Version history of R genetic analysis package (R/gap)

07/06/03 draft plan (home edition) shortly before RSS 2003

Version 0.1

11-01-2004

First submission to CRAN with Vignette and revised Rd


Version 0.2

12-01-2004

Change %lf and %lg to %f according to check by Prof Kurt Hornik


Version 0.3

13-01-2004 

Refine Vignette and change gap.demo.R


Version 0.4

14-01-2004

Create this file
Change DESCRIPTION
Correct author of mtdt
Delete hap.out in R directory
Add docoumentation of htrtable in gc.em
See also pfc rather than gif in gif.Rd
Add right bracket in dat1 of chow.test
Change ad to y in htr.Rd and the annotation in apoeapoc.Rd


Version 0.5

19-01-2004

To remove warnings earlier found in PC and pointed by Prof Brian Ripley
Resubmission to CRAN


22-1-2004

Add haplotype diversity to genecounting
Add default value to optrho in kbyl
Change "for" to "with" when describing fsnps


Version 0.6

28-1-2004

Changes for Mac OS X 10.3 (Panther) according to Michael Barmada (michael.barmada@hgen.pitt.edu):
. do_switch --> ndo_switch in hwe.hardy.c
. malloc.h --> malloc/malloc.h in gcontrol.c and makeped.c; but it seems ok to stick to stdlib.h
. add static to n_loci, etc. in hap.c, mia.c to avoid conflict

31-1-2004

Rename genecounting.R to gc.R and change lnl0 and lnl1 to l0 and l1
Add pgc function but with same problem as hwe.hardy

1-2-2004

Fix error and handle.miss functions in pgc when with.id=0
Change cat() to c() in gap.demo.R to avoid generating data files
Merge muvar1 and muvar2 into muvar and add their synopsis


Version 0.7

2-2-2004

Warnings pointed by Kurt Hornik
Change %lf to %f in several places of pgc.c
Remove semicolon after } of rsort1


things to do,

1. hwe.hardy debug
2. hap.score to deal with more distributions and robust label handling
3. hap/hap.em to handle missing only one allele and add X chromosome code
4. joint genetic and environmental effects and mixed models
5. pca regression and htSNP
6. permutation tests/LD statistics as in EHPLUS

Further to add: path/segregation/linkage analysis programs
