Version 3.4.1

.version.json

@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "GitHub",
-  "message": "3.4.0.6",
+  "message": "3.4.1",
   "color": "blue"
 }

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: grpreg
 Title: Regularization Paths for Regression Models with Grouped Covariates
-Version: 3.4.0.6
-Date: 2024-06-13
+Version: 3.4.1
+Date: 2024-09-02
 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"),
@@ -25,5 +25,5 @@ License: GPL-3
 URL: https://pbreheny.github.io/grpreg/, https://github.com/pbreheny/grpreg
 LazyData: TRUE
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8

NEWS.md

@@ -1,3 +1,8 @@
+# grpreg 3.4.1 (2024-09-02)
+  * Fixed: Fixed some broken URLs
+  * Internal: Updated citation format to bibentry()
+  * Internal: Now using R_Calloc for _R_USE_STRICT_R_HEADERS_ compatibility
+
 # grpreg 3.4.0 (2021-07-22)
   * New: Suite of tools for additive modeling, most notably expand_spline()
     and plot_spline() (thank you to Ryan Kurth for her work on this project)

R/grpreg.R

@@ -44,7 +44,7 @@
 #' following:
 #' \itemize{
 #'   \item [Models and loss functions](https://pbreheny.github.io/grpreg/articles/models.html)
-#'   \item [Penalties](https://pbreheny.github.io/grpreg/articles/penalties.htmlPenalties)
+#'   \item [Penalties](https://pbreheny.github.io/grpreg/articles/penalties.html)
 #' }
 #'   
 #' For the bi-level selection methods, a locally approximated coordinate

R/grpsurv.R

@@ -12,7 +12,7 @@
 #' P_\lambda(\beta)}{Q(\beta|X, y) = (1/n)*L(\beta|X, y) + P(\beta, \lambda),}
 #' where the loss function L is the negative partial log-likelihood (half the
 #' deviance) from the Cox regression model.
-#' [See here for more details](https://pbreheny.github.io/ncvreg/articles/models.html).
+#' [See here for more details](https://pbreheny.github.io/grpreg/articles/models.html).
 #' 
 #' Presently, ties are not handled by \code{grpsurv} in a particularly
 #' sophisticated manner.  This will be improved upon in a future release of

inst/CITATION

@@ -1,32 +1,42 @@
 citHeader("If you use any of the L2-norm penalties (penalty='grLasso', 'grMCP', or 'grSCAD'), cite the Statistics and Computing article.  If you use the group exponential lasso (penalty='gel'), cite the Biometrics article.  If you use the composite MCP (penalty='cMCP') or group bridge penalties, cite the Statistics and its Interface (2009) article; note that the penalty is referred to as the 'group MCP' in the original article, but it would be better to refer to it as 'composite MCP' in future works.")
 
-citEntry(entry="Article",
-	 author = personList(as.person("Patrick Breheny"),
-	 	  	     as.person("Jian Huang")),
-         title = "Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors",
-         journal = "Statistics and Computing",
-         year = "2015",
-         volume = "25",
-         pages = "173-187",
-         textVersion = "Breheny P and Huang J (2015). Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors. Statistics and Computing, 25: 173-187.")
+bibentry(
+  bibtype = "Article",
+  author = c(
+    person("Patrick", "Breheny"),
+    person("Jian", "Huang")
+  ),
+  title = "Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors",
+  journal = "Statistics and Computing",
+  year = 2015,
+  volume = 25,
+  number = 2,
+  pages = "173--187",
+  doi = "10.1007/s11222-013-9424-2",
+  url = "https://dx.doi.org/10.1007/s11222-013-9424-2")
 
-citEntry(entry="Article",
-	 author = personList(as.person("Patrick Breheny")),
-         title = "The group exponential lasso for bi-level variable selection",
-	 year = "2015",
-         journal = "Biometrics",
-         volume = "71",
-         pages = "731-740",
-         textVersion = "Breheny P (2015). The group exponential lasso for bi-level variable selection. Biometrics, 71: 731-740.")
+bibentry(
+  bibtype = "Article",
+  author = person("Patrick", "Breheny"),
+  title = "The group exponential lasso for bi-level variable selection",
+  journal = "Biometrics",
+  year = 2015,
+  volume = 71,
+  number = 3,
+  pages = "731--740",
+  doi = "10.1111/biom.12300",
+  url = "https://dx.doi.org/10.1111/biom.12300")
 
-citEntry(entry="Article",
-	 author = personList(as.person("Patrick Breheny"),
-	 	  	     as.person("Jian Huang")),
-         title = "Penalized methods for bi-level variable selection.",
-         journal = "Statistics and its interface",
-         year = "2009",
-         volume = "2",
-         pages = "369-380",
-         textVersion = "Breheny, P. and Huang, J. (2009) Penalized methods for
-  bi-level variable selection.  Statistics and its interface, 2: 369-380.")
+bibentry(
+  bibtype = "Article",
+  author = c(
+    person("Patrick", "Breheny"),
+    person("Jian", "Huang")
+  ),
+  title = "Penalized methods for bi-level variable selection",
+  journal = "Statistics and Its Interface",
+  year = 2009,
+  volume = 2,
+  pages = "369--380",
+  doi = "10.4310/sii.2009.v2.n3.a10")