automation

bd9eda70 · Armin Rauschenberger · 117c76d2 · bd9eda70 · bd9eda70 · bd9eda70
Commit bd9eda70 authored Nov 04, 2020 by Armin Rauschenberger
25 changed files
--- a/DESCRIPTION
+++ b/DESCRIPTION
 Package: starnet
-Version: 0.0.4
+Version: 0.0.5
 Title: Stacked Elastic Net
 Description: Implements stacked elastic net regression (Rauschenberger 2020, <doi:10.1093/bioinformatics/btaa535>). The elastic net generalises ridge and lasso regularisation (Zou 2005, <doi:10.1111/j.1467-9868.2005.00503.x>). Instead of fixing or tuning the mixing parameter alpha, we combine multiple alpha by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>).
 Depends: R (>= 3.0.0)
-Imports: glmnet, survival, cornet, joinet, Matrix
+Imports: glmnet, survival, cornet, Matrix
 Suggests: knitr, testthat, rmarkdown
 Enhances: CVXR, mvtnorm
 Authors@R: person("Armin","Rauschenberger",email="armin.rauschenberger@uni.lu",role=c("aut","cre"))

--- a/R/functions.R
+++ b/R/functions.R
@@ -185,7 +185,7 @@ starnet <- function(y,X,family="gaussian",nalpha=21,alpha=NULL,nfolds=10,foldid=
  #--- tune base lambdas ---
  for(i in seq_len(nalpha)){
-    fit <- joinet:::.mean.function(link[[i]],family=family)
+    fit <- .mean.function(link[[i]],family=family)
    base[[i]]$cvm <- apply(fit,2,function(x) .loss(y=y,x=x,family=family,type.measure=type.measure,foldid=foldid))
    base[[i]]$id.min <- which.min(base[[i]]$cvm)
    base[[i]]$lambda.min <- base[[i]]$lambda[base[[i]]$id.min]
@@ -234,7 +234,7 @@ starnet <- function(y,X,family="gaussian",nalpha=21,alpha=NULL,nfolds=10,foldid=
        glm <- .glm(y=y[foldid!=k],X=hat[foldid!=k,],family=family,intercept=intercept,lower.limit=TRUE,upper.limit=upper.limit,unit.sum=unit.sum)
        link[foldid==k] <- glm$alpha + hat[foldid==k,] %*% glm$beta
      }
-      y_hat <- joinet:::.mean.function(x=link,family=family)
+      y_hat <- .mean.function(x=link,family=family)
      cvm <- .loss(y=y,x=y_hat,family=family,type.measure=type.measure,foldid=foldid)
    } else {
      cvm <- 0
@@ -360,7 +360,7 @@ predict.starnet <- function(object,newx,type="response",nzero=NULL,...){
  if(type=="link"){
    return(frame)
  } else  if(type=="response"){
-    frame <- lapply(frame,function(y) joinet:::.mean.function(y,family=x$info$family))
+    frame <- lapply(frame,function(y) .mean.function(y,family=x$info$family))
    return(as.data.frame(frame))
  } else {
    stop("Invalid type.",call.=FALSE)
@@ -997,6 +997,21 @@ glmnet.auc <- get("auc",envir=asNamespace("glmnet"))
  return(foldid)
 }
+# This function is a copy from joinet!
+.mean.function <- function(x,family){
+  if(family %in% c("gaussian","cox")){
+    return(x)
+  } else if(family=="binomial"){
+    return(1/(1+exp(-x)))
+  } else if(family=="poisson"){
+    return(exp(x))
+  } else {
+    stop("Family not implemented.",call.=FALSE)
+  }
+}
 #y <- c(0,0,0,0,0,0,0,0,1,1)
 #for(nfolds in 1:10){
 #  folds <- .folds(y=y,nfolds=nfolds)

--- a/cran-comments.md
+++ b/cran-comments.md
-Reason for resubmission: error on r-patched-solaris-x86.
+Reason for resubmission: removed archived dependency.
\ No newline at end of file
-(I actually think the problem is the R package glmnet on this machine.)
\ No newline at end of file
--- a/docs/404.html
+++ b/docs/404.html
@@ -71,7 +71,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/articles/article.html
+++ b/docs/articles/article.html
@@ -31,7 +31,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/articles/script.html
+++ b/docs/articles/script.html
@@ -31,7 +31,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>
@@ -82,7 +82,7 @@
      <h1 data-toc-skip>Stacked Elastic Net</h1>
                        <h4 class="author">Armin Rauschenberger</h4>
-            <h4 class="date">21 October 2020</h4>
+            <h4 class="date">04 November 2020</h4>
      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/starnet/blob/master/vignettes/script.Rmd"><code>vignettes/script.Rmd</code></a></small>
      <div class="hidden name"><code>script.Rmd</code></div>

