Change name of vignette

DESCRIPTION

@@ -31,8 +31,10 @@ RoxygenNote: 6.0.1
 Suggests: 
     knitr,
     rmarkdown,
-    bookdown,
-    prettydoc,
     testthat,
     MASS
-VignetteBuilder: knitr
+VignetteBuilder: 
+    knitr,
+    bookdown,
+    prettydoc
+

R/sparseEigen-package.R

@@ -18,8 +18,8 @@
 #' \href{https://cran.r-project.org/web/packages/sparseEigen/README.html}{CRAN-README}.
 #'
 #' For more details see the vignette:
-#' \href{https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.html}{GitHub-html-vignette},
-#' \href{https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.pdf}{GitHub-pdf-vignette}, and
+#' \href{https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.html}{GitHub-html-vignette},
+#' \href{https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.pdf}{GitHub-pdf-vignette}, and
 #' \href{https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf}{CRAN-pdf-vignette}.
 #'
 #' @author Konstantinos Benidis and Daniel P. Palomar

README.Rmd

@@ -1,10 +1,10 @@
 ---
 output:
-  md_document:
-    variant: markdown_github
   html_document:
     variant: markdown_github
     keep_md: true
+  md_document:
+    variant: markdown_github
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -62,7 +62,7 @@ citation("sparseEigen")
 ```
 
 ## Vignette
-For more detailed information, please check the vignette: [GitHub-html-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.html), [GitHub-pdf-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.pdf),
+For more detailed information, please check the vignette: [GitHub-html-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.html), [GitHub-pdf-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.pdf),
 [CRAN-pdf-vignette](https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf).
 
 ## Usage of `spEigen()`
@@ -165,5 +165,5 @@ Package: [CRAN](https://CRAN.R-project.org/package=sparseEigen) and [GitHub](htt
 
 README file: [GitHub-readme](https://rawgit.com/dppalomar/sparseEigen/master/README.html) and [CRAN-readme](https://cran.r-project.org/web/packages/sparseEigen/README.html).
 
-Vignette: [GitHub-html-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.html), [GitHub-pdf-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.pdf),
+Vignette: [GitHub-html-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.html), [GitHub-pdf-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.pdf),
 [CRAN-pdf-vignette](https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf).

README.html

@@ -147,7 +147,7 @@ <h2>Installation</h2>
 </div>
 <div id="vignette" class="section level2">
 <h2>Vignette</h2>
-<p>For more detailed information, please check the vignette: <a href="https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.html">GitHub-html-vignette</a>, <a href="https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.pdf">GitHub-pdf-vignette</a>, <a href="https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf">CRAN-pdf-vignette</a>.</p>
+<p>For more detailed information, please check the vignette: <a href="https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.html">GitHub-html-vignette</a>, <a href="https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.pdf">GitHub-pdf-vignette</a>, <a href="https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf">CRAN-pdf-vignette</a>.</p>
 </div>
 <div id="usage-of-speigen" class="section level2">
 <h2>Usage of <code>spEigen()</code></h2>
@@ -210,7 +210,7 @@ <h2>Usage of <code>spEigenCov()</code></h2>
 <h2>Links</h2>
 <p>Package: <a href="https://CRAN.R-project.org/package=sparseEigen">CRAN</a> and <a href="https://github.com/dppalomar/sparseEigen">GitHub</a>.</p>
 <p>README file: <a href="https://rawgit.com/dppalomar/sparseEigen/master/README.html">GitHub-readme</a> and <a href="https://cran.r-project.org/web/packages/sparseEigen/README.html">CRAN-readme</a>.</p>
-<p>Vignette: <a href="https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.html">GitHub-html-vignette</a>, <a href="https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.pdf">GitHub-pdf-vignette</a>, <a href="https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf">CRAN-pdf-vignette</a>.</p>
+<p>Vignette: <a href="https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.html">GitHub-html-vignette</a>, <a href="https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.pdf">GitHub-pdf-vignette</a>, <a href="https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf">CRAN-pdf-vignette</a>.</p>
 </div>
 </div>
 

README.md

@@ -1,17 +1,38 @@
+---
+output:
+  html_document:
+    variant: markdown_github
+    keep_md: true
+  md_document:
+    variant: markdown_github
+---
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-sparseEigen
-===========
 
-Computation of sparse eigenvectors of a matrix (aka sparse PCA) with running time 2-3 orders of magnitude lower than existing methods and better final performance in terms of recovery of sparsity pattern and estimation of numerical values.
 
-Can handle covariance matrices as well as data matrices with real or complex-valued entries. Different levels of sparsity can be specified for each individual ordered eigenvector and the method is robust in parameter selection. See vignette for a detailed documentation and comparison, with several illustrative examples.
 
-The package is based on the paper: K. Benidis, Y. Sun, P. Babu, and D. P. Palomar (2016), "Orthogonal Sparse PCA and Covariance Estimation via Procrustes Reformulation," IEEE Transactions on Signal Processing, <https://doi.org/10.1109/TSP.2016.2605073>.
+# sparseEigen
+
+Computation of sparse eigenvectors of a matrix (aka sparse PCA)
+    with running time 2-3 orders of magnitude lower than existing methods and
+    better final performance in terms of recovery of sparsity pattern and 
+    estimation of numerical values. 
+
+Can handle covariance matrices as well as data matrices with real or 
+    complex-valued entries. Different levels of sparsity can be specified 
+    for each individual ordered eigenvector and the method is robust in 
+    parameter selection. See vignette for a detailed documentation and 
+    comparison, with several illustrative examples. 
+
+The package is based on the paper:
+    K. Benidis, Y. Sun, P. Babu, and D. P. Palomar (2016), "Orthogonal Sparse PCA 
+    and Covariance Estimation via Procrustes Reformulation," IEEE Transactions on 
+    Signal Processing, <https://doi.org/10.1109/TSP.2016.2605073>.
+
 
-Installation
-------------
+## Installation
 
-``` r
+```r
 # Installation from CRAN
 install.packages("sparseEigen")
 
@@ -29,17 +50,14 @@ package?sparseEigen
 citation("sparseEigen")
 ```
 
