fix broken links

Author: zdk123

.Rbuildignore

@@ -5,3 +5,6 @@
 ^.*cran-comments.md$
 ^.*revdep.*
 ^CRAN-RELEASE$
+^CRAN-SUBMISSION$
+^doc$
+^Meta$

DESCRIPTION

@@ -5,8 +5,8 @@ Encoding: UTF-8
 Authors@R: c(person("Zachary", "Kurtz", role = c("aut", "cre"), email="[email protected]"),
              person("Christian", "M\u00FCller", role = c("aut", "ctb"), email="[email protected]"))
 Description: Model selection for penalized graphical models using the Stability Approach to Regularization Selection ('StARS'), with options for speed-ups including Bounded StARS (B-StARS), batch computing, and other stability metrics (e.g., graphlet stability G-StARS). Christian L. Müller, Richard Bonneau, Zachary Kurtz (2016) <arXiv:1605.07072>.
-URL: http://github.com/zdk123/pulsar, http://arxiv.org/abs/1605.07072
-BugReports: http://github.com/zdk123/pulsar/issues
+URL: https://github.com/zdk123/pulsar, https://arxiv.org/abs/1605.07072
+BugReports: https://github.com/zdk123/pulsar/issues
 Depends:
     R (>= 3.2.0)
 License: GPL (>= 2)
@@ -32,5 +32,5 @@ Imports:
     utils,
     tools,
     Matrix
-RoxygenNote: 7.1.0
+RoxygenNote: 7.2.1
 VignetteBuilder: knitr

R/mcPulsarSelect.R

@@ -150,7 +150,7 @@
 #' }
 #' @importFrom Matrix mean triu
 #' @importFrom parallel mclapply
-#' @references Müller, C. L., Bonneau, R., & Kurtz, Z. (2016). Generalized Stability Approach for Regularized Graphical Models. arXiv. http://arxiv.org/abs/1605.07072
+#' @references Müller, C. L., Bonneau, R., & Kurtz, Z. (2016). Generalized Stability Approach for Regularized Graphical Models. arXiv. https://arxiv.org/abs/1605.07072
 #' @references Liu, H., Roeder, K., & Wasserman, L. (2010). Stability approach to regularization selection (stars) for high dimensional graphical models. Proceedings of the Twenty-Third Annual Conference on Neural Information Processing Systems (NIPS).
 #' @references Zhao, T., Liu, H., Roeder, K., Lafferty, J., & Wasserman, L. (2012). The huge Package for High-dimensional Undirected Graph Estimation in R. The Journal of Machine Learning Research, 13, 1059–1062.
 #' @seealso \code{\link{batch.pulsar}} \code{\link{refit}}

R/pulsar-package.R

@@ -15,7 +15,7 @@
 #' @name pulsar-package
 #' @seealso \code{\link{pulsar-function}}, \code{\link{pulsar}}, \code{\link{batch.pulsar}}
 #' @docType package
-#' @references Müller, C. L., Bonneau, R. A., & Kurtz, Z. D. (2016).Generalized Stability Approach for Regularized Graphical Models.arXiv: http://arxiv.org/abs/1605.07072.
+#' @references Müller, C. L., Bonneau, R. A., & Kurtz, Z. D. (2016).Generalized Stability Approach for Regularized Graphical Models.arXiv: https://arxiv.org/abs/1605.07072.
 NULL
 
 #' Graphical model functions for pulsar
@@ -118,5 +118,5 @@ NULL
 #' @name pulsar-function
 #' @aliases pulsar-function
 #' @seealso \code{\link{pulsar}}, \code{\link{batch.pulsar}}, \pkg{huge}, \pkg{Matrix}
-#' @references Müller, C. L., Bonneau, R. A., & Kurtz, Z. D. (2016). Generalized Stability Approach for Regularized Graphical Models. arXiv: http://arxiv.org/abs/1605.07072.
+#' @references Müller, C. L., Bonneau, R. A., & Kurtz, Z. D. (2016). Generalized Stability Approach for Regularized Graphical Models. arXiv: https://arxiv.org/abs/1605.07072.
 NULL

inst/CITATION

@@ -11,11 +11,11 @@ bibentry(header="To cite pulsar in publications use:",
   arxivId = "1605.07072",
   eprint = "1605.07072",
   month = "May",
-  url = "http://arxiv.org/abs/1605.07072",
+  url = "https://arxiv.org/abs/1605.07072",
   year = "2016",
 
   textVersion  =
   paste("M\u00FCller, C. L., Bonneau, R. A., & Kurtz, Z. D. (2016).",
         "Generalized Stability Approach for Regularized Graphical Models.",
-        "arXiv. Retrieved from http://arxiv.org/abs/1605.07072.")
+        "arXiv. Retrieved from https://arxiv.org/abs/1605.07072.")
 )

