Version 3.3.1

.gitignore

@@ -1,2 +1,3 @@
 vignettes/*.html
 docs
+.Rproj.user

.travis.yml

@@ -2,6 +2,7 @@ language: r
 r_packages:
   - glmnet
   - ncvreg
+  - survival
 
 script:
   - R CMD build .

.version.json

@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "GitHub",
-  "message": "3.3.0.2",
+  "message": "3.3.1",
   "color": "blue"
-}
+}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: grpreg
 Title: Regularization Paths for Regression Models with Grouped Covariates
-Version: 3.3.0.2
-Date: 2020-07-08
+Version: 3.3.1
+Date: 2021-03-26
 Authors@R: c(
   person("Patrick", "Breheny", role=c("aut","cre"), email="[email protected]", comment=c(ORCID="0000-0002-0650-1119")),
   person("Yaohui", "Zeng", role="ctb"))
@@ -14,9 +14,9 @@ Description: Efficient algorithms for fitting the regularization path of linear
   includes group selection methods such as group lasso, group MCP, and
   group SCAD as well as bi-level selection methods such as the group
   exponential lasso, the composite MCP, and the group bridge.
-BugReports: http://github.com/pbreheny/grpreg/issues
+BugReports: https://github.com/pbreheny/grpreg/issues
 License: GPL-3
-URL: http://pbreheny.github.io/grpreg, https://github.com/pbreheny/grpreg
+URL: https://pbreheny.github.io/grpreg/, https://github.com/pbreheny/grpreg
 LazyData: TRUE
 RoxygenNote: 7.0.2
 Encoding: UTF-8

NEWS → NEWS.md

@@ -1,3 +1,7 @@
+# grpreg 3.3.1 (2021-03-26)
+  * Fixed: AUC() now compatible with survival 3.2.10
+  * Internal: Fixed memory leak
+
 # grpreg 3.3.0 (2020-06-10)
   * Fixed: sqrt(K) no longer hard-coded into discarding rules (thank you to Dan
     Kessler for pointing this out)

R/auc.R

@@ -3,9 +3,13 @@ AUC.cv.grpsurv <- function(obj, ...) {
   if (!requireNamespace("survival", quietly = TRUE)) {
     stop("The 'survival' package is needed for AUC() to work. Please install it.", call. = FALSE)
   }  
+  if (packageVersion("survival") < "3.2.10") stop("AUC.cv.ncvsurv requires version 3.2.10 of 'survival' package or higher", call.=FALSE)
   S <- survival::Surv(obj$fit$time, obj$fit$fail)
-  res <- apply(obj$Y, 2, survival::survConcordance.fit, y = S)
-  num <- res['concordant',] + 0.5*res['tied.risk',] + 0.5*res['tied.time',]
-  num/sum(res[1:4,1])
+  res <- apply(obj$Y, 2, concord, y = S)
+  num <- res['concordant',] + 0.5*res['tied.x',] + 0.5*res['tied.y',] + 0.5*res['tied.xy',]
+  num/sum(res[,1])
 }
 AUC <- function(obj, ...) UseMethod("AUC")
+concord <- function(x, y) {
+  survival::concordancefit(y, -x)$count
+}

man/grpreg-package.Rd

@@ -58,22 +58,22 @@
     \item Breheny, P. and Huang, J. (2009) Penalized methods for
     bi-level variable selection.  \emph{Statistics and its interface},
     \strong{2}: 369-380.
-    \url{http://myweb.uiowa.edu/pbreheny/pdf/Breheny2009.pdf}
+    \url{https://myweb.uiowa.edu/pbreheny/pdf/Breheny2009.pdf}
 
     \item Huang J., Breheny, P. and Ma, S. (2012). A selective
     review of group selection in high dimensional
     models. \emph{Statistical Science}, \strong{27}: 481-499.
-    \url{http://myweb.uiowa.edu/pbreheny/pdf/Huang2012.pdf}
+    \url{https://myweb.uiowa.edu/pbreheny/pdf/Huang2012.pdf}
 
     \item Breheny, P. and Huang, J. (2015) Group descent algorithms for
     nonconvex penalized linear and logistic regression models with
     grouped predictors.  \emph{Statistics and Computing}, \strong{25}:
     173-187.
-    \url{http://dx.doi.org/10.1007/s11222-013-9424-2}
+    \doi{10.1007/s11222-013-9424-2}
 
