automation

f4df6530 · Armin Rauschenberger · e40f30d3 · f4df6530 · f4df6530 · f4df6530
Commit f4df6530 authored Aug 07, 2019 by Armin Rauschenberger
15 changed files
--- a/DESCRIPTION
+++ b/DESCRIPTION
 Package: joinet
-Version: 0.0.1
-Title: Multivariate Regression
+Version: 0.0.2
+Title: Multivariate Regression through Stacked Generalisation
 Description: Implements high-dimensional multivariate regression by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>). For positively correlated outcomes, a single multivariate regression is typically more predictive than multiple univariate regressions. Includes functions for model fitting, extracting coefficients, outcome prediction, and performance measurement.
 Depends: R (>= 3.0.0)
 Imports: glmnet, palasso, cornet
 Suggests: knitr, testthat, MASS
-Enhances: RColorBrewer, spls, SiER, MRCE
+Enhances: spls, SiER, MRCE
 Authors@R: person("Armin","Rauschenberger",email="a.rauschenberger@vumc.nl",role=c("aut","cre"))
 VignetteBuilder: knitr
 License: GPL-3
 LazyData: true
 Language: en-GB
 RoxygenNote: 6.1.1
-URL: https://github.com/rauschenberger/mixnet
-BugReports: https://github.com/rauschenberger/mixnet/issues
+URL: https://github.com/rauschenberger/joinet
+BugReports: https://github.com/rauschenberger/joinet/issues
--- a/R/functions.R
+++ b/R/functions.R
@@ -80,7 +80,7 @@
 #' \eqn{q} \code{\link[glmnet]{cv.glmnet}}-like objects.
 #' 
 #' @seealso
-#' Type \code{browseVignettes("joinet")} for examples.
+#' \code{\link{cv.joinet}}, \code{browseVignettes("joinet")}
 #' 
 #' @examples
 #' n <- 50; p <- 100; q <- 3

--- a/docs/articles/article.html
+++ b/docs/articles/article.html
@@ -30,7 +30,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -77,7 +77,7 @@
      <h1>Stacked Elastic Net</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/mixnet/blob/master/vignettes/article.Rmd"><code>vignettes/article.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/joinet/blob/master/vignettes/article.Rmd"><code>vignettes/article.Rmd</code></a></small>
      <div class="hidden name"><code>article.Rmd</code></div>

    </div>

--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -60,7 +60,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>


--- a/docs/articles/vignette.html
+++ b/docs/articles/vignette.html
@@ -30,7 +30,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -77,7 +77,7 @@
      <h1>Multivariate Elastic Net</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/mixnet/blob/master/vignettes/vignette.Rmd"><code>vignettes/vignette.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/joinet/blob/master/vignettes/vignette.Rmd"><code>vignettes/vignette.Rmd</code></a></small>
      <div class="hidden name"><code>vignette.Rmd</code></div>

    </div>

--- a/docs/authors.html
+++ b/docs/authors.html
@@ -60,7 +60,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>


--- a/docs/index.html
+++ b/docs/index.html
@@ -5,11 +5,11 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Multivariate Regression • joinet</title>
+<title>Multivariate Regression through Stacked Generalisation • joinet</title>
 <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous">
 <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="Multivariate Regression">
+<script src="pkgdown.js"></script><meta property="og:title" content="Multivariate Regression through Stacked Generalisation">
 <meta property="og:description" content="Implements high-dimensional multivariate regression by stacked generalisation (Wolpert 1992 &lt;doi:10.1016/S0893-6080(05)80023-1&gt;). For positively correlated outcomes, a single multivariate regression is typically more predictive than multiple univariate regressions. Includes functions for model fitting, extracting coefficients, outcome prediction, and performance measurement.">
 <meta name="twitter:card" content="summary">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -30,7 +30,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -106,9 +106,9 @@
 <ul class="list-unstyled">
 <li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=joinet">https://cloud.r-project.org/package=joinet</a>
 </li>
-<li>Browse source code at <br><a href="https://github.com/rauschenberger/mixnet">https://github.com/rauschenberger/mixnet</a>
+<li>Browse source code at <br><a href="https://github.com/rauschenberger/joinet">https://github.com/rauschenberger/joinet</a>
 </li>
-<li>Report a bug at <br><a href="https://github.com/rauschenberger/mixnet/issues">https://github.com/rauschenberger/mixnet/issues</a>
+<li>Report a bug at <br><a href="https://github.com/rauschenberger/joinet/issues">https://github.com/rauschenberger/joinet/issues</a>
 </li>
 <li>Download package at <br><a href="https://github.com/rauschenberger/joinet">https://github.com/rauschenberger/joinet</a>
 </li>

