[#1928] Patch to accommodate changes in pedigreemm

Date:
2012-04-03 18:06 Priority:
3

State:
Open

Submitted by:
Roby Joehanes (robbyjo) Assigned to:
Nobody (None)

Component:
None Version:
None

Resolution:
None

Summary:
Patch to accommodate changes in pedigreemm

Detailed description
I have created a patch for the latest lmer.R (against SVN rev 1694, latest as of this posting) to accommodate calls by pedigreemm. I see that there is potentially a way to create a single "finalize" method instead of one for each lmer, glmer, and nlmer. I assume that nAGQ is 0 for lmer, correct? Or is it possible for glmer or nlmer to specify nAGQ=0? Also, it is possible to change lmer / glmer / nlmer to use the finalize method as necessary.

Comments:

Message
Date: 2012-07-06 17:53 Sender: Roby Joehanes Updated the patch to reflect changes on SVN rev 1784. The latest patch for pedigreemm (bundled inside lme4-patch-svn1724.zip) still works.
Date: 2012-06-20 21:16 Sender: Roby Joehanes Updated the patch to reflect changes on SVN rev 1767. The latest patch for pedigreemm (bundled inside lme4-patch-svn1724.zip) still works.
Date: 2012-05-21 22:58 Sender: Roby Joehanes Updated the patch to reflect changes on SVN rev 1752. The latest patch for pedigreemm (bundled inside lme4-patch-svn1724.zip) still works.
Date: 2012-05-11 19:45 Sender: Roby Joehanes Updated the patch to reflect changes on SVN rev 1724. I packaged the newest pedigreemm patch along with the lme4 patch into one zip file called lme4-patch-svn1724.zip. New pedigreemm patch allows specification of IBD matrix into the model.
Date: 2012-05-07 02:48 Sender: Roby Joehanes Updated the patch to reflect changes on SVN rev 1717. Patch for pedigreemm (against lme4 SVN rev 1706) still works.
Date: 2012-04-24 23:36 Sender: Roby Joehanes Updated the patch to reflect changes on SVN rev 1710. Patch for pedigreemm (against lme4 SVN rev 1706) still works .
Date: 2012-04-20 18:58 Sender: Roby Joehanes Updated the patch to reflect changes on SVN rev 1708. Patch for pedigreemm (against lme4 SVN rev 1706) still works for lme4 SVN rev 1708.
Date: 2012-04-17 18:39 Sender: Roby Joehanes Updated the patch to reflect changes on SVN rev 1706.
Date: 2012-04-04 20:24 Sender: Roby Joehanes Another update to the patch to accommodate random factors with numbers of levels exceeding the number of observations.
Date: 2012-04-04 16:43 Sender: Roby Joehanes Apparently, there is no patch tracker for pedigreemm project as of this writing. So, I'll just submit my patch here.
Date: 2012-04-04 16:41 Sender: Roby Joehanes Update to the patch. I will post the counterpart patch for pedigreemm in pedigreemm project's tracker.

Attached Files:

Attachments:

Size	Name	Date	By	Download
7 KiB	lme4-svn1767-patch.txt	2012-06-20 21:16	robbyjo	lme4-svn1767-patch.txt
7 KiB	lme4-svn1784-patch.txt	2012-07-06 17:53	robbyjo	lme4-svn1784-patch.txt
4 KiB	lmer-patch-for-pedigreemm.txt	2012-04-03 18:06	robbyjo	lmer-patch-for-pedigreemm.txt
4 KiB	lmer-patch-for-pedigreemm-v2.txt	2012-04-04 16:41	robbyjo	lmer-patch-for-pedigreemm-v2.txt
6 KiB	pedigreemm-patch-v3.txt	2012-04-04 16:43	robbyjo	pedigreemm-patch-v3.txt
5 KiB	lmer-patch-for-pedigreemm-v3.txt	2012-04-04 20:24	robbyjo	lmer-patch-for-pedigreemm-v3.txt
8 KiB	lme4-svn1706-patch.txt	2012-04-17 18:39	robbyjo	lme4-svn1706-patch.txt
6 KiB	pedigree-svn1706-patch.txt	2012-04-17 18:39	robbyjo	pedigree-svn1706-patch.txt
8 KiB	lme4-svn1708-patch.txt	2012-04-20 18:58	robbyjo	lme4-svn1708-patch.txt
8 KiB	lme4-svn1710-patch.txt	2012-04-24 23:36	robbyjo	lme4-svn1710-patch.txt
8 KiB	lme4-svn1717-patch.txt	2012-05-07 02:48	robbyjo	lme4-svn1717-patch.txt
4 KiB	lme4-patch-svn1724.zip	2012-05-11 19:45	robbyjo	lme4-patch-svn1724.zip
7 KiB	lme4-svn1752-patch.txt	2012-05-21 22:58	robbyjo	lme4-svn1752-patch.txt

Changes

Field	Old Value	Date	By
File Added	192: lme4-svn1784-patch.txt	2012-07-06 17:53	robbyjo
File Added	187: lme4-svn1767-patch.txt	2012-06-20 21:16	robbyjo
File Added	182: lme4-svn1752-patch.txt	2012-05-21 22:58	robbyjo
File Added	176: lme4-patch-svn1724.zip	2012-05-11 19:45	robbyjo
File Added	173: lme4-svn1717-patch.txt	2012-05-07 02:48	robbyjo
File Added	170: lme4-svn1710-patch.txt	2012-04-24 23:36	robbyjo
File Added	169: lme4-svn1708-patch.txt	2012-04-20 18:58	robbyjo
File Added	166: lme4-svn1706-patch.txt	2012-04-17 18:39	robbyjo
File Added	167: pedigree-svn1706-patch.txt	2012-04-17 18:39	robbyjo
File Added	165: lmer-patch-for-pedigreemm-v3.txt	2012-04-04 20:24	robbyjo
File Added	164: pedigreemm-patch-v3.txt	2012-04-04 16:43	robbyjo
File Added	163: lmer-patch-for-pedigreemm-v2.txt	2012-04-04 16:41	robbyjo
File Added	162: lmer-patch-for-pedigreemm.txt	2012-04-03 18:06	robbyjo