2008-08-20 19:06 warnes * DESCRIPTION, inst/NEWS: Bump version numer up and update NEWS file 2008-08-20 19:04 warnes * R/makeGenotypes.R: Fix bug in makeGenoypes that caused it to ignore 'sep' when identifying potential genotype columns 2008-04-30 01:23 warnes * man/depreciated.Rd: Add complete reference to GeneticsDesign functions 2008-04-30 01:05 warnes * DESCRIPTION, inst/NEWS: Update for version 1.3.3 2008-04-30 00:54 warnes * R/genotype.R, R/locus.R: Replace obsolete (grr!) use of "$\" for atomic vectors 2008-04-30 00:53 warnes * R/power.casectl.R, man/depreciated.Rd, man/power.casectl.Rd: Mark power.casectl() as depreciated in favor of GeneticsDesign functions 2007-11-20 20:30 warnes * R/expectedGenotypes.R: Add extra error checking to expectedGenotypes() 2007-11-20 20:27 warnes * DESCRIPTION, inst/NEWS: Update NEWS and DESCRIPTION for genetics 1.3.2 2007-11-20 20:25 warnes * man/power.casectl.Rd: Fix documentation of kp and alpha arguments to power.casectl() 2007-11-20 20:24 warnes * R/hapmcmc.R: Add set argument to hapshuffle 2007-11-20 20:23 warnes * R/power.casectl.plot.R: Add explicit variable definition to avoid R CMD CHECK warning 2007-11-20 20:23 warnes * R/zzz.R: Package startup message states package is OBSOLETE 2007-11-20 20:20 warnes * R/genotype.R, tests/test.NA.R: Bug fix and regression test for assignment of NA to element of existing genotype object 2007-09-12 10:41 ggorjan * DESCRIPTION, NAMESPACE, R/genotype.R, R/summary.genotype.R, inst/NEWS, man/genotype.Rd: - fixes in genotypeOrder to ensure all genotype/haplotype combinations are used. - genotypeOrder<- is now exported 2007-08-21 14:37 warnes * ChangeLog, NEWS: Add softlinks into inst/ for ChangeLog and NEWS 2007-08-21 14:36 warnes * NEWS, inst/NEWS: Move Changelog (not in SVN) and NEWS to inst/ 2007-08-21 14:35 warnes * inst/ChangeLog, inst/NEWS: Remove softlinks in inst, doesn't work on windows 2007-08-20 18:30 warnes * inst/ChangeLog, inst/NEWS: Add softlinks in inst to NEWS and ChangeLog so these will get installed. 2007-08-08 14:59 warnes * DESCRIPTION: Bump minor version number since Gregor added new functions 2007-08-08 14:58 warnes * NEWS: Update NEWS file for new release 2007-08-08 14:56 warnes * DESCRIPTION: Update description for release, add credit to other contributors 2007-08-08 14:51 warnes * R/zzz.R: Add note referring users to the R-Genetics project homepage 2007-08-08 13:45 warnes * NAMESPACE, R/binsearch.R, man/binsearch.Rd: Move binsearch() to the gtools package 2007-08-08 13:38 warnes * R/binsearch.R: Correct bug in binsearch. Elipses were omitted from one cal to fun(). Bug reported by Matthew Walker 2007-07-25 07:32 ggorjan * NAMESPACE, NEWS, R/expectedGenotypes.R, R/genotype.R, R/groupGenotype.R, R/order.genotype.R, R/summary.genotype.R, man/expectedGenotypes.Rd, man/genotype.Rd, man/groupGenotype.Rd, man/order.genotype.Rd: groupGenotype(), some utility funcs, ... 2007-07-18 16:57 ggorjan * NEWS, R/genotype.R: Fixed genotype() with allow.partial.missing=FALSE when 'alleles' argument is passed Example: ## Old > x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B") > alleles <- c("A", "B") > genotype(x, alleles=alleles, allow.partial.missing=FALSE) [1] NA "A/NA" "A/A" NA "B/NA" "B/A" "B/B" Alleles: B A Warning message: Found data values not matching specified alleles. Converting to NA. in: genotype(x, alleles = alleles, allow.partial.missing = FALSE) ## New > genotype(x, alleles=alleles, allow.partial.missing=FALSE) [1] NA NA "A/A" NA NA "B/A" "B/B" Alleles: B A Warning message: Found data values not matching specified alleles. Converting to NA. in: genotype(x, alleles = alleles, allow.partial.missing = FALSE) > genotype(x, alleles=alleles, allow.partial.missing=TRUE) [1] NA "A/NA" "A/A" NA "B/NA" "B/A" "B/B" Alleles: B A Warning message: Found data values not matching specified alleles. Converting to NA. in: genotype(x, alleles = alleles, allow.partial.missing = TRUE) 2007-07-18 16:32 ggorjan * NEWS, R/genotype.R: There is no more warning in genotype() if 'a1' or 'a2' have NA value(s) and 'alleles'' argument is specified, since NA is NA anyway Here is the example: ## Old > x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B") > alleles <- c("A", "B", "C") > x <- genotype(x, alleles=alleles, reorder="yes") Warning message: Found data values not matching specified alleles. Converting to NA. in: genotype(x, alleles = alleles, reorder = "yes") > x [1] "C/C" "A/C" "A/A" NA "B/C" "A/B" "B/B" Alleles: A B C ## New > x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B") > alleles <- c("A", "B", "C") > x <- genotype(x, alleles=alleles, reorder="yes") > x [1] "C/C" "A/C" "A/A" NA "B/C" "A/B" "B/B" Alleles: A B C 2007-07-18 14:22 ggorjan * NEWS, R/diseq.R, man/diseq.Rd: really fixed printing of Obs vs Exp freqs 2007-07-18 12:51 ggorjan * R/expectedGenotypes.R, man/expectedGenotypes.Rd: sort produced genotypes 2007-07-18 12:19 ggorjan * R/expectedGenotypes.R: rollback one