2023-08-14 Ana Vazquez *[r107] DESCRIPTION Email, and version number update 2023-08-11 Paulino Perez Rodriguez *[r106] src/pedigree.c Package pedigreemm version 0.3-3 Package built using 83394/R 4.3.0; x86_64-pc-linux-gnu; 2022-12-03 04:01:43 UTC; unix Checked with rchk version 29e18222e1cfa67ba8e63bd3b22a25f78593c554 LLVM version 14.0.5 More information at https://github.com/kalibera/cran-checks/blob/master/rchk/PROTECT.md For rchk in docker image see https://github.com/kalibera/rchk/blob/master/doc/DOCKER.md Suspicious call (two or more unprotected arguments) to Rf_setAttrib at pedigree_chol pedigreemm/src/pedigree.c:46 The rchk tool detected a memory protection bug in the file pedigree.c (line 46) that was fixed in this version. Only three lines of code were modified: before: setAttrib(ans, install("F"), allocVector(REALSXP, n)); now has ben replaced with: SEXP tmp2 = PROTECT(allocVector(REALSXP, n)); setAttrib(ans, install("F"), tmp2); and a call to the UNPROTECT() macro was added at the end of the function: UNPROTECT(1); return ans; 2013-07-22 Ana Vazquez * [r105] man/pedigreemm.Rd: Add example. * [r104] R/pedigree.R: put labels to return of the functions relfactor, A and Ainverse * [r103] R/pedigree.R: added indexing in rownames(Zt)[rowsi] 2012-08-19 Ana Vazquez * [r102] man/editPed.Rd: Correction F by FALSE; new release. * [r101] R/pedigree.R: fix parentheses in the code 2012-08-17 Ana Vazquez * [r100] NAMESPACE: Include functions editPed getA getAInv * [r99] R/pedigree.R: created functions editPed getA getAInv getGenAncestors 2009-05-29 Douglas Bates * [r98] man/relfactor.Rd: Change man page for new default values * [r97] DESCRIPTION, R/pedigree.R: Correction to relfactor; new release. 2009-05-29 Ana Vazquez * [r96] man/relfactor.Rd: Cholesky() substituted by chol() * [r95] R/pedigree.R: * [r94] man/relfactor.Rd: bug in relfactor computation and modification in relfactor.Rd 2009-05-20 Douglas Bates * [r92] DESCRIPTION, man/pedigreemm-class.Rd: New release with corrected links for external S4 classes 2009-05-14 Douglas Bates * [r90] DESCRIPTION: New release * [r89] man/pedigreemm-class.Rd: Rather ugly fix for codoc complaint 2009-04-20 Ana Vazquez * [r88] R/pedigree.R: ZStar 2009-04-16 Douglas Bates * [r87] DESCRIPTION, R/pedigree.R: Adding lmer_Zstar, new version 2009-04-09 Ana Vazquez * [r86] man/pedCowsR.Rd: modification in pedCowsR.Rd 2009-03-10 Ana Vazquez * [r85] man/pedCowsR.Rd: adding documentation for pedCowsR 2009-03-04 Douglas Bates * [r84] R/pedigree.R, man/pedigreemm-class.Rd: Corrections to the ranef method 2009-02-26 Ana Vazquez * [r83] data/pedCowsR.rda: modified name in pedCowsR to avoid conflicts 2009-02-26 Douglas Bates * [r82] man/pedSires.Rd: Remove links to the dC object * [r81] NAMESPACE: Export the Dmat function * [r80] R/pedigree.R: Remove diff markings 2009-02-25 Ana Vazquez * [r79] data/pedCows.rda, data/pedCowsR.rda: adding a reduced pedCows called pedCowsR * [r78] data/pedCows.rda: new file pedCows.rda 2009-02-25 Douglas Bates * [r77] man/pedigreemm-class.Rd, man/pedigreemm.Rd: * [r76] R/pedigree.R: Define ranef method for the pedigreemm class 2009-02-23 Ana Vazquez * [r75] man/inbreeding.Rd: modifications in inbreeding.Rd * [r74] man/Dmat.Rd: adding the manual for Dmat function * [r73] man/Dmat.Rd: adding the manual for Dmat function * [r72] R/pedigree.R, data/dC.rda, data/mp.rda, data/pedCow.rda, man/dC.Rd, man/mp.Rd, man/pedCow.Rd: d 2009-02-16 Ana Vazquez * [r71] data/mastitis.rda, data/milk.rda, data/pedCows.rda: update of file names mastitis, milk, pedCows * [r70] man/mastitis.Rd, man/milk.Rd, man/pedCows.Rd: update of names mastitis, milk, pedCows 2009-02-10 Douglas Bates * [r69] R/pedigree.R: Switch pedigreemm to return class pedigreemm * [r68] R/pedigree.R: Updates for Dmat and inbreeding 2009-01-27 Ana Vazquez * [r67] man/dC.Rd: dC documentation * [r66] man/mp.Rd: mp documentation * [r65] data/mp.rda: mp with id and sire as factors 2009-01-26 Douglas Bates * [r64] DESCRIPTION, NAMESPACE, R/AllClass.R, R/pedigree.R, man/inbreeding.Rd, man/mp.Rd, man/pedCow.Rd, man/pedigree-class.Rd, man/relfactor.Rd: Changes prior to initial release of package * [r63] man/pedCow.Rd, man/pedCow5.Rd: Move to correct name 2009-01-09 Douglas Bates * [r62] NAMESPACE: Export the pedigreemm function * [r61] R/lmerZStar.R, R/pedigree.R: Initial form of pedigreemm (currently undocumented) * [r60] NAMESPACE: Import