--- a/docs/articles/starnet.html
+++ b/docs/articles/starnet.html
@@ -31,7 +31,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/index.html
+++ b/docs/index.html
@@ -31,7 +31,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>
@@ -98,6 +98,7 @@
 <h2 class="hasAnchor">
 <a href="#reference" class="anchor"></a>Reference</h2>
 <p>A Rauschenberger, E Glaab, MA van de Wiel (2020). “Predictive and interpretable models via the stacked elastic net”. <em>Bioinformatics</em>, btaa535. <a href="https://doi.org/10.1093/bioinformatics/btaa535">doi: 10.1093/bioinformatics/btaa535</a>.</p>
+<p><a href="https://CRAN.R-project.org/package=starnet"><img src="https://www.r-pkg.org/badges/version/starnet" alt="CRAN version"></a> <a href="https://CRAN.R-project.org/package=starnet"><img src="https://cranlogs.r-pkg.org/badges/starnet" alt="CRAN RStudio mirror downloads"></a> <a href="https://CRAN.R-project.org/package=starnet"><img src="https://cranlogs.r-pkg.org/badges/grand-total/starnet" alt="Total CRAN downloads"></a></p>
 </div>
  </div>

--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -71,7 +71,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
  article: article.html
  script: script.html
  starnet: starnet.html
-last_built: 2020-10-21T05:34Z
+last_built: 2020-11-04T14:04Z
--- a/docs/reference/coef.starnet.html
+++ b/docs/reference/coef.starnet.html
@@ -73,7 +73,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>
@@ -163,8 +163,8 @@ respectively.</p>
 <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'>y</span> <span class='kw'>&lt;-</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='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'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='starnet.html'>starnet</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>)</div><div class='output co'>#&gt; <span class='error'>Error in loadNamespace(name): there is no package called 'joinet'</span></div><div class='input'><span class='no'>coef</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>object</span>)</div><div class='output co'>#&gt; <span class='error'>Error in coef(object): object 'object' not found</span></div><div class='input'>
+<span class='no'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='starnet.html'>starnet</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>)
-</div></pre>
+<span class='no'>coef</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>object</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">

--- a/docs/reference/cv.starnet.html
+++ b/docs/reference/cv.starnet.html
@@ -72,7 +72,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/dot-cv.glmnet.html
+++ b/docs/reference/dot-cv.glmnet.html
@@ -73,7 +73,7 @@ with different handling of sparsity constraints." />
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/dot-loss.html
+++ b/docs/reference/dot-loss.html
@@ -72,7 +72,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/dot-simulate.html
+++ b/docs/reference/dot-simulate.html
@@ -72,7 +72,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/glmnet.auc.html
+++ b/docs/reference/glmnet.auc.html
@@ -72,7 +72,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/predict.starnet.html
+++ b/docs/reference/predict.starnet.html
@@ -72,7 +72,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/print.starnet.html
+++ b/docs/reference/print.starnet.html
@@ -72,7 +72,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/starnet-package.html
+++ b/docs/reference/starnet-package.html
@@ -75,7 +75,7 @@ we combine multiple alphas by stacked generalisation." />
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/starnet.html
+++ b/docs/reference/starnet.html
@@ -72,7 +72,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/docs/reference/weights.starnet.html
+++ b/docs/reference/weights.starnet.html
@@ -73,7 +73,7 @@ i.e. the weights for the base learners." />
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">starnet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

--- a/tests/testthat/test.R
+++ b/tests/testthat/test.R
@@ -61,12 +61,12 @@ for(family in c("gaussian","binomial","poisson")){
      a <- pred$stack
      coef <- coef.starnet(object=object)
-      b <- joinet:::.mean.function(coef$alpha + list$X %*% coef$beta,family=family)
+      b <- .mean.function(coef$alpha + list$X %*% coef$beta,family=family)
      pred <- predict.starnet(object=object,newx=list$X,type="link")
      weights <- weights.starnet(object=object)
      sub <- pred[,grepl(pattern="alpha",x=colnames(pred))]
-      c <- joinet:::.mean.function(weights[1] + as.matrix(sub) %*% weights[-1],family=family)
+      c <- .mean.function(weights[1] + as.matrix(sub) %*% weights[-1],family=family)
      cond <- all(abs((a-b)<1e-06) & abs((a-c)<1e-06) & abs((b-c)<1e-06))
@@ -166,7 +166,7 @@ for(family in c("gaussian","binomial","poisson","mgaussian","multinomial","cox")
          y_hat[foldid==k,] <- stats::predict(object=glmnet,newx=X1,type="response")
      } else {
          temp <- stats::predict(object=glmnet,newx=X1,type="link")
-          y_hat[foldid==k] <- joinet:::.mean.function(temp,family=family)
+          y_hat[foldid==k] <- .mean.function(temp,family=family)
      }
      beta[[k]] <- coef(glmnet)
      pred[[k]] <- predict(glmnet,newx=X,type="link")