part 2007-07-18 12:09 ggorjan * R/plot.genotype.R, man/plot.genotype.Rd: fixing S3 type of documentation + minor fix 2007-07-18 12:08 ggorjan * man/genotype.Rd, man/locus.Rd, man/print.LD.Rd, man/summary.genotype.Rd: fixing S3 type of documentation 2007-07-18 11:57 ggorjan * NEWS, man/power.casectl.Rd: Fixed documentation of power.casectrl() to match its code 2007-07-18 11:49 ggorjan * DESCRIPTION, NEWS, R/expectedGenotypes.R: added gtools to Depends as needed by expectedGenotypes() + some minor fixes 2007-06-17 01:27 warnes * man/power.casectl.Rd: Update with Michael's latest changes 2007-06-17 01:25 warnes * R/power.casectl.plot.R: Move old code from power.casectl.R to power.casectl.plot.R 2007-06-17 01:24 warnes * R/power.casectl.R: Update with Michael's latest changes 2007-05-29 19:35 warnes * NEWS: Add display of observed vs expected table to print.HWE.test() 2007-05-29 19:34 warnes * DESCRIPTION, man/HWE.test.Rd: Add display of observed vs expected table to print.HWE.test() 2007-05-29 19:29 warnes * R/HWE.test.R: Add display of observed vs expected table to print.HWE.test() 2006-12-05 18:22 warnes * man/undocumented.Rd: Remove typo/dupliucate alias entry for ci.balance 2006-12-05 17:45 warnes * NEWS: Update NEWS file for 1.2.0 and 1.2.1 2006-11-14 22:20 ggorjan * trunk/GeneticsBase/DESCRIPTION, trunk/GeneticsBase/R/convert.R, trunk/GeneticsBase/TODO.txt, trunk/GeneticsBase/data/ALZH.ped, trunk/GeneticsBase/data/CAMP.ped, trunk/GeneticsBase/data/CAMPZ.phe, trunk/GeneticsBase/data/qtl.ped, trunk/GeneticsBase/data/qtl.phe, trunk/GeneticsBase/data/xbat.ped, trunk/GeneticsBase/data/xbat.phe, trunk/GeneticsBase/man/fastGrid.Rd, trunk/GeneticsBase/man/makeMarkerInfo.Rd, trunk/GeneticsBase/man/makeTransTable.Rd, trunk/GeneticsBase/man/makeTransTableList.Rd, trunk/GeneticsBase/src/convert.c, trunk/PopGenetics/R/HWE.test.data.frame.R, trunk/PopGenetics/R/expectedGenotypes.R, trunk/PopGenetics/R/plot.genotype.R, trunk/PopGenetics/inst/doc/example_data.csv, trunk/PopGenetics/man/expectedGenotypes.Rd, trunk/PopGenetics/man/plot.genotype.Rd, trunk/fbat/DESCRIPTION, trunk/fbat/data/CAMP.ped, R/HWE.test.data.frame.R, R/expectedGenotypes.R, R/plot.genotype.R, inst/doc/example_data.csv, man/expectedGenotypes.Rd, man/plot.genotype.Rd: Removing executable property 2006-11-11 04:10 warnes * DESCRIPTION: Update version number 2006-11-11 04:09 warnes * DESCRIPTION, inst/doc/genetics_article.tex, man/HWE.exact.Rd, man/HWE.test.Rd, man/LD.Rd, man/binsearch.Rd, man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd, man/gregorius.Rd, man/homozygote.Rd, man/locus.Rd, man/makeGenotypes.Rd, man/print.LD.Rd, man/summary.genotype.Rd, man/write.pop.file.Rd: Update my email address 2006-10-02 13:21 weiliang_qiu * DESCRIPTION: add the 'BioCViews' tag with 'Genetics' as the keyword to the DESCRIPTION file 2006-03-10 18:19 nj7w * R/write.pedigree.file.R: Fixed a bug in function allele.number, as pointed out by Chris Wallace 2005-11-10 15:28 warnes * man/HWE.exact.Rd, man/HWE.test.Rd, man/LD.Rd, man/binsearch.Rd, man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd, man/gregorius.Rd, man/homozygote.Rd, man/locus.Rd, man/makeGenotypes.Rd, man/print.LD.Rd, man/summary.genotype.Rd, man/write.pop.file.Rd: Update my email address 2005-11-09 17:05 warnes * DESCRIPTION: Update version number and release date 2005-11-09 17:04 warnes * R/HWE.test.R, R/LD.R, R/ci.balance.R, R/diseq.R, man/diseq.Rd: Add R^2 to HWE and LD estimates 2005-11-08 20:54 warnes * R/summary.genotype.R: Fix Heterozygosity correction, per Christopher Carlson : > My second question is with regard to the summary.genotype > function. The value you return for Heterozygosity (Hu) appears to be > 2pq*(n/(n-1)), but with n as the number of individuals. I believe > that the proper correction is for n/(n-1) where n is the number of > chromosomes, not the number of individuals. For a reasonable number > of samples the difference is subtle, but it threw off my Tajima's D > estimates when I used Hu to calculate nucleotide diversity. 2005-10-04 23:43 warnes * DESCRIPTION, NAMESPACE, R/diseq.R, R/expectedGenotypes.R, R/power.casectl.R, R/print.LD.R, R/zzz.R: Move all dependency checking into DESCRIPTION and NAMESPACES. 2005-10-04 16:30 warnes * R/plot.genotype.R: Fix handling of the 'type' argument. 2005-10-04 16:28 warnes * R/plot.genotype.R: Correct the handling of the 'what' argument. 2005-10-04 15:17 warnes * DESCRIPTION: Forgot to increment version 2005-10-04 15:15 warnes * DESCRIPTION: Update email address, version number, and date. 2005-10-04 15:13 warnes * R/diseq.R: Return NA and issue a warning if diseq() called on a marker with only one observed allele. 2005-09-14 18:45 ggorjan * R/plot.genotype.R: Now plot percentage by default i.e. no need for argument in function call. 2005-08-18 19:39 nj7w * R/genotype.R: Fix bug in heterozygote when more than one allele.name is provided 2005-03-13 01:23 warnes * R/library.R, man/library.Rd: Remove old backport of library() commanad that is no longer needed. 