-Vignette
---------
-
-For more detailed information, please check the vignette: [GitHub-html-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.html), [GitHub-pdf-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.pdf), [CRAN-pdf-vignette](https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf).
-
-Usage of `spEigen()`
---------------------
+## Vignette
+For more detailed information, please check the vignette: [GitHub-html-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.html), [GitHub-pdf-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.pdf),
+[CRAN-pdf-vignette](https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf).
 
+## Usage of `spEigen()`
 We start by loading the package and generating synthetic data with sparse eigenvectors:
 
-``` r
+```r
 library(sparseEigen)
 set.seed(42)
 
@@ -66,62 +84,62 @@ R <- V %*% diag(lmd) %*% t(V)
 # with the constructed covariance matrix
 X <- MASS::mvrnorm(n, rep(0, m), R)  # random data with underlying sparse structure
 ```
-
 Then, we estimate the covariance matrix with `cov(X)` and compute its sparse eigenvectors:
 
-``` r
+```r
 # computation of sparse eigenvectors
 res_standard <- eigen(cov(X))
 res_sparse <- spEigen(cov(X), q)
 ```
 
 We can assess how good the estimated eigenvectors are by computing the inner product with the original eigenvectors (the closer to 1 the better):
 
-``` r
+```r
 # show inner product between estimated eigenvectors and originals
 abs(diag(t(res_standard$vectors) %*% V[, 1:q]))  #for standard estimated eigenvectors
 #> [1] 0.9215392 0.9194898 0.9740871
 abs(diag(t(res_sparse$vectors) %*% V[, 1:q]))    #for sparse estimated eigenvectors
 #> [1] 0.9986937 0.9988146 0.9972078
 ```
 
-Finally, the following plot shows the sparsity pattern of the eigenvectors (sparse computation vs. classical computation): <img src="man/figures/README-unnamed-chunk-6-1.png" width="75%" style="display: block; margin: auto;" />
+Finally, the following plot shows the sparsity pattern of the eigenvectors (sparse computation vs. classical computation):
+<img src="man/figures/README-unnamed-chunk-6-1.png" width="75%" style="display: block; margin: auto;" />
 
-Usage of `spEigenCov()`
------------------------
+## Usage of `spEigenCov()`
 
 The function `spEigenCov()` requires more samples than the dimension (otherwise some regularization is required). Therefore, we generate data as previously with the only difference that we set the number of samples to be `n=600`.
 
+
+
 Then, we compute the covariance matrix through the joint estimation of sparse eigenvectors and eigenvalues:
 
-``` r
+```r
 # computation of covariance matrix
 res_sparse2 <- spEigenCov(cov(X), q)
 ```
 
 Again, we can assess how good the estimated eigenvectors are by computing the inner product with the original eigenvectors:
 
-``` r
+```r
 # show inner product between estimated eigenvectors and originals
 abs(diag(t(res_sparse2$vectors[, 1:q]) %*% V[, 1:q]))    #for sparse estimated eigenvectors
 #> [1] 0.9997197 0.9996029 0.9992848
 ```
 
 Finally, we can compute the error of the estimated covariance matrix (sparse eigenvector computation vs. classical computation):
 
-``` r
+```r
 # show error between estimated and true covariance 
 norm(cov(X) - R, type = 'F') #for sample covariance matrix
 #> [1] 48.42514
 norm(res_sparse2$cov - R, type = 'F') #for covariance with sparse eigenvectors
 #> [1] 25.74865
 ```
 
-Links
------
-
+## Links
 Package: [CRAN](https://CRAN.R-project.org/package=sparseEigen) and [GitHub](https://github.com/dppalomar/sparseEigen).
 
 README file: [GitHub-readme](https://rawgit.com/dppalomar/sparseEigen/master/README.html) and [CRAN-readme](https://cran.r-project.org/web/packages/sparseEigen/README.html).
 
-Vignette: [GitHub-html-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.html), [GitHub-pdf-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors.pdf), [CRAN-pdf-vignette](https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf).
+Vignette: [GitHub-html-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.html), [GitHub-pdf-vignette](https://rawgit.com/dppalomar/sparseEigen/master/vignettes/SparseEigenvectors-vignette.pdf),
+[CRAN-pdf-vignette](https://cran.r-project.org/web/packages/sparseEigen/vignettes/SparseEigenvectors.pdf).

vignettes/.gitignore

@@ -1,2 +1,2 @@
-SparseEigenvectors_cache
-SparseEigenvectors_files
+SparseEigenvectors-vignette_cache
+SparseEigenvectors-vignette_files