Commit b8a86ac9 authored by Roman Flury's avatar Roman Flury

cleanups

parent 086716cb
Pipeline #980 passed with stage
in 4 seconds
spam/.Rproj.user spam/.Rproj.user
spam/docs/
.Rhistory .Rhistory
.RData .RData
.DS_Store .DS_Store
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...@@ -7,7 +7,7 @@ LIBPATH = #export R_LIBS_USER=$(shell pwd)/lib:/usr/sepp1.5.1/drwho/pack-a/r-3.2 ...@@ -7,7 +7,7 @@ LIBPATH = #export R_LIBS_USER=$(shell pwd)/lib:/usr/sepp1.5.1/drwho/pack-a/r-3.2
#RSCRIPT := $(LIBPATH) Rscript #RSCRIPT := $(LIBPATH) Rscript
#LIBPATH = export R_LIBS_USER=$(shell pwd)/lib:/usr/sepp1.5.1/drwho/pack-a/r-devel-99-ro/amd64-linux-ubuntu14.04/lib/R/library:/home/furrer/R/x86_64-pc-linux-gnu-library/3.5:/usr/lib/R-devel/lib/R/library && #LIBPATH = export R_LIBS_USER=$(shell pwd)/lib:/usr/sepp1.5.1/drwho/pack-a/r-devel-99-ro/amd64-linux-ubuntu14.04/lib/R/library:/home/furrer/R/x86_64-pc-linux-gnu-library/3.5:/usr/lib/R-devel/lib/R/library &&
R := $(LIBPATH) R-99 ## On I-MATH servers: daily built devel version R := $(LIBPATH) R ## On I-MATH servers: daily built devel version
RSCRIPT := $(LIBPATH) Rscript-99 ## On I-MATH servers: daily built devel version RSCRIPT := $(LIBPATH) Rscript ## On I-MATH servers: daily built devel version
.SUFFIXES: .Rnw .R .Rout .tex .pdf .c .o .so .f .SUFFIXES: .Rnw .R .Rout .tex .pdf .c .o .so .f
...@@ -84,9 +84,9 @@ ...@@ -84,9 +84,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
</a> </a>
</li> </li>
<li> <li>
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...@@ -84,9 +84,9 @@ ...@@ -84,9 +84,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
</a> </a>
</li> </li>
<li> <li>
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...@@ -54,9 +54,9 @@ ...@@ -54,9 +54,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
</a> </a>
</li> </li>
<li> <li>
...@@ -81,7 +81,7 @@ ...@@ -81,7 +81,7 @@
<h1>Illustrations and Examples</h1> <h1>Illustrations and Examples</h1>
<h4 class="author">Reinhard Furrer, Roman Flury</h4> <h4 class="author">Reinhard Furrer, Roman Flury</h4>
<h4 class="date">2018-10-05</h4> <h4 class="date">2018-10-11</h4>
<div class="hidden name"><code>spam.Rmd</code></div> <div class="hidden name"><code>spam.Rmd</code></div>
...@@ -118,20 +118,20 @@ Smat ...@@ -118,20 +118,20 @@ Smat
<span class="co">#&gt; [2,] 0 2 0</span> <span class="co">#&gt; [2,] 0 2 0</span>
<span class="co">#&gt; [3,] 1 0 3</span> <span class="co">#&gt; [3,] 1 0 3</span>
<span class="co">#&gt; Class 'spam' (32-bit)</span> <span class="co">#&gt; Class 'spam' (32-bit)</span>
Smat <span class="op">%*%</span><span class="st"> </span><span class="kw">t</span>(Smat) Smat %*%<span class="st"> </span><span class="kw">t</span>(Smat)
<span class="co">#&gt; [,1] [,2] [,3]</span> <span class="co">#&gt; [,1] [,2] [,3]</span>
<span class="co">#&gt; [1,] 10 0 6</span> <span class="co">#&gt; [1,] 10 0 6</span>
<span class="co">#&gt; [2,] 0 4 0</span> <span class="co">#&gt; [2,] 0 4 0</span>
<span class="co">#&gt; [3,] 6 0 10</span> <span class="co">#&gt; [3,] 6 0 10</span>
<span class="co">#&gt; Class 'spam' (32-bit)</span> <span class="co">#&gt; Class 'spam' (32-bit)</span>
Fmat <span class="op">%*%</span><span class="st"> </span><span class="kw">t</span>(Smat) Fmat %*%<span class="st"> </span><span class="kw">t</span>(Smat)
<span class="co">#&gt; [,1] [,2] [,3]</span> <span class="co">#&gt; [,1] [,2] [,3]</span>
<span class="co">#&gt; [1,] 10 0 6</span> <span class="co">#&gt; [1,] 10 0 6</span>
<span class="co">#&gt; [2,] 0 4 0</span> <span class="co">#&gt; [2,] 0 4 0</span>
<span class="co">#&gt; [3,] 6 0 10</span> <span class="co">#&gt; [3,] 6 0 10</span>
<span class="co">#&gt; Class 'spam' (32-bit)</span></code></pre></div> <span class="co">#&gt; Class 'spam' (32-bit)</span></code></pre></div>
<p>Hence, the user should not be worried which objects are sparse matrices and which are not. Of course not all operations result in sparse objects again,</p> <p>Hence, the user should not be worried which objects are sparse matrices and which are not. Of course not all operations result in sparse objects again,</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rep</span>(<span class="dv">1</span>, <span class="dv">3</span>) <span class="op">%*%</span><span class="st"> </span>Smat <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rep</span>(<span class="dv">1</span>, <span class="dv">3</span>) %*%<span class="st"> </span>Smat