2005-03-12 21:57 warnes * R/summary.genotype.R: Change 'persons' to 'samples' so that we aren't human-specific. 2005-03-12 21:54 warnes * DESCRIPTION, NAMESPACE, man/expectedGenotypes.Rd, man/plot.genotype.Rd: Fixes to pass R CMD check after addition of expectedGenotypes() and plot.genotype(). 2005-03-12 20:23 warnes * R/plot.genotype.R, man/plot.genotype.Rd: Add plot.genotype() contributed by Gregor GORJANC 2005-03-12 20:22 warnes * R/expectedGenotypes.R, man/expectedGenotypes.Rd: Add expectedGenotypes() contributed by Gregor GORJANC 2005-03-09 19:49 warnes * man/makeGenotypes.Rd: Add description of the use of the 'method' argument, and an example showing the use of 'method=as.genotype.allele.count'. 2005-03-02 18:14 nj7w * NAMESPACE: Fixed NAMESPACE file to import na.omit function explicitly from stats package. 2004-12-23 01:34 warnes * R/HWE.test.data.frame.R, inst/doc/LD.pdf, inst/doc/example_data.csv, inst/doc/genetics_article.pdf: Check in some files that seem to have been overlooked in the past. 2004-12-23 01:21 warnes * NEWS: Update for 1.1.2 (and 1.1.1). 2004-12-23 01:14 warnes * DESCRIPTION: Update version number. 2004-12-23 01:08 warnes * R/diseq.R: Remove debugging code that printed intermediate values (sometimes a lot of them). 2004-11-22 14:35 warnes * man/LD.Rd: Fix typos. 2004-11-15 16:36 warnes * DESCRIPTION: Update version. 2004-11-15 16:22 warnes * R/summary.genotype.R: Ensure that allele.freq table has the same ordering as allele.names. 2004-11-15 16:20 warnes * R/HWE.test.R: remove triplicate comment 2004-11-15 15:34 warnes * man/HWE.chisq.Rd: Make it clear that the Yates continuty correction is applied *only* when simulate.p.value=FALSE, so that the reported test statistics for simulate.p.value=FALSE and simulate.p.value=TRUE will differ. 2004-10-13 16:21 warnes * R/diseq.R, man/diseq.Rd: Attempt to fix/clarify HWE diseq. computations & synchronize documentation. 2004-09-21 21:45 warnes * DESCRIPTION, NAMESPACE, NEWS, R/power.casectl.R, man/HWE.chisq.Rd, man/HWE.exact.Rd, man/HWE.test.Rd, man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd, man/homozygote.Rd, man/locus.Rd, man/power.casectl.Rd, man/summary.genotype.Rd, man/undocumented.Rd: Updated to use a namespace and to work with the lastest gregmisc bundle (previously a package). 2004-09-17 18:46 warnes * man/HWE.chisq.Rd, man/HWE.exact.Rd, man/HWE.test.Rd, man/LD.Rd, man/binsearch.Rd, man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd, man/gregorius.Rd, man/homozygote.Rd, man/library.Rd, man/locus.Rd, man/makeGenotypes.Rd, man/power.casectl.Rd, man/print.LD.Rd, man/summary.genotype.Rd, man/undocumented.Rd, man/write.pop.file.Rd: Comments were incorrectly marked by '#' instead of '%'. 2004-09-16 22:15 warnes * R/power.casectl.R: Changes from Michael Man. 2004-09-16 21:33 warnes * man/diseq.Rd: Match changes to print.diseq revision 1.16, which restored ability to show Observed vs. Expected table by addition an additional potential value for the 'show' parameter: "table". 2004-09-16 21:22 warnes * NAMESPACE: Add namespace. 2004-09-15 18:32 warnesgr * R/diseq.R: Restore ability to show Observed vs. Expected table by addition an additional potential value for the 'show' parameter: "table". 2004-07-02 15:57 warnesgr * R/power.casectl.R, man/power.casectl.Rd: Add power.casectl provided by Micheal Man. 2004-05-25 19:40 warnesgr * DESCRIPTION, R/genotype.R, R/print.LD.R, man/HWE.test.Rd, man/binsearch.Rd, man/genotype.Rd, man/locus.Rd, man/makeGenotypes.Rd, man/undocumented.Rd: Many fixex. 2004-03-25 17:15 warnesgr * R/ci.balance.R, man/ci.balance.Rd: Remove unused '...' argument from ci.balance. 2004-02-02 15:55 warnesgr * R/ci.balance.R, R/diseq.R, man/ci.balance.Rd: - Rename ci.balance 'conf' parameter to 'confidence', and add 'alpha' parameter to remove R CMD check warning. - modify diseq.ci to pass confidence level to ci.balance. 2004-02-02 15:46 warnesgr * man/homozygote.Rd: remove extraneous period from argument to carrier.genotype. 2003-12-02 18:41 warnesgr * R/genotype.R: - remove depreciated (and error prone) use of codes(). 2003-12-02 18:37 warnesgr * R/print.LD.R: - Fixed bug: "D" was being reported when only "D'" was requested. 2003-11-24 17:32 warnesgr * man/write.pop.file.Rd: - Fix the last broken fix. 2003-11-24 17:22 warnesgr * man/write.pop.file.Rd: Changes to fix latex'ing problem. 2003-08-04 14:18 warnesgr * DESCRIPTION, NEWS: - Updated NEWS and DESCRIPTION for version 1.0.2 2003-08-04 13:48 warnesgr * R/summary.genotype.R: - Fixed a bug in Heterozygosity (H) and PIC calcuations caused by using allele count rather than allele proportions. Bug reported by Gerard Tromp . 2003-07-30 20:39 warnesgr * R/hapmcmc.R: - Added hapmcmc code submitted by David Duffy. 2003-06-06 09:27 warnesgr * man/binsearch.Rd, man/library.Rd, man/print.LD.Rd: - Fix fuction/documententation argument mismatch. - Fix lack of LF at the end of a couple of files. 