[Genabel-commits] r1255 - in pkg/GenABEL: . R

[noreply at r-forge.r-project.org]

Author: yurii
Date: 2013-06-29 13:06:44 +0200 (Sat, 29 Jun 2013)
New Revision: 1255

Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/R/polygenic.R
Log:
change nullification threshold in polygenic to 1e-8

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2013-06-29 10:49:38 UTC (rev 1254)
+++ pkg/GenABEL/CHANGES.LOG	2013-06-29 11:06:44 UTC (rev 1255)
@@ -1,6 +1,8 @@
 ***  v. 1.7-7
 
 (2013.06.29)
+Changed the 'polygenic' nullification threshold to 1e-8
+
 Added references for Grammar+ transformation
 
 Allowed for user-specified output data type in '*2databel' functions

Modified: pkg/GenABEL/R/polygenic.R
===================================================================
--- pkg/GenABEL/R/polygenic.R	2013-06-29 10:49:38 UTC (rev 1254)
+++ pkg/GenABEL/R/polygenic.R	2013-06-29 11:06:44 UTC (rev 1255)
@@ -309,9 +309,9 @@
 			eigres <- eigenOfRel
 		else
 			eigres <- eigen(relmat,symmetric=TRUE)
-		if (any(eigres$values<1e-16)) {
-			eigres$values[eigres$values<1e-16] <- 1e-16
-            msg <- paste("some eigenvalues close/less than 1e-16, setting them to 1e-16\nyou can also try option llfun='polylik' instead")
+		if (any(eigres$values<1e-8)) {
+			eigres$values[eigres$values<1e-8] <- 1e-8
+            msg <- paste("some eigenvalues close/less than 1e-8, setting them to 1e-8\nyou can also try option llfun='polylik' instead")
 			warning(msg)
 		}
 	} else stop("cannot be here...")