<span class="co">#&gt; [,1] [,2] [,3]</span> <span class="co">#&gt; [,1] [,2] [,3]</span>
<span class="co">#&gt; [1,] 4 2 4</span></code></pre></div> <span class="co">#&gt; [1,] 4 2 4</span></code></pre></div>
<p>However, other operations yield to different results when applied to full or sparse matrices</p> <p>However, other operations yield to different results when applied to full or sparse matrices</p>
...@@ -197,7 +197,7 @@ j &lt;-<span class="st"> </span><span class="kw">c</span>(<span class="dv">1</sp ...@@ -197,7 +197,7 @@ j &lt;-<span class="st"> </span><span class="kw">c</span>(<span class="dv">1</sp
A &lt;-<span class="st"> </span><span class="kw"><a href="../reference/spam.creation.html">spam</a></span>(<span class="dv">0</span>, <span class="dt">nrow =</span> <span class="dv">5</span>, <span class="dt">ncol =</span> <span class="dv">5</span>) A &lt;-<span class="st"> </span><span class="kw"><a href="../reference/spam.creation.html">spam</a></span>(<span class="dv">0</span>, <span class="dt">nrow =</span> <span class="dv">5</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)
A[<span class="kw"><a href="../reference/xybind.html">cbind</a></span>(i, j)] &lt;-<span class="st"> </span><span class="kw">rep</span>(<span class="fl">0.5</span>, <span class="kw">length</span>(i)) A[<span class="kw"><a href="../reference/xybind.html">cbind</a></span>(i, j)] &lt;-<span class="st"> </span><span class="kw">rep</span>(<span class="fl">0.5</span>, <span class="kw">length</span>(i))
A &lt;-<span class="st"> </span><span class="kw">t</span>(A) <span class="op">+</span><span class="st"> </span>A <span class="op">+</span><span class="st"> </span><span class="kw"><a href="../reference/diag.html">diag.spam</a></span>(<span class="dv">5</span>) A &lt;-<span class="st"> </span><span class="kw">t</span>(A) +<span class="st"> </span>A +<span class="st"> </span><span class="kw"><a href="../reference/diag.html">diag.spam</a></span>(<span class="dv">5</span>)
A A
<span class="co">#&gt; [,1] [,2] [,3] [,4] [,5]</span> <span class="co">#&gt; [,1] [,2] [,3] [,4] [,5]</span>
<span class="co">#&gt; [1,] 1.0 0.5 0.0 0.5 0.5</span> <span class="co">#&gt; [1,] 1.0 0.5 0.0 0.5 0.5</span>
...@@ -221,22 +221,22 @@ On the left side the associated graph to the matrix <span class="math inline">\( ...@@ -221,22 +221,22 @@ On the left side the associated graph to the matrix <span class="math inline">\(
<col width="96%"> <col width="96%">
</colgroup> </colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th>Step</th> <th align="left">Step</th>
<th>Description</th> <th align="left">Description</th>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td>[1]</td> <td align="left">[1]</td>
<td>Determine permutation and permute the input matrix <span class="math inline">\(\boldsymbol{A}\)</span> to obtain <span class="math inline">\(\boldsymbol{P}^T\boldsymbol{A}\boldsymbol{P}\)</span> <td align="left">Determine permutation and permute the input matrix <span class="math inline">\(\boldsymbol{A}\)</span> to obtain <span class="math inline">\(\boldsymbol{P}^T\boldsymbol{A}\boldsymbol{P}\)</span>
</td> </td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td>[2]</td> <td align="left">[2]</td>
<td>Symbolic factorization, where the sparsity structure of <span class="math inline">\(\boldsymbol{U}\)</span> is constructed</td> <td align="left">Symbolic factorization, where the sparsity structure of <span class="math inline">\(\boldsymbol{U}\)</span> is constructed</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td>[3]</td> <td align="left">[3]</td>
<td>Numeric factorization, where the elements of <span class="math inline">\(\boldsymbol{U}\)</span> are computed</td> <td align="left">Numeric factorization, where the elements of <span class="math inline">\(\boldsymbol{U}\)</span> are computed</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
......