2003-06-05 22:06 warnesgr * R/summary.genotype.R: - Added code to show number of alleles, number of individuals genotyped, heterogyosity, and poly. information content based on code contribued by David Duffy. 2003-06-04 21:22 warnesgr * R/plot.LD.R: - Modified string size to only leave vertical space for the number of elements that will be printed. 2003-06-04 21:22 warnesgr * R/genotype.R: - Somehow the assigment of the haplotype function got messed up. Fixed. 2003-06-04 21:21 warnesgr * man/print.LD.Rd: - Updated manual to match code - Replaced 'T' with 'TRUE' 2003-06-04 21:20 warnesgr * R/print.LD.R: - summary functions should have 'object' as the first parameter. 2003-06-04 20:26 warnesgr * DESCRIPTION, NEWS, TODO: Updates for release 1.0.1. 2003-06-04 20:20 warnesgr * R/plot.LD.R, R/print.LD.R, man/print.LD.Rd: - Fixed mislabeling of rows/columns in LDtable - Extended LDtable to handle resizing text to fit area - Extended LDtable to allow slection of what statistics are displayed, and which statistic is used for coloration. - Extended LDtable to allow all columns & rows to be shown - Added a larger example to documentation - Changed the name of some function parameters to be more clear and/or consistent - Added summary.LD.data.frame and print.LD.data.frame 2003-06-03 12:59 warnesgr * R/LD.R: - LD.genotype needs to reject haplotype objects since these are not yet supported by the code. 2003-06-03 11:41 warnesgr * R/genotype.R: - Fix handling of allele names when reorder="no". Apparently, unique() on a matrix now returns a matrix with unique *rows* removed, instead of a vector of unique *elements*. The consequence in this case was that genotype(...,reorder="no") was generating a list of alleles that was a matrix instead of a vector. 2003-05-30 16:08 warnesgr * man/locus.Rd: - added documentation for "value" option. 2003-05-30 15:52 warnesgr * R/library.R, R/zzz.R: - library.pos will now always be defined. Instead of conditionally defining library.pos, a check is made in .First.lib to see whether the system library function has a pos argument. If not, it uses library.pos instead of library to load dependencies. 2003-05-29 02:27 warnesgr * inst/doc/genetics_article.tex: - added ld to conclusion text 2003-05-29 02:23 warnesgr * inst/doc/genetics_article.tex: Updated for version 1.0.0 2003-05-29 02:22 warnesgr * DESCRIPTION, NEWS: - Updated for 0.7.0 2003-05-29 02:20 warnesgr * inst/doc/genetics_article.tex: - Final version to send to Fritz. 2003-05-29 01:55 warnesgr * inst/doc/example.R, inst/doc/genetics_article.tex, inst/doc/make_example_data.R: - Add R code to generate and demo genetics package 2003-05-29 00:36 warnesgr * R/locus.R: - All arguments are now optional. 2003-05-29 00:35 warnesgr * R/genotype.R: - Fix problem with NA's caused by grep bug in R <= 1.7.0. 2003-05-28 20:28 warnesgr * man/locus.Rd: - Add getmarker, getgene, locus<- , marker<-, and gene<- functions. 2003-05-28 20:26 warnesgr * man/write.pop.file.Rd: - Add URL for LinkDos 2003-05-28 20:26 warnesgr * man/undocumented.Rd: - Add alias for to shortsummary function. 2003-05-28 15:09 warnesgr * man/LD.Rd: - Added "locus<-", "marker<-", "gene<-", as well as "getgene", "getmarker" 2003-05-28 15:04 warnesgr * man/library.Rd: - renamed library() to library.pos(). Updated text to correcty note that the backport is from 1.8.0. 2003-05-28 15:01 warnesgr * R/write.pedigree.file.R: - Renamed write.pedigree to write.pedigree.file. - Added URL of LinkDos software. 2003-05-28 14:57 warnesgr * R/library.R, R/zzz.R: - Rename library to library.pos 2003-05-28 14:56 warnesgr * R/locus.R: - Added "locus<-", "marker<-", "gene<-", as well as "getgene", "getmarker" 2003-05-27 21:18 warnesgr * R/print.LD.R, man/print.LD.Rd: - Added show.all argument - Fixed code that omits blank row/column 2003-05-27 19:37 warnesgr * man/write.pop.file.Rd: - Add documentation for write.pop.file, write.pedigree.file, write.marker.file. 2003-05-27 18:45 warnesgr * man/diseq.Rd, man/genotype.Rd, man/makeGenotypes.Rd, man/summary.genotype.Rd: - Fix typos, update arguments to match changes to code 2003-05-27 18:43 warnesgr * R/library.R, man/library.Rd: - Added temporary copy of library() function. This copy will only be installed if the global library() function does not define a 'pos' argument. This code was backported from R-devel, and R 1.7.1 and later will include it as part of base. 2003-05-27 18:41 warnesgr * R/write.pedigree.file.R, R/write.pop.file.R: - Add utility functions to write pedigree, 'pop', and marker files which are used to transfer data to genetics applications. 2003-05-27 18:36 warnesgr * R/zzz.R: - Use new library function to load MASS in search position *3* before loading gregmisc. This prevents the genotype dataset in MASS from hiding the genotype function here. 2003-05-27 18:35 warnesgr * R/genotype.R: - fixed handling of genotype("") and similar - improvements to "[<-.genotype", it now automatically converts the second argument to a genotype object. 