version 1.2.7

cran · Nov 27, 2021 · f1bfd26 · f1bfd26
1 parent 8070ca2
commit f1bfd26
Show file tree

Hide file tree

Showing 11 changed files with 33 additions and 29 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,11 @@
 Package: st
-Version: 1.2.6
-Date: 2020-09-24
+Version: 1.2.7
+Date: 2021-11-26
 Title: Shrinkage t Statistic and Correlation-Adjusted t-Score
 Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
 Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
-Depends: R (>= 3.0.2), sda (>= 1.3.7), fdrtool (>= 1.2.15), corpcor (>=
-        1.6.9)
+Depends: R (>= 3.0.2), sda (>= 1.3.8), fdrtool (>= 1.2.17), corpcor (>=
+        1.6.10)
 Imports: graphics, stats
 Suggests: limma, samr
 Description: Implements the "shrinkage t" statistic 
@@ -15,8 +15,8 @@ Description: Implements the "shrinkage t" statistic
    It also offers a convenient interface  to a number of other regularized 
    t-statistics commonly employed in high-dimensional case-control studies.    
 License: GPL (>= 3)
-URL: http://www.strimmerlab.org/software/st/
-Packaged: 2020-09-24 09:21:16 UTC; strimmer
+URL: https://strimmerlab.github.io/software/st/
 NeedsCompilation: no
+Packaged: 2021-11-26 14:11:03 UTC; strimmer
 Repository: CRAN
-Date/Publication: 2020-09-24 12:00:03 UTC
+Date/Publication: 2021-11-27 06:00:02 UTC
diff --git a/MD5 b/MD5
@@ -1,6 +1,6 @@
-4e0e8c262406d287d75153428fc796af *DESCRIPTION
+3dc6fe4d914c21e2b151e0727de384f3 *DESCRIPTION
 2543f27fd118b19925495233c273b673 *NAMESPACE
-2293f3bfa32460a75b92ab5bf168e461 *NEWS
+6e867bb9a7b214a14496b8a5c6d0c825 *NEWS
 74c13d5ae0fa3848e60c41ede02f77cb *R/cst.R
 1b0a95b26dc21faf41f8c2cf90899e04 *R/efront.R
 6c975e6ea1790d9dbe55dfadb0d1375e *R/lait.R
@@ -13,12 +13,12 @@ ac063a48819c483610c21889a64b1097 *R/shrinkt.R
 55fa65345767d5aae5f8005fd517e3bd *R/studentt.R
 ff90f4bb74f287f7592fd381c3495e31 *data/choedata.rda
 31e3152696ea2051b995bf2aeb884e43 *man/choedata.Rd
-fd7208ff479c39c70090d0df7ae3b8f9 *man/cst.stat.Rd
-8d0ccb3b42f3927137ebffcfd101ae0d *man/diffmean.stat.Rd
-4e2cf0831d9d33f587607c86b39cc6b8 *man/lait.stat.Rd
-49e06f6c967c94d26f96a33a26e1794b *man/regularizedt.Rd
-67fe4570e2d8519e257de52aec488a88 *man/shrinkcat.stat.Rd
-2431962f940eec6c0b25e0dca38b8e75 *man/shrinkt.stat.Rd
+154631d53c1a60800daa7317b10ca4a5 *man/cst.stat.Rd
+08101dc14459772083aa4623c1ec0a92 *man/diffmean.stat.Rd
+029850973eb764b978f719ac6272a133 *man/lait.stat.Rd
+0cb3e87ee492c37953f0a62bd89f8f10 *man/regularizedt.Rd
+00912ac36c50726202539c53e8d40ad2 *man/shrinkcat.stat.Rd
+1d3d5621a1415bb5546f490605c1d12c *man/shrinkt.stat.Rd
 e1249b0d8b09882e5b4342dacc2ba7dd *man/st-internal.Rd
-4e7eacf6daa11cc4ba2e018f97aa709d *man/st.package.Rd
-a65f28d881e697005b08f68c86c72d6d *man/studentt.stat.Rd
+bebaaaca03a2ca81fe88e6212582c945 *man/st.package.Rd
+73370c6b26929c16e5c3c9fd62ecade7 *man/studentt.stat.Rd
diff --git a/NEWS b/NEWS
@@ -2,6 +2,10 @@
                  RELEASE HISTORY OF THE "st" PACKAGE
                =======================================
 
+		CHANGES IN `st' PACKAGE VERSION 1.2.7
+
+- update URLs.
+
 
 		CHANGES IN `st' PACKAGE VERSION 1.2.6
 

diff --git a/man/cst.stat.Rd b/man/cst.stat.Rd
@@ -38,7 +38,7 @@ See \url{https://arxiv.org/abs/math/0608061} for publication details.
 }
 \author{
 
-  Korbinian Strimmer (\url{http://www.strimmerlab.org}).
+  Korbinian Strimmer (\url{https://strimmerlab.github.io}).
 }
 \seealso{\code{\link{shrinkcat.stat}}, \code{\link{lait.stat}}.}
 

diff --git a/man/diffmean.stat.Rd b/man/diffmean.stat.Rd
@@ -44,7 +44,7 @@ to detect differentially regulated genes in replicated microarray experiments.
  FEBS Letters \bold{573}:83-9.
 }
 \author{
-  Korbinian Strimmer (\url{http://www.strimmerlab.org}).
+  Korbinian Strimmer (\url{https://strimmerlab.github.io}).
 
