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

Todo list:

. to be compatible with definitions in genetics
. standard error of haplotypes
. phase routine to include hap, genecounting or PHASE
. hap/hap.em to handle missing only one allele and X Chromsome data
. joint genetic and environmental effects and mixed models
. pca regression and htSNP
. linkage analysis programs
. C/Fortran calls to .Call, etc.
. NEXUS format, C++ from GDA site

Version 1.0-8

4-4-2006

Add heritability estimate to twinan90
Remove unused definitions according to compiling error from Kurt Hornik
Temporarily disable dependence on R/genetics due to problems with mvtnorm

Version 1.0-7

1-4-2006

Remove comments about haplo.score in gap.Rnw
Add twinan90 by Chris Williams
Add byrow=TRUE to a number of matrix() calls

Version 1.0-6

12-2-2006

fix bug in genecounting when multiple runs of chromosome X data is used
Add example to pedtodot as in R News and Bioinformatics

Version 1.0-5

16-1-2006

Drop pathmix and pointer

Version 1.0-4

13-12-2005

Add ccize

Version 1.0-3

24-7-2005

genecounting (gc.c):
Change nhet2 from short to long (int)
Change ll() in gc.c according to report by Iris Grossman on a "Crazy" data

hwe.hardy:
Fix bug report by Lize van der Merwe <lize.van.der.merwe@mrc.ac.za> on data
three=c("A/A",rep("A/B",4),rep("B/B",4),rep("A/C",14),rep("B/C",28),rep("C/C",49))
g3=genotype(three)
hwe.hardy(g3)

It benefits from the original author of HWE ("Guo, Sun-Wei" <swguo@mail.mcw.edu>)

17-4-2005

Refine 2ld.R and 2ld.c according to the C program 2LD 
Revisit pfm.sim.f (f95 -PIC -xlibmil -xO5 -dalign -c by Brian Ripley).

Version 1.0-2

14-4-2005

Done with genecounting involving Chromosome X data.
Comment on code for hrt which is useless and causes crashes.
Move fine controls of genecounting and hap to gc.control/hap.control.

18-3-2005

Version 0.8-4

add NAMESPACE
change bt, gcontrol, mtdt
add pedtodot
add datasets mao, nep499, snca, cf, fa, crohn
modify hwe.hardy by Gregor Gorjanc <Gregor.Gorjanc@bfro.uni-lj.si>,
which requires package genetics
change onLoad to .onLoad

Version 0.8-3

8-11-2004

adapt haplo.score fully for hap.score
create examples for hwe.hardy using pgc, etc.
add gcp
modify gc.em, hap.em to allow for any allele labels
change hwe to accept allele, genotype and genotype count more naturally
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 go 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