vignette

R/functions.R

@@ -273,12 +273,14 @@ joinet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev
 #' with \eqn{n} rows (samples) and \eqn{q} columns (variables).
 #' 
 #' @examples
+#' if(!grepl('SunOS',Sys.info()['sysname'])){
 #' n <- 50; p <- 100; q <- 3
 #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
 #' Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
 #' Y[,1] <- 1*(Y[,1]>median(Y[,1]))
 #' object <- joinet(Y=Y,X=X,family=c("binomial","gaussian","gaussian"))
 #' predict(object,newx=X)
+#' }
 #' 
 predict.joinet <- function(object,newx,type="response",...){
   if(length(list(...))!=0){warning("Ignoring argument.",call.=FALSE)}
@@ -345,7 +347,6 @@ predict.joinet <- function(object,newx,type="response",...){
 #' 
 #' @examples
 #' if(!grepl('SunOS',Sys.info()['sysname'])){
-#' 1+1
 #' n <- 50; p <- 100; q <- 3
 #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
 #' Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
@@ -414,11 +415,13 @@ coef.joinet <- function(object,...){
 #' in the row on the outcomes in the column.
 #' 
 #' @examples
+#' if(!grepl('SunOS',Sys.info()['sysname'])){
 #' n <- 50; p <- 100; q <- 3
 #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
 #' Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
 #' object <- joinet(Y=Y,X=X)
 #' weights(object)
+#' }
 #' 
 weights.joinet <- function(object,...){
   if(length(list(...))!=0){warning("Ignoring argument.",call.=FALSE)}

R/pkgname.R

@@ -37,6 +37,7 @@
 #' Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
 #' # n samples, p inputs, q outputs
 #' 
+#' if(!grepl('SunOS',Sys.info()['sysname'])){
 #' #--- model fitting ---
 #' object <- joinet(Y=Y,X=X)
 #' # slot "base": univariate
@@ -58,6 +59,7 @@
 #' # cross-validated loss
 #' # row "base": univariate
 #' # row "meta": multivariate
+#' }
 #' 
 NULL
 

docs/pkgdown.yml

@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   article: article.html
   joinet: joinet.html
-last_built: 2020-11-02T15:36Z
+last_built: 2020-11-02T17:32Z
 

docs/reference/coef.joinet.html

@@ -156,7 +156,6 @@ in a matrix with \(p\) rows (inputs) and \(q\) columns.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='kw'>if</span>(!<span class='fu'><a href='https://rdrr.io/r/base/grep.html'>grepl</a></span>(<span class='st'>'SunOS'</span>,<span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span>()[<span class='st'>'sysname'</span>])){
-<span class='fl'>1</span>+<span class='fl'>1</span>
 <span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>100</span>; <span class='no'>q</span> <span class='kw'>&lt;-</span> <span class='fl'>3</span>
 <span class='no'>X</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n</span>*<span class='no'>p</span>),<span class='kw'>nrow</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>ncol</span><span class='kw'>=</span><span class='no'>p</span>)
 <span class='no'>Y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>replicate</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>q</span>,<span class='kw'>expr</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>mean</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/colSums.html'>rowSums</a></span>(<span class='no'>X</span>[,<span class='fl'>1</span>:<span class='fl'>5</span>])))

docs/reference/joinet-package.html

@@ -160,6 +160,7 @@ to open the vignette.</p>
 <span class='no'>Y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>replicate</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>q</span>,<span class='kw'>expr</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>mean</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/colSums.html'>rowSums</a></span>(<span class='no'>X</span>[,<span class='fl'>1</span>:<span class='fl'>5</span>])))
 <span class='co'># n samples, p inputs, q outputs</span>
 
+<span class='kw'>if</span>(!<span class='fu'><a href='https://rdrr.io/r/base/grep.html'>grepl</a></span>(<span class='st'>'SunOS'</span>,<span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span>()[<span class='st'>'sysname'</span>])){
 <span class='co'>#--- model fitting ---</span>
 <span class='no'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='joinet.html'>joinet</a></span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='no'>Y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)
 <span class='co'># slot "base": univariate</span>
@@ -180,7 +181,8 @@ to open the vignette.</p>
 <span class='no'>loss</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='cv.joinet.html'>cv.joinet</a></span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='no'>Y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)
 <span class='co'># cross-validated loss</span>
 <span class='co'># row "base": univariate</span>
-<span class='co'># row "meta": multivariate</span></div></pre>
+<span class='co'># row "meta": multivariate</span>
+}</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">