     \item Breheny, P. (2015) The group exponential lasso for bi-level
     variable selection. \emph{Biometrics}, \strong{71}: 731-740.
-    \url{http://dx.doi.org/10.1111/biom.12300}
+    \doi{10.1111/biom.12300}
   }
 }
 \author{Patrick Breheny}

man/grpreg.Rd

@@ -190,21 +190,21 @@ tau = 1/3, group.multiplier, warn=TRUE, returnX = FALSE, ...)
     \item Breheny, P. and Huang, J. (2009) Penalized methods for
     bi-level variable selection.  \emph{Statistics and its interface},
     \strong{2}: 369-380.
-    \url{http://myweb.uiowa.edu/pbreheny/pdf/Breheny2009.pdf}
+    \url{https://myweb.uiowa.edu/pbreheny/pdf/Breheny2009.pdf}
 
     \item Huang J., Breheny, P. and Ma, S. (2012). A selective
     review of group selection in high dimensional
     models. \emph{Statistical Science}, \strong{27}: 481-499.
-    \url{http://myweb.uiowa.edu/pbreheny/pdf/Huang2012.pdf}
+    \url{https://myweb.uiowa.edu/pbreheny/pdf/Huang2012.pdf}
 
     \item Breheny, P. and Huang, J. (2015) Group descent algorithms for
     nonconvex penalized linear and logistic regression models with grouped
     predictors.  \emph{Statistics and Computing}, \strong{25}: 173-187.
-    \url{http://dx.doi.org/10.1007/s11222-013-9424-2}
+    \doi{10.1007/s11222-013-9424-2}
 
     \item Breheny, P. (2015) The group exponential lasso for bi-level
     variable selection. \emph{Biometrics}, \strong{71}: 731-740.
-    \url{http://dx.doi.org/10.1111/biom.12300}
+    \doi{10.1111/biom.12300}
   }
 }
 

man/grpsurv.Rd

@@ -123,27 +123,27 @@ not correspond to the ith row of \code{X}):
     \item Breheny, P. and Huang, J. (2009) Penalized methods for
     bi-level variable selection.  \emph{Statistics and its interface},
     \strong{2}: 369-380.
-    \url{http://myweb.uiowa.edu/pbreheny/pdf/Breheny2009.pdf}
+    \url{https://myweb.uiowa.edu/pbreheny/pdf/Breheny2009.pdf}
 
     \item Huang J., Breheny, P. and Ma, S. (2012). A selective
     review of group selection in high dimensional
     models. \emph{Statistical Science}, \strong{27}: 481-499.
-    \url{http://myweb.uiowa.edu/pbreheny/pdf/Huang2012.pdf}
+    \url{https://myweb.uiowa.edu/pbreheny/pdf/Huang2012.pdf}
 
     \item Breheny, P. and Huang, J. (2015) Group descent algorithms for
     nonconvex penalized linear and logistic regression models with grouped
     predictors.  \emph{Statistics and Computing}, \strong{25}: 173-187.
-    \url{http://dx.doi.org/10.1007/s11222-013-9424-2}
+    \doi{10.1007/s11222-013-9424-2}
 
     \item Breheny, P. (2015) The group exponential lasso for bi-level
     variable selection. \emph{Biometrics}, \strong{71}: 731-740.
-    \url{http://dx.doi.org/10.1111/biom.12300}
+    \doi{10.1111/biom.12300}
 
     \item Simon N, Friedman JH, Hastie T, and Tibshirani R. (2011)
     Regularization Paths for Cox's Proportional Hazards Model via
     Coordinate Descent.  \emph{Journal of Statistical Software},
     \strong{39}: 1-13.
-    \url{http://www.jstatsoft.org/v39/i05}
+    \url{https://www.jstatsoft.org/v39/i05}
   }
 }
 \author{Patrick Breheny}

pkgdown/_pkgdown.yml

@@ -21,6 +21,8 @@ navbar:
         href: articles/web/penalties.html
     - text: Functions
       href: reference/index.html
+    - text: News
+      href: news/index.html
   right:
     github:
       icon: fa-github fa-lg