2003-05-27 18:33 warnesgr * R/diseq.R: - Add call item to diseq.object giving original function call - Fixed bug in testing for 2 x 2 allele case 2003-05-27 18:32 warnesgr * R/plot.LD.R, R/print.LD.R, man/print.LD.Rd: - Add plot and print methods for LD objects. 2003-05-27 18:30 warnesgr * R/LD.R: - Found and fixed bug in likelihood computation. The count table needed to be organized with high-frequency alleles in the upper left corner instead of the lower right corner. 2003-05-22 17:25 warnesgr * R/HWE.chisq.R, R/HWE.exact.R, R/HWE.test.R, R/LD.R, R/binsearch.R, R/ci.balance.R, R/genotype.R, R/gregorius.R, R/locus.R, R/makeGenotypes.R, R/plot.LD.R, R/print.LD.R, R/summary.genotype.R, R/zzz.R: - Remove CVS Log tag, which was eating up too much space. Just use 'cvs log' to get the comments if needed! 2003-05-22 16:22 warnesgr * R/LD.R, R/plot.LD.R, R/print.LD.R: - moved LD printing functions to print.LD.R - moved LD plotting functions to plot.LD.R - fixed problems in print.LD.data.frame - enhanced plot.LD.data.frame - other small changes 2003-05-21 20:03 warnesgr * R/makeGenotypes.R: - Remove stray character that caused a syntax error. 2003-05-21 20:03 warnesgr * R/summary.genotype.R: - Fix handling of genotype summary when called from summary.data.frame. Was broken by too-broad search and replace... but the changes motivated enhancements. ;^) 2003-05-21 19:57 warnesgr * DESCRIPTION, R/zzz.R: - Added dependency on gregmisc package. 2003-05-21 19:46 warnesgr * R/LD.R, man/LD.Rd, man/print.LD.Rd: - Improvements to LD code and documentation. 2003-05-20 16:46 warnesgr * R/makeGenotypes.R, man/makeGenotypes.Rd: - Reduce stringency for considering a variable a genotype. 2003-05-20 16:43 warnesgr * R/LD.R, man/LD.Rd: - Add code & (incomplete) docs for linkage disequilibrium 2003-05-16 18:39 warnesgr * DESCRIPTION, R/makeGenotypes.R, inst/doc/Rnews.sty, inst/doc/genetics_article.tex, man/makeGenotypes.Rd: - Updated to version 0.7.0 - Made changes to pass R CMD check 2003-05-16 15:50 warnesgr * R/makeGenotypes.R, man/makeGenotypes.Rd: - Added makeGenotypes/makeHaplotypes to help convert variables in dataframes to genotype/haplotype variables. 2003-04-07 20:30 warnesgr * R/diseq.R, man/diseq.Rd: - Flipped sign of D, D', r. Now D matches sign given in Weir's book, and r has the proper sign. 2003-03-07 14:52 warnesgr * R/HWE.exact.R, man/HWE.exact.Rd: - Modified HWE.exact to return an object of class 'htest' - Noted this change in the man file and added HWE.chisq to list of links and to example code. 2003-03-07 14:49 warnesgr * DESCRIPTION: - Updated version number to 0.6.7. 2003-03-07 14:47 warnesgr * man/HWE.test.Rd: - Added links to HWE.chisq, HWE.exact, genotype to see also seciton. - Slighlty modified example code. 2003-03-07 14:44 warnesgr * NEWS: - New file 2003-03-07 14:33 warnesgr * R/genotype.R, man/genotype.Rd: - Added nallele function to compute the number of alleles. 2003-03-07 14:32 warnesgr * R/HWE.chisq.R, R/HWE.test.R, man/HWE.chisq.Rd, man/HWE.test.Rd: - Created HWE.chisq, HWE.chisq.genotype and corresponding man page. - Moved computation of Chisquare test for HWE from HWE.test.genotype to HWE.chisq.genotype. - Added option (on by default) to compute the exact p-value using HWE.exact. This is on by default when nallele=2 2003-02-03 16:13 warnesgr * DESCRIPTION, inst/doc/genetics_article.tex, man/HWE.exact.Rd, man/binsearch.Rd, man/gregorius.Rd: - Fixed typos and R CMD check warnings. - Updated version number - Removed 'data' directory to fix new R CMD check warning. 2002-12-11 21:29 warnesgr * R/binsearch.R: - fixed typo 2002-12-11 21:07 warnesgr * R/binsearch.R, R/gregorius.R, man/binsearch.Rd, man/gregorius.Rd: - Moved binsearch() into a separate file and added documentation. - Simplified and documented binsearch() code. - binsearch() now detects whether the function is increasing or decreasing and acts accordingly. - Updated gregorius() to use the modified binsearch. 2002-12-10 20:36 warnesgr * man/gregorius.Rd: - Updated title/description 2002-12-10 20:33 warnesgr * R/gregorius.R, man/gregorius.Rd: - Implemented gregorius() function, replacing data frame gregorius. - Re-created corresponding help page. 2002-12-02 17:23 warnesgr * man/gregorius.Rd: - Added cvs tags to header of gregorius.Rd 2002-12-02 17:13 warnesgr * data, data/00Index, data/gregorius.R, man/gregorius.Rd: - Added data set (and documentation) 'gregorius' which contains necessary samples sizes to detect alleles. 2002-12-02 16:16 warnesgr * man/HWE.exact.Rd: - Added HWE.exact.Rd. 2002-12-02 16:12 warnesgr * R/HWE.exact.R: - Now returnes only the computed P-value. 2002-12-02 15:40 warnesgr * R/HWE.exact.R: - Added code for HWE.exact, based on contributed function by David Duffy 2002-11-27 15:32 warnesgr * DESCRIPTION, R/HWE.test.R, R/diseq.R, R/genotype.R, TODO, inst/doc/genetics_article.tex, man/HWE.test.Rd, man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd, man/locus.Rd, man/summary.genotype.Rd, man/undocumented.Rd: Correct spelling errors and typos. 