--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -60,7 +60,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -106,7 +106,7 @@
  <div class="col-md-9 contents">
    <div class="page-header">
      <h1>Changelog <small></small></h1>
-      <small>Source: <a href='https://github.com/rauschenberger/mixnet/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
+      <small>Source: <a href='https://github.com/rauschenberger/joinet/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
    </div>

    <div id="joinet-001-2019-07-31" class="section level2">

--- a/docs/reference/coef.joinet.html
+++ b/docs/reference/coef.joinet.html
@@ -65,7 +65,7 @@ the coefficients from the base learners.)" />
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -111,7 +111,7 @@ the coefficients from the base learners.)" />
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Extract Coefficients</h1>
-    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/mixnet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/joinet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
    <div class="hidden name"><code>coef.joinet.Rd</code></div>
    </div>


--- a/docs/reference/cv.joinet.html
+++ b/docs/reference/cv.joinet.html
@@ -63,7 +63,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -109,7 +109,7 @@
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Model comparison</h1>
-    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/mixnet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/joinet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
    <div class="hidden name"><code>cv.joinet.Rd</code></div>
    </div>


--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -60,7 +60,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>


--- a/docs/reference/joinet.html
+++ b/docs/reference/joinet.html
@@ -63,7 +63,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -109,7 +109,7 @@
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Multivariate Elastic Net Regression</h1>
-    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/mixnet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/joinet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
    <div class="hidden name"><code>joinet.Rd</code></div>
    </div>

@@ -206,7 +206,7 @@ ridge renders dense models (<code>alpha</code>\(=0\))</p>
    
    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>

-    <div class='dont-index'><p>Type <code><a href='https://www.rdocumentation.org/packages/utils/topics/browseVignettes'>browseVignettes("joinet")</a></code> for examples.</p></div>
+    <div class='dont-index'><p><code><a href='cv.joinet.html'>cv.joinet</a></code>, <code><a href='https://www.rdocumentation.org/packages/utils/topics/browseVignettes'>browseVignettes("joinet")</a></code></p></div>
    

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>

--- a/docs/reference/predict.joinet.html
+++ b/docs/reference/predict.joinet.html
@@ -63,7 +63,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -109,7 +109,7 @@
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Make Predictions</h1>
-    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/mixnet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/joinet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
    <div class="hidden name"><code>predict.joinet.Rd</code></div>
    </div>


--- a/docs/reference/weights.joinet.html
+++ b/docs/reference/weights.joinet.html
@@ -64,7 +64,7 @@ i.e. the weights for the base learners." />
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.2</span>
      </span>
    </div>

@@ -110,7 +110,7 @@ i.e. the weights for the base learners." />
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Extract Weights</h1>
-    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/mixnet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/joinet/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
    <div class="hidden name"><code>weights.joinet.Rd</code></div>
    </div>


--- a/man/joinet.Rd
+++ b/man/joinet.Rd
@@ -77,5 +77,5 @@ Armin Rauschenberger, Enrico Glaab (2019)
 \emph{Manuscript in preparation}.
 }
 \seealso{
-Type \code{browseVignettes("joinet")} for examples.
+\code{\link{cv.joinet}}, \code{browseVignettes("joinet")}
 }