Version history of the R genetic analysis package (R/gap) Version 1.5-3 25-08-2023 Depends: R (>= 2.10), gap.datasets (>= 0.0.6) as suggested by Uwe Ligges Version 1.5-2 21-08-2023 circos.mhtplot(2)/labelManhattan/mhtplot: to italicise gene labels On METAL_forestplot(): 1. Revise examples, 2. Accommodate `metafor` for EE/FE models, 3. \insertRef{} Extend gc.lambda() for -log10(P) and drop -log10(P)<2 for IL-12B plot in gap.Rmd Amend circos.mhtplot2() with an addtional track Add ci2ms() for PhenoScanner/GWAS Catalog lookup and refine h2_mzdz() Drop genetics/GeneticsDesign reference in pbsize2() and backslash (\%) in tscc() Rename SNP functions and document hg18/19/38 Reorganize DESCRIPTION, adding Roxygen: list(markdown = TRUE), and document in Markdown Import/amend in line with Rdpack/Remove INDEX to suppress error message/ and \insertRef Refine gap.Rmd and shinygap.Rmd Revise CITATION for the new style Version 1.5-1 22-01-2023 Add rationale, @graham21 and @vosa21 for cs() together with minor changes in gap.Rmd gcx.c: 49, 1209, short * to short int [] hap.h:37, hap_c.c: 1001, char * Modify mhtplot.trunc() Export several internal functions Fix logp.Rd Version 1.5 12-01-2023 Apply bookdown to shinygap.Rmd Suggest mets in gap.examples instead Initialize r=0 at lines 252, 695 of gcontrol_c.c Remove "typedef enum{false=0,true=1} boolean" in pgc.h and use false/true=0/1 in pgc_c.c Modify gap.Rmd Version 1.4-2 09-01-2023 Only use %s as in makeped_c.c/fscanf("%s",&response) Add "and" in gap.Rmd Summary Version 1.4-1 08-01-2023 Increase all 1s, 2s to 3s as in makeped_c.c/fscanf("%1s",&response) Fix typo `constrast` in gap.Rmd Version 1.4 07-01-2023 Suggest bookdown Version 1.3-2 07-01-2023 gap.Rmd now uses bookdown with `convert -resize 60% IL.12B-mhtplot.trunc.png IL-12B.png` and appropriate citations Rename `gsmr` to `mr` with the test data reading from the console Replace path.package() with find.package() Move `...` from pdf() to meta() in METAL_forestplot() sprintf --> snprintf following https://developer.r-project.org/blosxom.cgi/R-devel/2022/12/04 Simplify miamiplot2 code Export makeped() Document/export hap.control(), KCC() due to query from Cecil Asa-Atiemo Fix LLVM clang >= 15 is used in C23 mode (https://www.stats.ox.ac.uk/pub/bdr/C23/): gcontrol_c.c r variables not used, makeped_c.c fscanf() may overflow, pgc.h enum expects identifier Version 1.3-1 20-10-2022 Remove README.md and mask miamiplot2 example Version 1.3 20-10-2022 Fix a function declaration without a prototype in C [-Wstrict-prototypes] Generate NAMESPACE by roxygen2 and add README.md Add mr_forestplot() Add qtlClassifier(), pedtodot_verbatim(), miamiplot2()/labelManhattan() Add circos.mhtplot2(); Clarification of YAML declaration in gap.Rmd Add cex.axis to axis(1) in mhtplot.trunc() & notes on adjustment data Drop Cox.est, Cox.T, Dev* for hwe.cc from NAMESPACE and export fbsize Drop (p) and add options to get qtl2plot(), qtl2plotly() and qtl3plotly(). Mask circos.cnvplot due to excessive running time. Redocument grid2d, klem, metareg, mtdt, plot.hap.score, print.hap.score. Revise grid2d, qtl(2|3)dplt(ly)() so as to accommodate TSS. Suggests: DiagrammeR, DOT, manhattanly, readr Version 1.2.3-6 10-05-2022 Switch back to three-character maintainer name. Version 1.2.3-5 09-05-2022 Mask circos.mhtplot due to running time > 5s Merge first name Version 1.2.3-4 09-05-2022 Drop URL for "Approximations for Mean and Variance of a Ratio" by Howard Seltman due to