version 1.2.3

cran · Nov 14, 2014 · 47b9149 · 47b9149
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,11 @@
 Package: st
-Version: 1.2.2
-Date: 2014-04-18
-Title: Shrinkage t Statistic and CAT Score
+Version: 1.2.3
+Date: 2014-11-14
+Title: Shrinkage t Statistic and Correlation-Adjusted t-Score
 Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
-Maintainer: Korbinian Strimmer <strimmer@uni-leipzig.de>
-Depends: R (>= 2.15.1), sda (>= 1.3.3), fdrtool (>= 1.2.12)
+Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
+Depends: R (>= 2.15.1), sda (>= 1.3.3), fdrtool (>= 1.2.12), corpcor
+        (>= 1.6.7)
 Suggests: limma, samr
 Description: This package implements the "shrinkage t" statistic 
    introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage estimate
@@ -14,7 +15,7 @@ Description: This package implements the "shrinkage t" statistic
    employed in high-dimensional case-control studies.    
 License: GPL (>= 3)
 URL: http://strimmerlab.org/software/st/
-Packaged: 2014-04-18 14:39:31 UTC; strimmer
+Packaged: 2014-11-14 01:47:30 UTC; strimmer
 NeedsCompilation: no
 Repository: CRAN
-Date/Publication: 2014-04-18 19:43:20
+Date/Publication: 2014-11-14 08:16:40
diff --git a/MD5 b/MD5
@@ -1,12 +1,12 @@
-393e73c76fdc9f3e04f756de77c6c9e7 *DESCRIPTION
-76c5d6190d48a6202c7a1019777ea6d7 *NAMESPACE
-36413384d3cf94795ec03e3aaaf53540 *NEWS
+cf7906731db166c40b3487f5d1ca5372 *DESCRIPTION
+b4552ce40f3bd48c9feea4cc9adf7c14 *NAMESPACE
+9adf66f7d1ecf3cc1539fcdd051ef5f7 *NEWS
 74c13d5ae0fa3848e60c41ede02f77cb *R/cst.R
 1b0a95b26dc21faf41f8c2cf90899e04 *R/efront.R
 6c975e6ea1790d9dbe55dfadb0d1375e *R/lait.R
-57bde37fe67ba1efcf4f23a758625e40 *R/modt.R
+946c7b5de2765739d4abb4ae5e396df6 *R/modt.R
 22a82f065c20dd9502f3607276d90d81 *R/rankprod.stat.R
-1402cdc0d7210be6397867891fe37d73 *R/sam.R
+5a59fbd75feca94b8e5f6509c60b2448 *R/sam.R
 e87be2bd9f9c15264059e676c6a7c299 *R/samL1.R
 c0d8599fd7d6a1915918204e44356e42 *R/shrinkcat.R
 ac063a48819c483610c21889a64b1097 *R/shrinkt.R

diff --git a/NAMESPACE b/NAMESPACE
@@ -25,6 +25,7 @@ export(
 )
 import(
 "fdrtool",
-"sda"
+"sda",
+"corpcor"
 )
 
diff --git a/NEWS b/NEWS
@@ -3,6 +3,12 @@
                =======================================
 
 
+		CHANGES IN `st' PACKAGE VERSION 1.2.3
+
+- change of maintainer email address.
+- fixed the  "no visible global function definition" warnings.
+
+
 		CHANGES IN `st' PACKAGE VERSION 1.2.2
 
 - added import statement in NAMESPACE to address corresponding warnings

diff --git a/R/modt.R b/R/modt.R
@@ -1,8 +1,8 @@
-### modt.R  (2007-10-27)
+### modt.R  (2014-11-14)
 ###
 ###    Moderated t Statistic
 ###
-### Copyright 2006-2008 Rainer Opgen-Rhein and Korbinian Strimmer
+### Copyright 2006-2014 Rainer Opgen-Rhein and Korbinian Strimmer
 ###
 ###
 ### This file is part of the `st' library for R and related languages.
@@ -46,8 +46,8 @@ modt.fun <- function (L)
     {
       L = as.integer(L)
       d <- cbind(rep(1, length(L)), L)
-      fit <- lmFit(t(X), design=d)
-      eb.out <- ebayes(fit)
+      fit <- limma::lmFit(t(X), design=d)
+      eb.out <- limma::ebayes(fit)
       modt <- -eb.out$t[,2]
 
       return(modt) 

diff --git a/R/sam.R b/R/sam.R
@@ -1,8 +1,8 @@
-### sam.R  (2008-10-27)
+### sam.R  (2014-11-14)
 ###
 ###    SAM t Statistic
 ###
-### Copyright 2006-2008 Rainer Opgen-Rhein and Korbinian Strimmer
+### Copyright 2006-2014 Rainer Opgen-Rhein and Korbinian Strimmer
 ###
 ###
 ### This file is part of the `st' library for R and related languages.
@@ -44,7 +44,7 @@ sam.fun <- function(L)
    function(X)
     {
       dd = list(x=t(X),y=as.integer(L), logged2=TRUE)
-      out = samr(dd, resp.type="Two class unpaired", nperms=1)
+      out = samr::samr(dd, resp.type="Two class unpaired", nperms=1)
 
       return(out$tt) # SAM test statistic
     }