inst/gstars.bib

@@ -12,7 +12,7 @@ @article{Mazumder2012
 pages = {781--794},
 pmid = {25392704},
 title = {{Exact covariance thresholding into connected components for large-scale Graphical Lasso}},
-url = {http://arxiv.org/abs/1108.3829$\backslash$nhttp://jmlr.org/papers/v13/mazumder12a.html},
+url = {https://arxiv.org/abs/1108.3829$\backslash$nhttp://jmlr.org/papers/v13/mazumder12a.html},
 volume = {13},
 year = {2012}
 }
@@ -216,13 +216,11 @@ @article{Witten2011
 }
 @article{Ravikumar2011b,
 author = {Ravikumar, Pradeep and Wainwright, Martin J. and Raskutti, Garvesh and Yu, Bin},
-doi = {10.1214/11-EJS631},
 issn = {1935-7524},
 journal = {Electronic Journal of Statistics},
 number = {January 2010},
 pages = {935--980},
 title = {{High-dimensional covariance estimation by minimizing L1 -penalized log-determinant divergence}},
-url = {http://projecteuclid.org/euclid.ejs/1316092865},
 volume = {5},
 year = {2011}
 }
@@ -235,7 +233,6 @@ @article{Fiori2010
 }
 @article{Meinshausen:2010,
 author = {Meinshausen, N and B{\"{u}}hlmann, P},
-doi = {10.1111/j.1467-9868.2010.00740.x},
 file = {:Users/cmueller/Documents/Mendeley Desktop/Meinshausen, B{\"{u}}hlmann - 2010 - Stability selection.pdf:pdf},
 issn = {1467-9868},
 journal = {J. R. Stat. Soc. Ser. B Stat. Methodol.},
@@ -244,7 +241,6 @@ @article{Meinshausen:2010
 pages = {417--473},
 publisher = {Blackwell Publishing Ltd},
 title = {{Stability selection}},
-url = {http://dx.doi.org/10.1111/j.1467-9868.2010.00740.x},
 volume = {72},
 year = {2010}
 }
@@ -300,7 +296,7 @@ @article{Zhao2012
 keywords = {data-dependent model selection,estimation,glasso,high-dimensional undirected graph estimation,huge,lossless screening,lossy screening,semiparametric graph},
 pages = {1059--1062},
 title = {{The huge package for high-dimensional undirected graph estimation in r}},
-url = {http://dl.acm.org/citation.cfm?id=2343681},
+url = {https://dl.acm.org/doi/10.5555/2503308.2343681},
 volume = {13},
 year = {2012}
 }
@@ -365,7 +361,7 @@ @article{Banerjee2008
 keywords = {binary data,convex optimization,gaussian,graphical model,maximum likelihood estimation,model selection},
 pages = {485--516},
 title = {{Model selection through sparse maximum likelihood estimation for multivariate gaussian or binary data}},
-url = {http://dl.acm.org/citation.cfm?id=1390696},
+url = {https://dl.acm.org/doi/10.5555/1390681.1390696},
 volume = {9},
 year = {2008}
 }
@@ -458,7 +454,7 @@ @article{Foygel2010
 mendeley-groups = {PULSAR},
 pages = {1--14},
 title = {{Extended Bayesian Information Criteria for Gaussian Graphical Models}},
-url = {http://arxiv.org/abs/1011.6640},
+url = {https://arxiv.org/abs/1011.6640},
 year = {2010}
 }
 @article{Lafferty2012,
@@ -499,7 +495,7 @@ @inproceedings{Tandon2014
 file = {:Users/cmueller/Documents/Mendeley Desktop/Tandon, Ravikumar - 2014 - Learning Graphs with a Few Hubs.pdf:pdf},
 pages = {602--610},
 title = {{Learning Graphs with a Few Hubs}},
-url = {http://jmlr.org/proceedings/papers/v32/tandon14.html},
+url = {https://proceedings.mlr.press/v32/tandon14.html},
 year = {2014}
 }
 
@@ -513,7 +509,7 @@ @article{Hocevar2016
 journal = {arXiv 1601.06834},
 pages = {1--15},
 title = {{Combinatorial algorithm for counting small induced graphs and orbits}},
-url = {http://arxiv.org/abs/1601.06834},
+url = {https://arxiv.org/abs/1601.06834},
 year = {2016}
 }
 @article{Hsieh2014,
@@ -526,7 +522,7 @@ @article{Hsieh2014
 keywords = {Gaussian Markov,covariance,graphical model,optimization,random field,regularization},
 pages = {2911--2947},
 title = {{QUIC: Quadratic Approximation for Sparse Inverse Covariance Estimation}},
-url = {http://jmlr.org/papers/v15/hsieh14a.html},
+url = {https://jmlr.org/papers/v15/hsieh14a.html},
 volume = {15},
 year = {2014}
 }
@@ -561,7 +557,7 @@ @article{Lim2013c
 keywords = {lasso,model selection,parameter estimation,prediction},
 pages = {1--31},
 title = {{Estimation Stability with Cross Validation (ESCV)}},
-url = {http://arxiv.org/abs/1303.3128},
+url = {https://arxiv.org/abs/1303.3128},
 year = {2013}
 }
 @article{Poisson1837,