Version 3.5-2

Author: pbreheny

DESCRIPTION

@@ -1,11 +1,12 @@
 Package: ncvreg
 Version: 3.5-2
-Date: 2016-02-06
+Date: 2016-04-08
 Title: Regularization Paths for SCAD and MCP Penalized Regression Models
 Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
 Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
 Suggests: survival, parallel
 Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
 License: GPL-2
+BugReports: http://github.com/pbreheny/ncvreg/issues
 URL: http://myweb.uiowa.edu/pbreheny/publications/Breheny2011.pdf
 Depends:

NEWS

@@ -1,3 +1,9 @@
+3.5-2
+	* Fixed bug for ncvsurv with integer penalty factors
+	* Fixed rare numerical accuracy bug in cv fold assignments
+	* Fixed LOOCV bug introduced by bias-correction feature
+	* Added user interrupt checking
+
 3.5-1
 	* Fixed bug with penalty.factor for cv.ncvsurv when some columns may be
 	  degenerate

README.md

@@ -1,5 +1,5 @@
-[![version](http://www.r-pkg.org/badges/version/ncvreg)](http://cran.r-project.org/web/packages/ncvreg/index.html)
-[![downloads](http://cranlogs.r-pkg.org/badges/ncvreg)](http://cran.r-project.org/web/packages/ncvreg/index.html)
+[![version](http://www.r-pkg.org/badges/version/ncvreg)](https://cran.r-project.org/package=ncvreg)
+[![downloads](http://cranlogs.r-pkg.org/badges/ncvreg)](https://cran.r-project.org/package=ncvreg)
 [![codecov.io](https://codecov.io/github/pbreheny/ncvreg/coverage.svg?branch=master)](https://codecov.io/github/pbreheny/ncvreg?branch=master)
 
 `ncvreg` fits regularization paths for linear, logistic, or Poisson regression models with nonconvex penalties, in particular the minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalty.  Coordinate descent algorithms are used to fit the models.

tests/cv.ncvreg.R inst/tests/cv.ncvreg.R

@@ -10,8 +10,8 @@
   \tabular{ll}{
     Package: \tab ncvreg\cr
     Type: \tab Package\cr
-    Version: \tab 3.5-1\cr
-    Date: \tab 2016-02-067\cr
+    Version: \tab 3.5-2\cr
+    Date: \tab 2016-04-08\cr
     License: \tab GPL-2\cr}
   Accepts a design matrix \code{X} and vector of responses \code{y},
   produces the regularization path over a grid of values for the tuning

tests/cv.ncvsurv.R inst/tests/cv.ncvsurv.R

@@ -5,7 +5,7 @@
   Cox regression models over a grid of values for the regularization
   parameter lambda, with option for an additional L2 penalty.}
 \usage{
-ncvsurv(X, y, model=c("cox","aft"), penalty=c("MCP", "SCAD", "lasso"),
+ncvsurv(X, y, penalty=c("MCP", "SCAD", "lasso"),
 gamma=switch(penalty, SCAD=3.7, 3), alpha=1,
 lambda.min=ifelse(n>p,.001,.05), nlambda=100, lambda, eps=.001,
 max.iter=1000, convex=TRUE, dfmax=p, penalty.factor=rep(1, ncol(X)),
@@ -19,9 +19,6 @@ warn=TRUE, returnX=FALSE, ...)
     up time); the second column should be a binary variable with 1
     indicating that the event has occurred and 0 indicating (right)
     censoring.}
-  \item{model}{Either "cox" for a Cox proportional hazards model or
-    "aft" for an accelerated failure time (AFT) model.  Note: AFT models
-    are not yet implemented in this release of \code{ncvreg}.}
   \item{penalty}{The penalty to be applied to the model.  Either "MCP"
     (the default), "SCAD", or "lasso".}
   \item{gamma}{The tuning parameter of the MCP/SCAD penalty (see