Rd
index 1a4116a..248061b 100644
--- a/man/ridgeSIR.Rd
+++ b/man/ridgeSIR.Rd
@@ -19,20 +19,20 @@ ridgeSIR(x, y, H, d, mu2 = NULL)
}
\value{
S3 object of class \code{ridgeRes}: a list consisting of
-\itemize{
+\describe{
\item{\code{EDR}}{ the estimated EDR space (a p x d matrix)}
\item{\code{condC}}{ the estimated slice projection on EDR (a d x H
matrix)}
\item{\code{eigenvalues}}{ the eigenvalues obtained during the generalized
eigendecomposition performed by SIR}
\item{\code{parameters}}{ a list of hyper-parameters for the method:
- \itemize{
+ \describe{
\item{\code{H}}{ number of slices}
\item{\code{d}}{ dimension of the EDR space}
\item{\code{mu2}}{ regularization parameter for the ridge penalty}
}}
\item{\code{utils}}{ useful outputs for further computations:
- \itemize{
+ \describe{
\item{\code{Sigma}}{ covariance matrix for x}
\item{\code{slices}}{ slice number for all observations}
\item{\code{invsqrtS}}{ value of the inverse square root of the
@@ -60,16 +60,16 @@ res_ridge <- ridgeSIR(x, y, H = 10, d = 2, mu2 = 10^8)
}
\references{
-{Picheny, V., Servien, R. and Villa-Vialaneix, N. (2019)
+Picheny, V., Servien, R. and Villa-Vialaneix, N. (2019)
Interpretable sparse SIR for digitized functional data.
-\emph{Statistics and Computing}, \strong{29}(2), 255--267.}
+\emph{Statistics and Computing}, \strong{29}(2), 255--267.
}
\seealso{
\code{\link{sparseSIR}}, \code{\link{SISIR}},
\code{\link{tune.ridgeSIR}}
}
\author{
-{Victor Picheny, \email{victor.picheny@inrae.fr}\cr
+Victor Picheny, \email{victor.picheny@inrae.fr}\cr
Remi Servien, \email{remi.servien@inrae.fr}\cr
-Nathalie Vialaneix, \email{nathalie.vialaneix@inrae.fr}}
+Nathalie Vialaneix, \email{nathalie.vialaneix@inrae.fr}
}
diff --git a/man/sparseSIR.Rd b/man/sparseSIR.Rd
index b6af598..84e64c4 100644
--- a/man/sparseSIR.Rd
+++ b/man/sparseSIR.Rd
@@ -34,29 +34,31 @@ NULL, all available cores minus one are used}
}
\value{
S3 object of class \code{sparseRes}: a list consisting of
-\itemize{
+\describe{
\item{\code{sEDR}}{ the estimated EDR space (a p x d matrix)}
\item{\code{alpha}}{ the estimated shrinkage coefficients (a vector having
a length similar to \code{inter_len})}
\item{\code{quality}}{ a vector with various qualities for the model (see
Details)}
\item{\code{adapt_res}}{ if \code{adaptive = TRUE}, a list of two vectors:
- \itemize{
+ \describe{
\item{\code{nonzeros}}{ indexes of variables that are strong non zeros}
\item{\code{zeros}}{ indexes of variables that are strong zeros}
}}
\item{\code{parameters}}{ a list of hyper-parameters for the method:
- \itemize{
+ \describe{
\item{\code{inter_len}}{ lengths of intervals}
\item{\code{sel_prop}}{ if \code{adaptive = TRUE}, fraction of the
coefficients which are considered as strong zeros or strong non zeros}
}}
\item{\code{rSIR}}{ same as the input \code{object}}
\item{\code{fit}}{ a list for LASSO fit with:
- \itemize{
- \item{\code{glmnet}} result of the \code{\link[glmnet]{glmnet}} function
- \item{\code{lambda}} value of the best Lasso parameter by CV
- \item{\code{x}} exploratory variable values as passed to fit the model
+ \describe{
+ \item{\code{glmnet}}{ result of the \code{\link[glmnet]{glmnet}}
+ function}
+ \item{\code{lambda}}{ value of the best Lasso parameter by CV}
+ \item{\code{x}}{ exploratory variable values as passed to fit the
+ model}
}}
}
--
GitLab