server certificate verification failure Drop DOI with Cai & Zeng (2004) for its unusual entry Version 1.2.3-3 09-05-2022 Change cnvplot(cnv) to cnvplot(gap.datasets::cnv) Revise gap.Rmd to comply with csl. Version 1.2.3-2 06-05-2022 gap.Rmd Drop fig=TRUE from gap.Rnw since it causes problems Merge plogp.Rmd and functions.Rmd from pQTLtools Apply Sweave2knitr() to gap.Rnw and jss.Rnw and change gap.Rnw to gap.Rmd Add nature-genetics.csl from https://www.zotero.org/styles/nature-genetics with nocite Add the three functions related to linear regression shinygap Add inst/shinygap and therefore runshinygap Create R/global.R containing revised functions so it does not rely on R/gap Add split=FALSE to METAL_forestplot to accommodate individual plot(s). Make the first argument of sn() inside fbsize() as list() so as to handle vector input R R CMD build --compact-vignettes=gs+qpdf with ghostscript 9.56.1 suggested by Kurt Hornik DESCRIPTION/Description + inst/CITATION + bibentry amended with doi courtesy of instructions from Achim Zeileis Wed 06/10/2021 01:11. Depend: gap.datasets Imports: dplyr, ggplot2, plotly Suggests: htmlwidgets, rmarkdown, -gap.datasets Rename h2 to h2_mzdz to resolve conflict with shiny/htmltools Document circos.cis.vs.trans.plot(), circos.cnvplot(), miamiplot() Document logp(), log10p(), log10pvalue(), pqtl2dplot(), pvalue(), h2G(), h2GE(), h2l() Rename mhtplot2d/3d as pqtl2dplot/3dplotly, 3d version as run3d() and use .csv Drop strlen() since nchar() is ready to use Add allDuplicated and export grid2d() Add get_b_se(), get_pve_se(), get_sdy(), reverse_strand() Use of qnorm(log_p-log(2),lower.tail=FALSE,log.p=TRUE) for cs() when log_p is non-NULL 04-05-2021 Documentation through roxygen and suggests knitr 24-04-2021 Enable fig=TRUE in gap.Rnw to generate figures/reduce size of the package 23-04-2021 Revise gsmr() adding legend and Egger intercept Add cnvplot() trunc.mhtplot, and METAL_forestplot examples to gap.Rnw Version 1.2.3-1 21-04-2021 Remove URL from hwe.cc.Rd and http --> https in CITATION Version 1.2.3 20-04-2021 Remove (unused) # ftp:// from asplot after suggestion 19-04-2021 Revise log10pvalue() and mhtplot.trunc() on p values 17-04-2021 Simplify pvalue() 16-04-2021 Change arguments for qnorm() and fix a swapped UCL/LCL bug in gsmr() 14-04-2021 Add log10pvalue so as to enable mhtplot.trunc() to handle p, log10p, z 11-04-2021 Rework on mhtplot.trunc() to use Z so as to handle extremely small p values Drop qqman from suggests 10-04-2021 Relocate description on lsf.str() as Appendix and add library(gap) in gap.Rnw 09-04-2021 Add weighted.median(), mr.boot(), gsmr() which suggests metafor, cowplot 31-03-2021 Revise ESplot to use log(OR) as effect size, activate (...) option 22-03-2021 Add example for miamiplot in gap.Rnw 12-02-2021 Revise circos.cnvplot() excluding records with start>end 11-02-2021 Revise METAL_forestplot() 19-01-2021 Revise cs() to give the correct list of variants 10-01-2021 Revise ESplot() and therefore the vignette from Wendi's problem 20-10-2020 Add pvalue() to complement log10p() 05-08-2020 Fix issues in chr_pos_a1_a2() with vector input and suggest R/genetics 28-04-2020 Change colors for cis/trans signals in circos.cis.vs.trans.plot() 22-02-2020 Add bat data example for MCMCgrm on a query from Shengjing Song Merge d3json() to mhtplot3d(), drop the template, regress and suggest plotly 19-02-2020 Add details on N to METAL_forestplot.Rd due to query/flag of a typo from Savita