2002-11-13 20:18 warnesgr * DESCRIPTION: - Fix typo. 2002-11-12 19:59 warnesgr * DESCRIPTION, R/diseq.R, R/genotype.R: - Changes to remove warnings generated by 'R CMD check'. 2002-11-12 19:58 warnesgr * man/HWE.test.Rd, man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd, man/homozygote.Rd, man/locus.Rd, man/summary.genotype.Rd, man/undocumented.Rd: - Changes to remove warnings generated by 'R CMD check'. 2002-11-12 17:57 warnesgr * R/zzz.R: - diseq.ci now requires the combinat library instead of boot. 2002-11-12 05:53 warnesgr * examples/test.ci.R: - Checkin of test.ci.R 2002-11-12 05:31 warnesgr * DESCRIPTION: - Bump version number 2002-11-12 05:31 warnesgr * R/genotype.R, R/locus.R, man/diseq.Rd, man/genotype.Rd, man/homozygote.Rd: - Fix mismatches between documentation and code that we generating warning messages. 2002-11-11 22:56 warnesgr * R/diseq.R: - Added minval and maxval to ci.balnance call() in diseq.ci() - Fixed typo in output text. 2002-11-08 21:07 warnesgr * DESCRIPTION, R/genotype.R, R/summary.genotype.R, TODO, man/HWE.test.Rd, man/genotype.Rd, man/homozygote.Rd, man/locus.Rd, man/summary.genotype.Rd, man/undocumented.Rd: - DESCRIPTION: Updated version number and date - TODO: Updated todo list. 2002-11-08 19:54 warnesgr * tests, tests/ci.balance.R: Added tests for ci.balance() functon. 2002-11-08 19:53 warnesgr * R/ci.balance.R, R/diseq.R, man/ci.balance.Rd, man/diseq.Rd: - Moved ci.balance() to a separate file and created a documenation file for it. - Modified ci.balance to better annotate when it uses boundary values. - Modified diseq.ci to better provide warning message when the number of alleles is greater than 3. 2002-11-08 17:20 warnesgr * R/HWE.test.R, R/diseq.R: - Added test for more than two alleles to diseq.ci. If there are more than two, generate a warning message indicating that confidence intervals for values near 0 and 1 are ill-behaved. When 'correct=TRUE' use ci.balance to attempt to correct for this. - Modified HWE.test to display warnings from diseq.ci. 2002-11-07 19:13 warnesgr * R/diseq.R: - Fixed code so that gentypes with some listed allele not observed are handled properly. For example, if we have "A/A", and "A/B", but no "B/B", or worse yet when we know that "A" and "B" allels are both possible but we only see one. 2002-10-28 18:20 warnesgr * R/genotype.R: - Allow allele names to be specified for as.genotype.allele.count(). 2002-10-28 18:19 warnesgr * R/summary.genotype.R: - Fixed for syntax error in summary.genotype() 2002-10-28 18:19 warnesgr * R/HWE.test.R, R/diseq.R: - Lots of changes to the disequlibrim computation and confidence interval code. - D, D', and R are now computed - Overall values are reported *with sign* of the number of alleles is 2 - Bootstrapping code is now more efficient - Changes to HWE.test() and print.hwe.test() corresponding to the above changes 2002-10-24 21:43 warnesgr * DESCRIPTION, R/diseq.R, R/genotype.R, man/genotype.Rd: - Fixed bug as.genotype.alllele.count() introduced when 'harmonizing' methods with generics. - Added 'alleles' arguments to the as.genotype.alllele.count() function. - Added example code for as.genotype.alllele.count() to doc file. - Added explicit mention of as.genotype.alllele.count() to doc file. 2002-10-11 18:01 warnesgr * R/HWE.test.R, R/diseq.R, R/zzz.R: Updated version number. 2002-09-30 14:35 warnesgr * R/diseq.R: - Modified diseq() to retain sign on the overall disequlibrium estimate - Modified diseq.ci() to use percentile confidence intervals 2002-09-24 01:53 warnesgr * DESCRIPTION: - Updated version number - Added 'computing disequilibrium' to description text. 2002-09-24 01:32 warnesgr * R/HWE.test.R, R/diseq.R, R/genotype.R, R/zzz.R, man/HWE.test.Rd, man/diseq.Rd, man/genotype.Rd, man/summary.genotype.Rd: - 'Un-genericized' diseq() - Moved documentation of diseq() and diseq from HWE.test.Rd to diseq.Rd - Cleaned up HWE.test.Rd and diseq.Rd - Fixed broken class check in diseq() and diseq.ci() - Removed allele.count.default() -- this will force the user to explicitly call 'genotype' on the data to use allele.count(). - Added zzz.R to require package 'boot' 2002-09-24 00:02 WarnesGR * R/HWE.test.R, R/diseq.R, man/HWE.test.Rd: - Moved code that computed D-hat to diseq() and diseq.genotype() in diseq.R. - Added diseq.ci() to compute confidence interval for D-hat. - Added code to call diseq() and diseq.ci() from HWE.test() - Added arguments to HWE.test() and print.HWE.test() to control these new features - Added text to HWE.test.Rd documenting these new functions and arguments 2002-09-23 20:08 warnesgr * R/genotype.R: - Added as.genotype.table() 2002-06-27 18:46 warnesgr * inst/doc/genetics_article.tex: - More revisions. Hopefully last set before submission to publication review. 