...@@ -84,9 +84,9 @@ ...@@ -84,9 +84,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
</a> </a>
</li> </li>
<li> <li>
......
...@@ -59,9 +59,9 @@ ...@@ -59,9 +59,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
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<li> <li>
...@@ -107,7 +107,7 @@ ...@@ -107,7 +107,7 @@
<ul class="list-unstyled"> <ul class="list-unstyled">
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=spam">https://​cloud.r-project.org/​package=spam</a> <li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=spam">https://​cloud.r-project.org/​package=spam</a>
</li> </li>
<li>Report a bug at <br><a href="NA">NA</a> <li>Report a bug at <br><a href="https://git.math.uzh.ch/reinhard.furrer/spam/issues">https://​git.math.uzh.ch/​reinhard.furrer/​spam/​issues</a>
</li> </li>
</ul> </ul>
</div> </div>
......
...@@ -84,9 +84,9 @@ ...@@ -84,9 +84,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
</a> </a>
</li> </li>
<li> <li>
...@@ -118,6 +118,7 @@ ...@@ -118,6 +118,7 @@
</h1> </h1>
<p>SIGNIFICANT USER-VISIBLE CHANGES</p> <p>SIGNIFICANT USER-VISIBLE CHANGES</p>
<ul> <ul>
<li>New vignette including illustrations and examples</li>
<li>Improved documentation for covariance functions like <code><a href="../reference/cov.html">cov.exp()</a></code>.</li> <li>Improved documentation for covariance functions like <code><a href="../reference/cov.html">cov.exp()</a></code>.</li>
</ul> </ul>
<p>BUG FIXES</p> <p>BUG FIXES</p>
......
pandoc: 1.19.2.1 pandoc: 1.16.0.2
pkgdown: 1.1.0 pkgdown: 1.1.0
pkgdown_sha: ~ pkgdown_sha: ~
articles: articles:
spam: spam.html spam: spam.html
urls:
reference: https://www.math.uzh.ch/pages/spam//reference
article: https://www.math.uzh.ch/pages/spam//articles
...@@ -87,9 +87,9 @@ ...@@ -87,9 +87,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
</a> </a>
</li> </li>
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...@@ -90,9 +90,9 @@ ...@@ -90,9 +90,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
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...@@ -88,9 +88,9 @@ locations. See www.image.ucar.edu/GSP/Data/US.monthly.met/ for the source of the ...@@ -88,9 +88,9 @@ locations. See www.image.ucar.edu/GSP/Data/US.monthly.met/ for the source of the
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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github gitlab
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...@@ -88,9 +88,9 @@ ...@@ -88,9 +88,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
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...@@ -90,9 +90,9 @@ ...@@ -90,9 +90,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
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...@@ -88,9 +88,9 @@ ...@@ -88,9 +88,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
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...@@ -87,9 +87,9 @@ ...@@ -87,9 +87,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
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...@@ -87,9 +87,9 @@ ...@@ -87,9 +87,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
github gitlab
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...@@ -89,9 +89,9 @@ of class spam." /> ...@@ -89,9 +89,9 @@ of class spam." />
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
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...@@ -87,9 +87,9 @@ ...@@ -87,9 +87,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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...@@ -87,9 +87,9 @@ ...@@ -87,9 +87,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://git.math.uzh.ch/reinhard.furrer/spam"> <a href="https://git.math.uzh.ch/reinhard.furrer/spam">
<span class="fa fa-lg fa-github"></span> <span class="fa fa-lg fa-gitlab"></span>
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...@@ -88,9 +88,9 @@ ...@@ -88,9 +88,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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...@@ -87,9 +87,9 @@ ...@@ -87,9 +87,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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...@@ -88,9 +88,9 @@ ...@@ -88,9 +88,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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...@@ -87,9 +87,9 @@ ...@@ -87,9 +87,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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...@@ -87,9 +87,9 @@ ...@@ -87,9 +87,9 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
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