Karthikeyan 09-02-2020 Revise return values for mhtplot2d as id,chr1,pos1,chr2,pos2,x,y,log10p,target,gene,col Version 1.2.2 01-02-2020 Fix problem with inv_chr_pos_a1_a2(prefix=), return values from mhtplot2d Recompile R-devel with `CPPFLAGS="-D_FORTIFY_SOURCE=2 -fPIC" ./configure --enable-R-shlib' as informed by Kurt Hornik and then add ignore.h for `R CMD check --as-cran` 17-12-2019 Add chr_pos_a1_a2()/inv_chr_pos_a1_a2() 11-12-2019 Add snptest_sample() to output in SNPTEST sample file format 05-11-2019 Add makeRLEplot() from Caprion pilot data and function setup by Jimmy Peters 13-10-2019 Revise METAL_forestplot() adding dplyr_rsid() due to queries from Cismaru, Anca 07-10-2019 Add mhtplot2d() for 2D Manhattan plot 02-09-2019 Fix numerical issues and log_p= option for cs() 24-08-2019 Reverse compatibility with R 3.3.1 by changing family to family_ in pfc.f 14-08-2019 Fix bug in sentinels subsetting, i.e., pos --> u[[pos]] 25-06-2019 Add cs and suggest matrixStats 18-06-2019 Add logp and variance explained for sentinels.Rd 12-06-2019 Add z = option to mhtplot.trunc to handle P value = 0 Change sentinels.R for names other than "Chrom", "End", "MarkerName", "Effect", "StdErr" 06-06-2019 Revise sentinels.R, gap-package.Rd and both use OPGtbl Version 1.2.1 05-06-2019 Eventual foreign language check with export definitions followed by R-devel CMD INSTALL This is noted at the GitHub Computational-Statistics repository (INSTALL.md) Version 1.2 04-06-2019 Add sentinels function, further revision over C/Fortran code 31-05-2019 Split examples into gap.examples Version 1.1-27 30-05-2019 Fix hap_c.c and also pgc.h, pgc_c.c through Ripley's options to R CMD check --configure-args="", which are more restrictive than R-devel CMD check --as-cran and also CRAN check itself. Version 1.1-26 30-05-2019 Change size of tempname in hap_c.c Version 1.1-25 29-05-2019 Replace sprintf with snprintf in hap_c.c Version 1.1-24 29-05-2019 Suggest reshape and revise C/Fortran codes (from CRAN check) Version 1.1-23 27-05-2019 Suggest calibrate and rmeta, revise require() and pfc.f/pfc.sim.f with do/continue 25-05-2019 Suggest qqman, plotrix while adding mhtplot.trunc 23-05-2019 Suggest dplyr, forestplot, meta and add METAL_forestplot 10-05-2019 Add return total signals from cis.vs.trans.classification 08-05-2019 Add column and row totals for cis.vs.trans.classification 02-05-2019 Change circos.cis.vs.trans.plot so the chords are directional and two-coloured 22-01-2019 Revise cnvplot to handle Y chromosome 20-12-2018 Add circos.mhtplot, revise cnvplot and employ gc.lambda in qqunif.Rd 19-12-2018 Refine cis.vs.trans.plot and inf1.rda 18-12-2018 Add cnv/cnvplot/circos.cnvplot and therefore suggests circlize due to query from Zheng Ye Carry on with addition of circos.cis.vs.trans.plot Revise contact e-mail address in gap-package.Rd Add required(gap.datasets) to mhtplot.Rd 22-11-2018 Note https://ftp.hapmap.org/hapmap for asplot 20-11-2018 Add cis.vs.trans.classification as with jma.cojo.rda and inf1.rda 03-10-2018 Add log10p as in the SCALLOP/INF project 01-10-2018 Add gc.lambda and miamiplot as in CEU and invnormal as in GLGC-GIANT analysis plan 24-09-2018 Reset maxalleles to be 1000 in 2ld.c as requested by sjmack from GitHub 05-08-2018 Add ABO example contrasting HWE/HWD for hwe.jags.Rd 30-07-2018 Redirect URL/BugReports to GitHub 25-07-2018 Add h2.jags 24-07-2018 Add hwe.jags 17-07-2018 Revise asplot.Rd/gap.Rnw after query from Dhanaprakash Jambulingam