2002-06-27 18:46 warnesgr * R/HWE.test.R, examples/HWE_Test.R: - Allow user to specify parameters for the chisquare test. 2002-06-25 21:38 warnesgr * inst/doc/genetics_article.tex: - Fixed syntax errors - Some reorganization 2002-06-19 11:17 warnesgr * man/locus.Rd: - Fixed typo in \seealso. 2002-06-19 10:34 warnesgr * inst/doc/genetics_article.tex: Much enhancement, including addition of example section. 2002-06-19 00:13 warnesgr * R/HWE.test.R: - Fixed bug that caused 'Error: subscript out of bounds' when a 2 allele genotype had 1/1 and 1/2 but not 2/2. 2002-06-18 20:42 warnesgr * DESCRIPTION: Updated version. 2002-06-18 20:41 warnesgr * R/genotype.R, man/summary.genotype.Rd: - Fixed a bug in allele.count that resulted in infinite recuresion. - Modified documentation to match changed code. 2002-06-18 19:38 warnesgr * DESCRIPTION, R/genotype.R, R/summary.genotype.R, man/HWE.test.Rd, man/genotype.Rd, man/locus.Rd, man/summary.genotype.Rd: Changes to fix problems reported by R CMD check. 2002-05-06 18:35 swietm * 7, TODO: Testing CVS functionality. Removed addewd characters to TODO 2002-05-06 18:31 swietm * 7, TODO: This was a test to learn how to add and modify files using CVS 2002-04-09 00:49 warneg * inst, inst/doc, inst/doc/Rnews.sty, inst/doc/genetics_article.tex: - Initial checkin of article sources 2002-04-08 23:24 warneg * DESCRIPTION, man/homozygote.Rd: First checkin after moving repository from tuwein. 2002-04-08 23:23 warneg * man/genotype.Rd: - Noted that when the user specifies the alleles non-matching elements are converted to NAs. 2002-04-08 23:19 warneg * R/genotype.R: - Modified 'genotype' function so that when the user specifies the alleles non-matching elements are converted to NAs. 2002-02-21 03:09 warnes * R/genotype.R, man/genotype.Rd, man/undocumented.Rd: - Add as.factor.genotype. 2002-02-14 12:55 warnes * DESCRIPTION: Rephrased description. 2002-02-14 12:55 warnes * R/HWE.test.R, R/genotype.R: Fixed bugs in [.genotype and [.haplotype. - There was a serious typo that would have been cought had I just done R CMD check. - Revamped [.genotype and [.haplotype to work correctly and to avoid the overhead of calling genotype() or haplotype() when drop=T. I think these finally work properly. 2002-02-14 12:48 warnes * man/HWE.test.Rd, man/genotype.Rd, man/undocumented.Rd: - Added 'keywords' to HWE.test - Create undocumented.Rd to satisfy documentation requiremets for objects not otherwise included in documentation - Add 'alais' commands noting that 'genotype' and '[.haplotype' are documented here. 2002-02-14 12:37 warnes * man/genotype.Rd: - Small change to the example code. 2002-02-09 00:47 warnes * R/genotype.R: - Fixed the changes to "[.genotype" and "[.haplotype". I was incorrectly coping *all* of the attributes in the case of drop=T. This caused mis-labeling of the underlying factor levels. 2002-02-07 17:08 warnes * man/genotype.Rd: Added examples related to two bugs, - == with non-genotype/non-haplotype rhs, and - [...,drop=T] . 2002-02-07 16:57 warnes * R/genotype.R: Fixed two bugs 1) "[.genotype" and "[.haplotype" didn't have the 'drop' argument, so an error would be generated when used in a context that expected it (like lm(..., subset=something) ). I've implemented these so that drop=T not only drops unused factor levels, but also drops unused *allele* levels. 2) "==.genotype" and "==.haplotype" didn't handle second arguments that weren't genotypes / haplotypes, so x <- genotype( "A/B" ) x == "A/B" would generate an error. Solved by converting the y argument to a genotype / haplotype before the comparison. Note that if the lhs is a genotype this means x == "A/B" and x == "B/A" give the identical results. 2001-08-13 15:36 warnes * R/HWE.test.R: BUGFIX: Corrected problem where the allele order was not consistent between the first (Observed #) and second columns (Expected #) of the HWE.test table. This caused incorrect values for Obs-Exp to be calcuated, as well as incorrect D-hat estimates. Fortunately, it did not effect the correctness of the test statistic or p-value, since these were computed via the chisq function. 2001-08-03 11:33 warnes * DESCRIPTION, man/genotype.Rd: Minor changes. 2001-06-28 19:26 warnes * R/chisq.test.R: Will let Fritz and Kurt negotiate any changes/modifications to chisq.test. 2001-06-28 19:23 warnes * R/genotype.R: Minor change, mask off extra attributes when calling print() to dislplay genotype data. 2001-06-28 19:15 warnes * man/HWE.test.Rd: - Updated to match v1.4 of HWE.test.R. - Added CVS id and log fields to file. 2001-06-28 19:14 warnes * R/HWE.test.R: - Modified to use chisq.test(...,simulate.p.value=T,B=10000) to use simulated p-value so that assumptions underlying Chi-square approximation need not hold. This particularly useful for small sample sizes or when some allele pairs are not observed. - Now gives a table of observed counts, observed frequency, expected frequency, and disequilibrium statistic (D-hat) for each pair of alleles in addition to the overall disequilibrium statistic (D-hat). 