version 3.7

cran · Apr 9, 2012 · 2785286 · 2785286
1 parent 9dfb1cd
commit 2785286
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rrBLUP
 Title: Ridge regression and other kernels for genomic selection
-Version: 3.6
+Version: 3.7
 Author: Jeffrey Endelman
 Maintainer: Jeffrey Endelman <j.endelman@gmail.com>
 Description: One application is to estimate marker effects by ridge
@@ -11,6 +11,6 @@ Description: One application is to estimate marker effects by ridge
 Suggests: multicore
 License: GPL-3
 LazyLoad: yes
-Packaged: 2012-04-03 15:31:52 UTC; jeffendelman
+Packaged: 2012-04-09 20:10:22 UTC; jeffendelman
 Repository: CRAN
-Date/Publication: 2012-04-03 21:02:09
+Date/Publication: 2012-04-10 04:27:07
diff --git a/MD5 b/MD5
@@ -1,10 +1,10 @@
-909f5f0706ea232931f64ee54eccdd1f *DESCRIPTION
+c0676cc86141fd4e7f05f71b45b6d238 *DESCRIPTION
 9983baa53027ec7ecc5c44dc94318515 *NAMESPACE
-76fb9f9fdc5f599f1e738375331e9fc1 *NEWS
+564add1473e8322fc4fec2d6a89648d1 *NEWS
 3426a5afa2b38e987e53b354c267f488 *R/A.mat.R
 48dcf02533fd05c528f6c6ea2cd022fb *R/GWA.R
 f9b894abb6a3158ebfabe61486dccd94 *R/kinship.BLUP.R
-0d21c26c501e27b2d61363e369edb57c *R/mixed.solve.R
+60346207605422f7ea47a9848a817498 *R/mixed.solve.R
 b74e4e9e2c643e550a83c5ee4eb7e905 *inst/CITATION
 fbaf1e01452ed907bdb412ff35f3b067 *man/A.mat.Rd
 89ab7c69f6c5dbfca37b5220dd14525b *man/GWA.Rd

diff --git a/NEWS b/NEWS
@@ -1,3 +1,7 @@
+Changes in 3.7:
+
+* Improved handling of positive semi-definite kinship matrix in mixed.solve.
+
 Changes in 3.6:
 
 * Improved error handling in mixed.solve.

diff --git a/R/mixed.solve.R b/R/mixed.solve.R
@@ -44,23 +44,12 @@ if (n <= m + p) {
 } else {
   spectral.method <- "cholesky"
   if (!is.null(K)) {
+    diag(K) <- diag(K) + 1e-6
   	B <- try(chol(K),silent=TRUE)
-  	if (class(B)=="try-error") {
-         # K not positive definite
-         eig.K <- eigen(K,symmetric=TRUE)
-         if (min(eig.K$values) < -1e-6) {
-           stop("K not positive semi-definite")
-         } else {
-         # use pivoting
-         options(warn=-1) #disable warning
-         B <- chol(K,pivot=TRUE)
-         options(warn=0)
-         pivot <- attr(B,"pivot")         
-         B <- B[,order(pivot)]         
-         } #if min(eig.K)
-     } #if class(B)
+  	if (class(B)=="try-error") {stop("K not positive semi-definite.")}
   } # if is.null
 } 
+
 if (spectral.method=="cholesky") {
 if (is.null(K)) {
 	ZBt <- Z