the Matrix package to get generics and methods 2009-01-08 Ana Vazquez * [r59] data/pedCow.rda: pedCow.rda matching the mp.rda * [r58] data/mp.rda: mp.rda example with different identifications 2009-01-06 Douglas Bates * [r57] man/pedCow5.Rd: Add docs * [r56] man/sirePedigree.Rd: Add docs * [r55] DESCRIPTION: New release * [r54] R/lmerZStar.R, R/pedigree.R: Cleanup * [r53] data/dC.rda, data/dairyCattle.rda, data/pedSires.rda, data/sirePedigree.rda, man/dC.Rd, man/dairyCattle.Rd, man/pedSires.Rd: Removing large data frame and pedigree 2008-09-15 Ana Vazquez * [r52] data/pedCow.rda: pedigree for milk production example * [r51] data/mp.rda: small example milk production * [r50] data/pedSires.rda: pedigree for smaller example * [r49] data/dC.rda: smaller example for mastitis 2008-08-29 Douglas Bates * [r48] R/AllClass.R, R/pedigree.R: Updating of pedigree functions 2008-07-15 Ana Vazquez * [r47] inst/LSi1862_2dig.rda: Chol(ped) for sires of dairyCattle 2008-07-11 Ana Vazquez * [r46] data/dairyCattle.rda, data/sirePedigree.rda: dairyCattle and Pedigree with different labels 2008-07-11 Douglas Bates * [r44] DESCRIPTION, inst, inst/doc, inst/doc/Methods.txt: New version. Add inst/doc * [r43] R/lmerZStar.R: Move to the doFit = FALSE argument in lmer and glmer 2008-06-23 Douglas Bates * [r42] R/pedigree.R: Add the corrected version of Linv * [r41] man/dairyCattle.Rd: Correct the record count * [r40] NAMESPACE: Import the chol generic from Matrix * [r39] R/pedigree.R: Add a (hidden) Linv function 2008-06-18 Ana Vazquez * [r38] R/lmerZStar.R: fixing bug: FL$fl[[i]]$Zt instead of FL$trms[[i]]$Zt 2008-05-25 Douglas Bates * [r36] R/lmerZStar.R: Use FL$fl, not just FL after modifications to factor list generator 2008-05-19 Ana Vazquez * [r35] data/dairyCattle.rda: Remove repeated and incorrect observations. 2008-05-12 Douglas Bates * [r34] R/lmerZStar.R: update lmer_ZStar to new form of lmerFactorList value 2008-04-22 Douglas Bates * [r32] DESCRIPTION: new release * [r31] NAMESPACE, R/pedigree.R, man/pedigree-class.Rd, src/pedigree.c: Remove chol method, which was not working anyway and would be horribly expensive * [r30] data/dairyCattle.rda, man/dairyCattle.Rd: Remove redundant levels of the sire factor 2008-04-08 Douglas Bates * [r29] man/dairyCattle.Rd: Update documentation 2008-04-07 Douglas Bates * [r27] NAMESPACE, R/AllClass.R, R/pedigree.R: Add class pedinbred to calculate and store the inbreeding * [r26] src/pedigree.c: cleaned up code in pedigree_inbreeding * [r25] DESCRIPTION, data/pedigreeSires.rda, data/sirePedigree.rda, man/sirePed.Rd, man/sirePedigree.Rd: Move pedigrees to name sirePedigree; New release * [r24] man/sirePed.Rd: Commit changes prior to removing 2008-04-07 Ana Vazquez * [r22] data/pedigreeSires.rda: adding the pedigree of the sires. 2008-04-07 Douglas Bates * [r21] man/Holstein.Rd: Data set is no longer called Holstein * [r20] data/dairyCattle.Rd, man/dairyCattle.Rd: Move documentation file to man directory * [r19] data/dairyCattle.Rd: Remove horrible list of factor levels 2008-04-04 Ana Vazquez * [r18] data/dairyCattle.Rd: add dairyCattle.Rd file 2008-04-03 Ana Vazquez * [r17] data/dairyCattle.rda: add dairyCattle.rda and remove Holstein.rda * [r16] data/Holstein.rda, data/sirePed.rda: add dairyCattle.rda and remove Holstein.rda 2008-04-02 Douglas Bates * [r15] DESCRIPTION: Correct form of Maintainer: field; New release. 2008-03-26 Douglas Bates * [r13] man/Holstein.Rd, man/pedigree-class.Rd, man/sirePed.Rd: Documentation update * [r12] DESCRIPTION: New version * [r11] man/Holstein.Rd: Documentation for Holstein data set * [r10] data/Holstein.rda, data/pedigreeModif.txt, data/sirePed.rda: Add the sire pedigree data set * [r9] data/Holstein.rda, data/example.rda, data/example.txt: Move data set named "example" to "Holstein" 2008-03-25 Ana Vazquez * [r7] data, data/example.rda, data/example.txt, data/pedigreeModif.txt: adding example data and pedigree 2008-03-17 Douglas Bates * [r6] DESCRIPTION, R/lmerZStar.R: Modifications after testing the package * [r5] R/lmerZStar.R: Initial version of lmer_Zstar; updated dependencies * [r3] README: Remove unnecessary README 2008-03-11 Douglas Bates * [r2] pkg/DESCRIPTION, pkg/NAMESPACE, pkg/R/AllClass.R, pkg/R/pedigree.R, pkg/man/pedigree-class.Rd, pkg/man/pedigree.Rd, pkg/src, pkg/src/init.c, pkg/src/pedigree.c, pkg/src/pedigree.h: Initial version transferred from the lme4 package