2001-06-15 17:02 warnes * DESCRIPTION, R/HWE.test.R, R/chisq.test.R, R/genotype.R, TODO, examples/Genomics.examples, man/HWE.test.Rd, man/genotype.Rd, man/homozygote.Rd, man/locus.Rd, man/summary.genotype.Rd: - Modified HWE.test to use chisq.test. Added a modified version of chisq.test until the (minor) changes show up in ctest. - Fixed documentation links and alias omissions - Fixed getallele() to snag allele element or attribute if either is present. This makes it work for summary.genotype as well as for genotype. 2001-06-13 20:00 warnes * R/summary.genotype.R: - Added "allele.names" attribute. 2001-06-13 17:03 warnes * R/HWE.test.R, man/genotype.Rd: - Updated HWE.test.R to not assume that a summary.genotype object contains the original genotype object. - Removed a duplicate link to "allele.names" from genotype.Rd. 2001-05-30 22:15 warnes * man/HWE.test.Rd: Added HWE.test.Rd to document HWE.test. 2001-05-30 22:12 warnes * R/HWE.test.R, R/genotype.R, R/locus.R, TODO, examples/Genomics.examples, man/genotype.Rd, man/homozygote.Rd, man/summary.genotype.Rd: Updated documentation mostly. Added as.character.genotype(). 2001-05-30 22:03 warnes * man/locus.Rd: Initial version of locus.Rd. 2001-05-29 17:42 warnes * man/summary.genotype.Rd: Updated to note that row for NA is only present if the data contains NA. Corresponds to revision 1.2 of summary.genotype.R. 2001-05-29 17:38 warnes * man/genotype.Rd, man/summary.genotype.Rd: Modified seealso(). 2001-05-29 17:16 warnes * man/homozygote.Rd: Completed homozygote.Rd which documents homozygote(), heterozugote(), carrier(), allele(), and allele.cound(). 2001-05-29 10:27 leisch * R/summary.genotype.R: add NA line only if NA's are present 2001-05-26 00:28 warnes * man/homozygote.Rd: Partially completed man/homozygote.Rd containing documentation for homozygote(), heterozygote(), carrier(), allele.count(), and allele(). 2001-05-26 00:26 warnes * R/genotype.R: Removed allele.ind() and added "any" parameter to carrier(). When more than one allele is selected, or when no alleles are slected and any=F, carrier() now acts as allele.ind() did. Modified allele.count() to have similar behavior. 2001-05-25 23:39 warnes * man/genotype.Rd: Added man/genotype.Rd to document genotype and haplotype classes in R/genotype.R. 2001-05-25 23:37 warnes * R/genotype.R, R/summary.genotype.R, man, man/summary.genotype.Rd: Moved summary.genotype and print.summary.genotype into a separate file (R/summary.genotype.R). Added man/summary.genotype.Rd containing documentation for summary.genotype. 2001-05-22 20:26 warnes * R/Gene.R, R/Genomics.R: classes defined in Gene.R substantially rewritten and moved to locus.R. Contents of Genomics.R moved to genotype.R. 2001-05-22 20:23 warnes * examples/locus.example.R: Added more examples 2001-05-22 19:00 warnes * examples/locus.example.R: Initial checkin of test script for code in locus.R. 2001-05-22 18:58 warnes * R/locus.R: - Renamed "location.X" to "as.character.X" to better represent thier function. (Note as.character isn't generic at the moment, so these functions must be called directly.) - added function getlocus() to grab the appropriate locus field or attribute from an arbitrary object. 2001-05-22 18:53 warnes * R/genotype.R: - Renamed "genotype.R" from "Genomics.R". - Added slot for "locus" into genotype class. - Made allele.count, allele.ind, heterozygote, homozygote, and carrier return objects with the same class and created print.X routines. This enabled the next item.. - Made "locus" propagate to summary, HWE.test, allele, allele.count, allele.ind, heterozygote, homozygote, and carrier. This should make it easier to keep track of what locus each of these correspond to. **This may create unanticipated side effects** 2001-05-22 18:21 warnes * R/locus.R: Created classes for "locus", "gene", and "marker" along with basic methods is.X, print.X, and generic utility function "location", which formats the locus infromation for printing. 2001-05-16 12:58 leisch * R/Genomics.R: cosmetics 2001-05-16 12:55 leisch * R/Genomics.R: genotype: bugfix for non-character allele vectors (e.g., integers) a2 is now ignored if a1 is a genotype a1 can now also be a 2 column matrix of alleles 2001-05-10 16:15 leisch * DESCRIPTION: update 2001-05-10 16:07 leisch * R/Genomics.R: cosmetics 2001-05-07 13:22 warnes * examples, examples/Allele_Freq.R, examples/Allele_Freq.out, examples/Examples.new, examples/Examples.out, examples/Gene.examples, examples/Genomics.examples, examples/HWE_Test.R, examples/HWE_Test.out, examples/test.data.2.txt, examples/test.data.txt: Added example files, code, and output. 2001-05-07 13:21 warnes * R, R/Gene.R, R/Genomics.R: Imported R code for - Genotype and Haplotype classes, - corresponding summary function (gives allele and genotype frequencies) - Hardy-Weinburg Equilibrium testing. Also, a initial try at a Gene and Marker classes. 2001-05-03 13:07 leisch * ., DESCRIPTION: Initial revision