[Genabel-commits] r1802 - branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src

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

Author: lckarssen
Date: 2014-08-15 14:59:56 +0200 (Fri, 15 Aug 2014)
New Revision: 1802

Modified:
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/coxph_data.cpp
Log:
Remove debug print statements from the ProbABEL Cox PH code, now that bug #5726 is fixed.
Thanks to Luba Pardo and Joris Verkouteren from the Erasmus Medical Centre Rotterdam, Anne Grotenhuis from the Radboud Medical Centre Nijmegen, and Matthias Wuttke from the University Medical Centre Freiburg for their time and effort in reporting the bug, helping to nail down the problem and, testing of the fix.



Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/coxph_data.cpp
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/coxph_data.cpp	2014-08-12 11:08:03 UTC (rev 1801)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/coxph_data.cpp	2014-08-15 12:59:56 UTC (rev 1802)
@@ -438,16 +438,6 @@
 
     niter = maxiter;
 
-    cerr << snpinfo.name[cursnp]
-         << ": MAF = " << snpinfo.MAF[cursnp]
-         << "; Freq1 = " << snpinfo.Freq1[cursnp]
-         << "; Rsq = " << snpinfo.Rsq[cursnp]
-         << "; FLAG = " << flag
-         << "; niter = " << maxiter
-         << "; imat.nrow = " << imat.data.rows()
-         << "; X.nrow = " << X.nrow
-         << "; X.ncol = " << X.ncol
-         << "\n";
 
     // Check the results of the Cox fit; mirrored from the same checks
     // in coxph.fit.S and coxph.R from the R survival package.
@@ -523,9 +513,9 @@
         if (setToNAN)
         {
             // Cox regression failed
-            // sebeta[i] = NAN;
-            // beta[i]   = NAN;
-            // loglik    = NAN;
+            sebeta[i] = NAN;
+            beta[i]   = NAN;
+            loglik    = NAN;
         } else {
             sebeta[i] = sqrt(imat.get(i, i));
             loglik = loglik_int[1];