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

Todo list:

. add examples from Abbas (memory problem!)
. standard error of haplotypes
. genecounting on X chromosome
. hap/hap.em to handle missing only one allele
. joint genetic and environmental effects and mixed models
. pca regression and htSNP
. path/segregation/linkage analysis programs
. C/Fortran calls to .Call, etc.
. NEXUS format, C++ from GDA site

Version 0.8-3

8-11-2004

to adapt haplo.score fully for hap.score
to create examples for hwe.hardy using pgc, etc.
to add gcp
to modify gc.em, hap.em to allow for any allele labels
to change hwe to accept allele, genotype and genotype count more naturally
to change digit2 and digitm from int to void because of a complaint by Brian Ripley

Version 0.8-2

16-8-2004

Add keyword as required by R 2.x
Change hwe.hardy.c, pgc.h and makeped.c according to gcc -Wall -pedantic

Version 0.8-1

5-6-2004

add kin.matrix to kin.morgan using algorithm similar to g2a
replace tril/triu in mtdt with standard function lower.tri/upper.tri
add resid and scale prob in genecounting
relabel gret in pgc.Rd as cdata
delete comma in pfc.R and fix problem with loop index in pfc.f
add pfc.sim


Version 0.8

4-2-2004

Crashes by hwe.hardy goes away, chi-squared tests to be implemented

8-2-2004

Add hwe, decided any details should go to the R code itself

17-2-2004

Add static to outfile in pgc.h and hap.c, pointed by Jan de Leeuw (deleeuw@stat.ucla.edu)

21-2-2004

Completion of the first comprehensive analysis of data on Parkinson's disease and SNCA markers from
Abbas Parsian (parsian@louisville.edu) (HWE, haplotype frequency estimation, score tests, Fisher's
exact test, hwde, genetics) and gap obtained comparable results with SAS combined with hwe of 
Jurg Ott (ott@rockefeller.edu) but dealing with missing data; this could be released as an example
later on. It was decided that auxiliary functions are better added after the actual linkage analysis
codes are working.

Fix lr statistic in gc.em.R due to rename of lnlx to lx

26-2-2004

Reverse the order of version history in this file (starting from the most recent)


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


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 0.5

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 0.4

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 0.3

13-01-2004 

Refine Vignette and change gap.demo.R


Version 0.2

12-01-2004

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


Version 0.1

11-01-2004

First submission to CRAN with Vignette and revised Rd

07/06/03

draft plan (home edition) shortly before RSS 2003
