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

Version 1.1-8
26-02-2013	Remove attach/detach in gc.em.R filter through --as-cran with installation of qpdf

Version 1.1-7
26-02-2013	Rmove \synopsis in muvar.Rd from CRAN check results
25-02-2013	Add mhtplot2 after the Nature Genetics paper on heart rate
		Add l51 following a side project at the work place
		Suggest coxme, pedigreemm, regress
15-09-2012	Remove .tm_properties according to CRAN check
06-08-2012	Add AE3 function, mfblong.rda, and CITATION, suggesting nlme

Version 1.1-6
15-03-2012	Change version to MAKEPED_VERSION in makeped.c according to Prof Brian Ripley
14-03-2012	Add inst/doc/results, figures to .Rinstignore
		Revise mtdt2

Version 1.1-5
14-03-2012	Add .Rinstignore
		Remove Sweave.sty in inst/doc and reorganse sub-directories there
13-03-2012	Change env to envir and lapply to sapply in tscc

Version 1.1-4
13-03-2012	Withdraw twinan90 to comply with new R CMD check
		Suppress write statements in pfc.f, pfc.sim.f; replace stop with rexit
		Replace fprintf(stderr,) with REprintf(), printf() with Rprint(), exit() with error()
		Restore allele.recode, geno.recode
		Remove Hmisc and suggests kinship2

Version 1.1-3
06-12-2011	Revise gap.Rnw to be compatible with kinship_1.1.2
30-11-2011	Revise hwe.cc components and therefore NAMESPACE according to Wang, Li [li.wang@vanderbilt.edu]
		Suggest rms instead of Design in DESCRIPTIOIN and therefore modify hap.score.R
11-11-2011	Add examples of HWE for multiple markers as done for Roger Vallejo [Roger.Vallejo@ARS.USDA.GOV]
03-10-2011	Add url to twinan90 example and .png example for mhtplot
29-08-2011	Revise asplot to allow for is.na(RSQR) and add NCBI2R example
12-08-2011	Revise asplot as with the package vignette
09-06-2011	Activate ylab, according to Marcel den Hoed [marcel.denhoed@mrc-epid.cam.ac.uk]
03-06-2011	Replace snca.RData with PD.rda
31-05-2011	Refine mhtplot and documentation according to Franco, Luis Miguel [lfranco@bcm.edu]
04-05-2011	Tidy up some loose ends from Version 1.1-2

Version 1.1-2
03-05-2011	Modify package vignette after cross-check with package kinship
01-05-2011	Revise kin.morgan (finally) with bug-fix as reported by Lukas Keller [lukas.keller@ieu.uzh.ch]
14-04-2011	Add --resave-data option when running R CMD build

Version 1.1-1
10-12-2010	Add into vignette results from pbsize/fbsize/ccsize and figures as produced by asplot, ESplot, mhtplot, and qqunif
25-11-2010	Add type argument to mht.control() so that it is appropriate for lod score analysis
23-11-2010	Clarify colors and hcolors in mhtplot
19-11-2010	Add /usr/share/texlive/texmf-dist/tex/latex/ltxmisc/a4wide.sty under Fedora 13
		and Comment on \usepackage{a4wide/amsmath/epsfig} in gap.Rnw enable build/check
		Change some table() calls to unique in Mhtplot to keep genes in order

Version 1.1-0
17-11-2010	Enable rotated ticks on the x-axis and retain cutoffs argument after HaemGenRBC plot
14-11-2010	Relocate highlight region in mhtplot after the usual data points
05-11-2010	Remove attach/detach data statements in mtdt2 due to bug-fix in BradleyTerry2
03-11-2010	Further reivision of mhtplot using real data from Tuomas.Kilpelainen@mrc-epid.cam.ac.uk
07-07-2010	Revise mhtplot at suggestion of Peter Ehlers [ehlers@ucalgary.ca]
30-06-2010	Replace qqplot within gcontrol2 by qqunif

Version 1.0-23
24-06-2010	Refine keywords
23-06-2010	Add masize for sample size calculation in mediation analysis
08-06-2010	Add references to apoeapoc following a query from Breitling Lutz [l.breitling@Dkfz-Heidelberg.de]
27-05-2010	Rename abc as ab, pending addition of a formal abc
14-05-2010	Add hwe.cc based on codes by Chang Yu [chang.yu@vanderbilt.edu]
29-04-2010	Add ACE.R for ACE, AE, CE and E twin models using OpenMx and create h2
20-04-2010      Add mtdt2 calling BradleyTerry2
01-04-2010	Add klem with .C("kbylem") for LD statistics based on imputed SNPs to be calculated
24-03-2010	Fix problems of no specification of ylim=NULL at mhtplot
03-01-2010	Add example data to comp.score and refine makeped example

Version 1.0-22
01-01-2010	Refine ccsize, fbsize and pbsize
21-11-2009	Add outfile and outfileonly arguments to read.ms.output

Version 1.0-21
20-11-2009	Fix bug on read.ms.output when nsam==1 and make mhtplot to accommodate generic data as pointed
		by Dagmar Kapell [Dagmar.Kapell@sac.ac.uk]
19-11-2009	Add function read.ms.output after work on EJHG paper and revise link to qqfun from qqunif
10-11-2009	Add function abc based on EPIC-Norfolk data for QQR for Shengxu Li [shengxu.li@mrc-epid.cam.ac.uk]
08-11-2009	Add confidence interval option to qqunif as required by Andy Wood [arwood@pms.ac.uk]
28-08-2009	Remove references to qqline, qqplot of stats in qqfun.Rd and depreciated power.casectrl of genetics