docs/reference/predict.joinet.html

@@ -159,12 +159,14 @@ The slots <code>base</code> and <code>meta</code> each contain a matrix
 with \(n\) rows (samples) and \(q\) columns (variables).</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>100</span>; <span class='no'>q</span> <span class='kw'>&lt;-</span> <span class='fl'>3</span>
+    <pre class="examples"><div class='input'><span class='kw'>if</span>(!<span class='fu'><a href='https://rdrr.io/r/base/grep.html'>grepl</a></span>(<span class='st'>'SunOS'</span>,<span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span>()[<span class='st'>'sysname'</span>])){
+<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>100</span>; <span class='no'>q</span> <span class='kw'>&lt;-</span> <span class='fl'>3</span>
 <span class='no'>X</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n</span>*<span class='no'>p</span>),<span class='kw'>nrow</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>ncol</span><span class='kw'>=</span><span class='no'>p</span>)
 <span class='no'>Y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>replicate</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>q</span>,<span class='kw'>expr</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>mean</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/colSums.html'>rowSums</a></span>(<span class='no'>X</span>[,<span class='fl'>1</span>:<span class='fl'>5</span>])))
 <span class='no'>Y</span>[,<span class='fl'>1</span>] <span class='kw'>&lt;-</span> <span class='fl'>1</span>*(<span class='no'>Y</span>[,<span class='fl'>1</span>]<span class='kw'>&gt;</span><span class='fu'><a href='https://rdrr.io/r/stats/median.html'>median</a></span>(<span class='no'>Y</span>[,<span class='fl'>1</span>]))
 <span class='no'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='joinet.html'>joinet</a></span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='no'>Y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>,<span class='kw'>family</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"binomial"</span>,<span class='st'>"gaussian"</span>,<span class='st'>"gaussian"</span>))
-<span class='fu'><a href='https://rdrr.io/r/stats/predict.html'>predict</a></span>(<span class='no'>object</span>,<span class='kw'>newx</span><span class='kw'>=</span><span class='no'>X</span>)</div><div class='output co'>#&gt; $base
+<span class='fu'><a href='https://rdrr.io/r/stats/predict.html'>predict</a></span>(<span class='no'>object</span>,<span class='kw'>newx</span><span class='kw'>=</span><span class='no'>X</span>)
+}</div><div class='output co'>#&gt; $base
 #&gt;             [,1]         [,2]        [,3]
 #&gt;  [1,] 0.41837245 -1.928585385 -2.49734037
 #&gt;  [2,] 0.73430703 -1.232615541 -1.92258279

docs/reference/weights.joinet.html

@@ -154,11 +154,13 @@ which are the effects of the outcomes
 in the row on the outcomes in the column.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>100</span>; <span class='no'>q</span> <span class='kw'>&lt;-</span> <span class='fl'>3</span>
+    <pre class="examples"><div class='input'><span class='kw'>if</span>(!<span class='fu'><a href='https://rdrr.io/r/base/grep.html'>grepl</a></span>(<span class='st'>'SunOS'</span>,<span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span>()[<span class='st'>'sysname'</span>])){
+<span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>50</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>100</span>; <span class='no'>q</span> <span class='kw'>&lt;-</span> <span class='fl'>3</span>
 <span class='no'>X</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='no'>n</span>*<span class='no'>p</span>),<span class='kw'>nrow</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>ncol</span><span class='kw'>=</span><span class='no'>p</span>)
 <span class='no'>Y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>replicate</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>q</span>,<span class='kw'>expr</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>mean</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/colSums.html'>rowSums</a></span>(<span class='no'>X</span>[,<span class='fl'>1</span>:<span class='fl'>5</span>])))
 <span class='no'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='joinet.html'>joinet</a></span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='no'>Y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)
-<span class='fu'><a href='https://rdrr.io/r/stats/weights.html'>weights</a></span>(<span class='no'>object</span>)</div><div class='output co'>#&gt;                      y1          y2         y3
+<span class='fu'><a href='https://rdrr.io/r/stats/weights.html'>weights</a></span>(<span class='no'>object</span>)
+}</div><div class='output co'>#&gt;                      y1          y2         y3
 #&gt; (Intercept) -0.04720442 -0.15165929 0.26901703
 #&gt; V1           0.00000000  0.01158793 0.65726908
 #&gt; V2           0.55230103  0.71134918 0.45932382

man/coef.joinet.Rd

@@ -25,7 +25,6 @@ the coefficients from the base learners.)
 }
 \examples{
 if(!grepl('SunOS',Sys.info()['sysname'])){
-1+1
 n <- 50; p <- 100; q <- 3
 X <- matrix(rnorm(n*p),nrow=n,ncol=p)
 Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))

man/joinet-package.Rd

@@ -28,6 +28,7 @@ X <- matrix(rnorm(n*p),nrow=n,ncol=p)
 Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
 # n samples, p inputs, q outputs
 
+if(!grepl('SunOS',Sys.info()['sysname'])){
 #--- model fitting ---
 object <- joinet(Y=Y,X=X)
 # slot "base": univariate
@@ -49,6 +50,7 @@ loss <- cv.joinet(Y=Y,X=X)
 # cross-validated loss
 # row "base": univariate
 # row "meta": multivariate
+}
 
 }
 \references{

man/predict.joinet.Rd

@@ -26,11 +26,13 @@ with \eqn{n} rows (samples) and \eqn{q} columns (variables).
 Predicts outcome from features with stacked model.
 }
 \examples{
+if(!grepl('SunOS',Sys.info()['sysname'])){
 n <- 50; p <- 100; q <- 3
 X <- matrix(rnorm(n*p),nrow=n,ncol=p)
 Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
 Y[,1] <- 1*(Y[,1]>median(Y[,1]))
 object <- joinet(Y=Y,X=X,family=c("binomial","gaussian","gaussian"))
 predict(object,newx=X)
+}
 
 }

man/weights.joinet.Rd

@@ -24,10 +24,12 @@ Extracts coefficients from the meta learner,
 i.e. the weights for the base learners.
 }
 \examples{
+if(!grepl('SunOS',Sys.info()['sysname'])){
 n <- 50; p <- 100; q <- 3
 X <- matrix(rnorm(n*p),nrow=n,ncol=p)
 Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
 object <- joinet(Y=Y,X=X)
 weights(object)
+}
 
 }