Remove URL in crohn.Rd as it is unavailable Change hap_c.c for complaints over %03d 13-07-2018 Remove twinan90 from INDEX|man/gap-package.Rd 08-06-2018 Minor changes Version 1.1-22 06-06-2018 Replace email address Tidy up inst/tests Version 1.1-21 23-01-2018 Amend URL and makeped example Version 1.1-20 24-11-2017 Resize by removing programs available from GitHub Revise gap.Rnw Version 1.1-19 23-11-2017 Remove a4wide.sty from gap.Rnw and rnews.Rnw Drop www.graphviz.org Version 1.1-18 23-11-2017 Enlarge c[3] to c[7] from CRAN check and Prof Ripley Version 1.1-17 19-04-2017 Change fac(8000) to fac(0:8000) in pfc.sim.f for error from R 3.4 as alerted by Rainer Johannes 02-03-2017 Drop \url from hap.Rd, mia.Rd/revise url in CITATION Add import statements to NAMESPACE as suggested by R CMD check --as-cran Change useDynLib(gap) to useDynLib(gap, .registration = TRUE) run tools::package_native_routine_registration_skeleton("gap") to /src 13-03-2016 Replace URL with desktop service version 05-01-2016 Add InterAct code snipets to inst/tests/h2 10-12-2015 Extend h2GE to handle multiple GxE's 06-06-2015 Reset width=8.5in for h2.Rnw. Version 1.1-16 06-06-2015 Change h2.Rnw to h2.pdf generated locally as it would invoke multicore computing. Version 1.1-15 05-06-2015 Revise h2.Rnw Version 1.1-14 04-06-2015 Drop R2OpenBUGS and coda Revise h2.Rnw Version 1.1-13 03-06-2015 Revise gap.Rnw Title case compliance Add information on suggested packages through require() Add meyer data and example code Replace uniform RNG to be R's in hap and hwe.hardy Update h2.Rnw adding contents on MCMCglmm, MCMCgrm, OpenBUGS and JAGS Suggest bdsmatrix, Matrix, MCMCglmm, R2OpenBUGS, R2jags and drop NCBI2R Update references.txt (no) and crohn.Rd Version 1.1-12 18-08-2014 Revise packageStartupMessage and NAMESPACE Use scope operator for external function calls as suggested by Prof Ripley Add Repository to DESCRIPTION according to R CMD check --as-cran replace "<=" with "<" at line 502 of makeped.c according to Prof Brian Ripley Version 1.1-11 18-08-2014 Use Unit URL, suggest mets and add INDEX, use of packageStartupMessage Add WriteGRMSAS and SAS code for l51 Add ReadGRM/WriteGRM/ReadGRMPCA/ReadGRMPLINK/h2G/h2GE/VR and revise .Rd files Revise demo/gap.R and kin.morgan.c in accordance with recent changes Move doc/ to tests/ as in kinship to make room for vignettes Replace gets() by fgets() in makeped.c as suggested by Fedora 19 Add source codes of associate R functions for cross-checking, e.g., 2ld (first full release of GENECOUNTING source code) Enhance the resolutions of figures in gap.Rnw by mixing pdf/png formats Add rnews.Rnw, pedtodot.Rnw, jss.Rnw and h2.Rnw as additional vignettes Version 1.1.10 30-09-2013 Create vignettes subdirectory for associate files from inst/doc Remove url from DESCRIPTION Add functions during experiments with GCTA Add chicken GWAS example from Titan to vignette Wrap lines longer than 100 characters Version 1.1-9 03-08-2013 Revise example in mhtplot in reply to query from Titan [mailto:lone9@qq.com] Further revision on cutoffs to mhtplot 08-04-2013 Replace .file.path(.package.path) with system.file 27-02-2013 Add SOLAR code for l51.Rd Reorder columns in mdata as in mhtplot2.Rd so that gene annotations are produced 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 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" ) 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 , 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