Version 1.0-20
26-08-2009	Rename kbyl as LDkl in geneecounting.Rd, add references to vignette for b2r/mvmeta 

Version 1.0-19
25-08-2009	Attempt to do away with warning from 2ld.c

Version 1.0-18
25-08-2009	Remove braces for enumerate items in genecounting.Rd and hap.Rd
18-08-2009	Add b2r in order for meta-analysis via correlations to be conducted
17-08-2009	Add arguments alpha and beta to fbsize as needed by Tetyana Zayats [zayatst@Cardiff.ac.uk]
		Add mvmeta from an earlier test, pending on further work on using linear regression estimates
11-08-2009	Suggests pedigree package
23-07-2009	Fix subscript for QW in metareg as pointed by Emmanouela Repapi [er82@leicester.ac.uk]
08-06-2009	Revise mhtplot documentation example according to Meg Rose [mrose19@jhu.edu]
03-01-2009	Fix link to Citations.txt
		Modify gap-package.Rd and mhtplot.Rd

Version 1.0-17
02-01-2009	Remove braces from Rd files according to CRAN check

Version 1.0-16
02-01-2009	Refine asplot and mhtplot
01-01-2009	Modify mhtplot with real position, colors for available chromosomes, default cutoffs and gap
31-12-2008	Remove psfig.sty from gap.Rnw
14-11-2008	Change pos <- data[,2] to pos <- 1:length(data[,2]) according to Aron Chiang
07-11-2008	Add 'base' to mhtplot as pointed by Aron Chiang [Yutin.A.Chiang@uth.tmc.edu]
		Add detach(hapdat) to gc.em according to Jose Osorio [Jose.OSORIOYFORTEA@limagrain.com]
		Add comments on permutation test of r2 as for Sofiane MEZMOUK [Sofiane.MEZMOUK@biogemma.com]
20-08-2008	Revise links to LDkl in gc.em.Rd and hap.em.Rd
                Add HapDesign and HapFreqSE by Andrea Foulkes
23-04-2008	add mzdz.dat

Version 1.0-15
10-04-2008	Rename tbyt/kbyl as LD22/LDkl and fix hap.c
07-04-2008	Add ESplot for Grace Jing Wang's query
28-03-2008	Add regional association plot (asplot)
25-03-2008	Add qqfun according to qq.plot of package car by John Fox
22-03-2008	Add gcontrol2 (experimental)
21-03-2008	Remove labels "chr" in mhtplot
20-03-2008	Swap order of x, y in qqunif
14-03-2008	Create mhtplot for Manhattan plot of genomewide p values
                Add example to qqunif for highlighting p values above certain threshold
10-03-2008	Revise pedtodot according to pedigrees from Jinliang Wang/Richard Mott
07-03-2008	Add Fisher's method for meta-analysis to metap
06-03-2008	Replace get() with data[""] in metap/metareg
		Refine metap.Rd to make it consistent with the GIANT example
		Document some functions in gap-internal.Rd
		Provide option for file of haplotype assignment
04-03-2008	Add metap, and modify metareg to accept multiple records
		Add PARn, snp.ES, snp.HWE, snp.PAR
03-03-2008	Add metareg
02-03-2008      Add citations.txt to inst/doc

Version 1.0-14
01-03-2008	Add pbsize2 and make an internal function from pexp/fexp
                Add jss07.pdf to inst/doc
                Add mao.dat to inst/tests and therefore modify genecounting.Rd
27-02-2008	Change license to GPL (>=2) as suggested by Kurt Hornik
20-02-2008	Correct reference as suggested by Mark N Grote
		Change V = -1.,2.1,.1 to J = 1,32, V=-1+0.1*(J-1) in twinan90.f

Version 1.0-13
01-08-2007	Refine BFDP,FPRP,qqunif

Version 1.0-12
16-06-2007	Add haplo.stats to Suggest and remove associate functions
28-07-2007	Add BFDP,FPRP,qqunif

Version 1.0-11
12-06-2007	Add gap-package.Rd and reformat this file with tabs
18-04-2007	Add comp.score
08-04-2007	DESCRIPTION:
		Suggests: Design, Hmisc

Version 1.0-10
02-01-2007	Remove P1 in powerj of tscc function
		Rename mi.inference to micombine to avoid confusion
11-10-2006	add \method markup to plot.hap.score and print.hap.score

Version 1.0-9
21-9-2006	Add Design, Hmisc to DESCRIPTION as required by R 2.4.0
		Add more summary statistics to twinan90
		Add mi.inference to mia
		Add power calculation for joint analysis of two-stage design
		Add recent references to gap.Rnw

Version 1.0-8
04-04-2006	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
01-04-2006	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
12-02-2006	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
16-01-2006	Drop pathmix and pointer

Version 1.0-4
13-12-2005	Add ccsize

Version 1.0-3
24-07-2005	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>)
17-04-2005	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
14-04-2005	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.

Version 0.8-4
18-03-2005	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
08-11-2004	Ddapt 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
16-08-2004	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
05-06-2004	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
04-02-2004	Crashes by hwe.hardy go away, chi-squared tests to be implemented
08-02-2004	Add hwe, decided any details should go to the R code itself
17-02-2004	Add static to outfile in pgc.h and hap.c, pointed by Jan de Leeuw (deleeuw@stat.ucla.edu)
21-02-2004	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

26-02-2004	Reverse the order of version history in this file (starting from the most recent)

Version 0.7
02-02-2004	Warnings pointed by Kurt Hornik
		Change %lf to %f in several places of pgc.c
		Remove semicolon after } of rsort1

Version 0.6
28-01-2004	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

31-01-2004	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

01-02-2004	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
07-06-2003	Draft plan (home edition) shortly before RSS 2003