   This function is in part based on code from Henry Wirth.
 }

diff --git a/man/lait.stat.Rd b/man/lait.stat.Rd
@@ -49,7 +49,7 @@ Bioinformatics \bold{24}:666-673.
 }
 \author{
 
-  Verena Zuber and Korbinian Strimmer (\url{http://www.strimmerlab.org}).
+  Verena Zuber and Korbinian Strimmer (\url{https://strimmerlab.github.io}).
 }
 \seealso{\code{\link{shrinkcat.stat}}, \code{\link{cst.stat}}.}
 

diff --git a/man/regularizedt.Rd b/man/regularizedt.Rd
@@ -63,12 +63,12 @@ and relative to the shrinkage t statistic in Opgen-Rhein and Strimmer (2007).
  differentially expressed genes by a distribution-free shrinkage 
  approach.  
  Statist. Appl. Genet. Mol. Biol. \bold{6}:9.
- (\url{https://doi.org/10.2202/1544-6115.1252})  
+ <DOI:10.2202/1544-6115.1252> 
 }
 \author{
   Rainer Opgen-Rhein 
   and
-  Korbinian Strimmer (\url{http://www.strimmerlab.org}).
+  Korbinian Strimmer (\url{https://strimmerlab.github.io}).
 }
 \seealso{\code{\link{diffmean.stat}}, \code{\link{studentt.stat}}, \code{\link{shrinkt.stat}}, \code{\link{shrinkcat.stat}}.}
 

diff --git a/man/shrinkcat.stat.Rd b/man/shrinkcat.stat.Rd
@@ -62,12 +62,12 @@ shrinkcat.fun(L, lambda, lambda.var, lambda.freqs, var.equal=TRUE,
 \references{
 Zuber, V., and K. Strimmer. 2009.  Gene ranking and biomarker discovery under correlation.
 Bioinformatics 25: 2700-2707.
-\url{https://doi.org/10.1093/bioinformatics/btp460}.
+<DOI:10.1093/bioinformatics/btp460>
 }
 \author{
   Verena Zuber 
   and
-  Korbinian Strimmer (\url{http://www.strimmerlab.org}).
+  Korbinian Strimmer (\url{https://strimmerlab.github.io}).
 }
 \seealso{\code{\link[sda]{catscore}}, \code{\link{shrinkt.stat}}, \code{\link{cst.stat}}, \code{\link{lait.stat}}.}
 

diff --git a/man/shrinkt.stat.Rd b/man/shrinkt.stat.Rd
@@ -55,12 +55,12 @@ shrinkt.fun(L, lambda.var, lambda.freqs, var.equal=TRUE, verbose=TRUE)
  differentially expressed genes by a distribution-free shrinkage 
  approach.  
  Statist. Appl. Genet. Mol. Biol. \bold{6}:9.
- (\url{https://doi.org/10.2202/1544-6115.1252})  
+ <DOI:10.2202/1544-6115.1252>  
 }
 \author{
   Rainer Opgen-Rhein, Verena Zuber, 
   and
-  Korbinian Strimmer (\url{http://www.strimmerlab.org}).
+  Korbinian Strimmer (\url{https://strimmerlab.github.io}).
 }
 \seealso{\code{\link{studentt.stat}},
          \code{\link{diffmean.stat}},

diff --git a/man/st.package.Rd b/man/st.package.Rd
@@ -14,9 +14,9 @@ This package implements the "shrinkage t" statistic
 }
 
 \author{Rainer Opgen-Rhein, Verena Zuber, and 
-        Korbinian Strimmer (\url{http://www.strimmerlab.org/})}
+        Korbinian Strimmer (\url{https://strimmerlab.github.io/})}
 \references{
-  See website: \url{http://www.strimmerlab.org/software/st/}
+  See website: \url{https://strimmerlab.github.io/software/st/}
 }
 \keyword{univar}
 \seealso{

diff --git a/man/studentt.stat.Rd b/man/studentt.stat.Rd
@@ -32,7 +32,7 @@ d}
 
 \author{
   Verena Zuber and
-  Korbinian Strimmer (\url{http://www.strimmerlab.org}).
+  Korbinian Strimmer (\url{https://strimmerlab.github.io}).
 }
 \seealso{\code{\link{shrinkt.stat}}, \code{\link{shrinkcat.stat}}.}