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| + | ====== Updates and changes to WOMBAT ====== | ||
| + | |||
| + | This page tries to keep track of what has been changed in WOMBAT and when — including `bug' fixes. | ||
| + | |||
| + | ==== 2014 ==== | ||
| + | |||
| + | == 10/09/2014 == | ||
| + | |||
| + | Some minor bug fixes. Added option to store *.gin matrix in core. | ||
| + | |||
| + | ==== 2013 ==== | ||
| + | |||
| + | == 19/11/2013 == | ||
| + | |||
| + | Fixed bug affecting runs using the --snap option when multiple SNPs were fitted simultaneously. | ||
| + | |||
| + | == 4/9/2013 == | ||
| + | |||
| + | Added: trial versions compiled for Windows (both 32 and 64 bit) using the gfortran cross-compiler on a Linux host. These have all the features of the Linux versions, but had very little testing - beware! | ||
| + | |||
| + | == 22/7/2013 == | ||
| + | |||
| + | Added: [[wombat:ex17page|Example 17]] to illustrate approximation of sampling variances for complicated functions of covariances via sampling from a multivariate normal distribution. | ||
| + | |||
| + | == 19/3/2013 == | ||
| + | |||
| + | Linux versions updated: Changed sparse matrix computations to take advantage of "supernodes" - this speeds up computations but can require quite a bit more memory. Run time option ** −−old** is provided to switch back to the previous scheme. | ||
| + | |||
| + | The speed up achieved varies greatly with the "quality" of the BLAS and LAPACK routines used - best for the I7 (MKL library) and LF64 (ATLAS library) versions, not quite so good for the PATH64/32 or LF95 versions which are compiled on older machines with only the reference libraries. | ||
| + | |||
| + | == 1/3/2013 == | ||
| + | |||
| + | Added run option ** −−dense**; aimed at analyses with a dense, user-defined covariance matrix among random effects (e.g. genomic relationship matrix); not everything works yet; dense calculations rely on LAPACK and BLAS libraries. also new: 64bit version compiled for I7 processor using Intel ifort compiler and MKL library. | ||
| + | |||
| + | |||
| + | ==== 2012 ==== | ||
| + | |||
| + | ==15/08/2012 == | ||
| + | |||
| + | Downloads updated. New: facility to fit "social" genetic effects & [[wombat:ex16page|Example 16]] to illustrate it. | ||
| + | |||
| + | == 21/5/2012 == | ||
| + | |||
| + | Berenice H. reported that WOMBAT scrambled the starting values supplied for certain types of random regression models. Fixed. | ||
| + | |||
| + | == 19/4/2012 == | ||
| + | Update downloads. New option** −−pool**: allows pooling of estimates from part analyses using penalized maximum likelihood; illustrated in [[wombat:ex15page|Example 15]]. | ||
| + | ==== 2011 ==== | ||
| + | |||
| + | == 25/9/2011 == | ||
| + | Updated Linux versions and examples. New: Example13 & Example14, option TSELECT for RPTCOV, −−nonly for analysis of first n records only, | ||
| + | −−nolsq to skip LSQ analysis for fixed effects and **−−snap** for GWAS analysis. | ||
| + | |||
| + | == 24/2/2011 == | ||
| + | |||
| + | Added section on fitting imprinting effects to [[wombat:specialanalyses|Specialized analyses]]; added example4/D to illustrate. | ||
| + | |||
| + | ==22/2/2011 == | ||
| + | Revamped options for penalized estimation; updated manual, Linux versions & example5/D. | ||
| + | |||
| + | ==== 2010 ==== | ||
| + | |||
| + | == 14/4/2010 == | ||
| + | Updated linux versions: option MRR enabled (full rank analyses only) -- beware, has only been tested for a simple bivariate case. | ||
| + | New special option RPTCOV & new option ONE for random regression basis functions. | ||
| + | |||
| + | ==== 2009 ==== | ||
| + | |||
| + | == 4/12/2009 === | ||
| + | New options: ''−−redped'' switches on pedigree reduction for sire model; ''IDE'' as code for basis functions for random regression models; data subset selection for specified range of values of a covariable. | ||
| + | |||
| + | == 4/8/2009 == | ||
| + | John K. noted that fitting correlated random effects did not work for effects with the GIN option; fixed. | ||
| + | |||
| + | |||
| + | == 5/4/2009 == | ||
| + | Changed rules for sire model analyses: require "subject" identifier in data & model part of parameter file. | ||
| + | |||
| + | == 31/03/2009 == | ||
| + | Romain D. reported a problem for an analysis with many dependencies among fixed effects -- increased limit and improved fault trapping for exceeding the maximum number. | ||
| + | |||
| + | == 27/03/2009 == | ||
| + | Added checks for sorting of data file; new SPECIAL option CLONES. Analyses with very low (<10% but >0%) proportions of repeated records for a trait are no longer accepted. | ||
| + | |||
| + | == 21/01/2009 == | ||
| + | Changes made last year caused WOMBAT to no longer recognise the ''DIAG'' option for random effect covariance matrices; fixed. Option ''––choozhz'' was only recognised for animal model analyses; now enabled for sire models as well. | ||
| + | |||
| + | ==== 2008 ==== | ||
| + | |||
| + | == 17/10/2008 == | ||
| + | |||
| + | Christie I. reported that the COVZER option did not work properly for multivariate analyses with numbers of covariates differing between traits. | ||
| + | Klint G. found that the Windows versions had problems if data and pedigree file were the same. Both fixed. | ||
| + | |||
| + | Added facility to read in "pre-defined" inbreeding coefficients from the pedigree file. | ||
| + | |||
| + | |||
| + | == 26/8/2008 == | ||
| + | Fixed bug which affected convergence of reduced rank analyses under a sire model with known maternal grand sires. | ||
| + | |||
| + | == 13/8/2008 == | ||
| + | Fixed bug which caused WOMBAT to ignore some of the effects chosen to be set to zero through the ''ZEROUT'' directive, and improved `automatic' identification of dependencies among fixed effects somewhat. | ||
| + | |||
| + | == 30/7/2008 == | ||
| + | WOMBAT now stops if it finds repeated records for a trait for less than 20% of individuals, under the assumption that this is due to careless data preparation. For the rare cases were this is a planned scenario, this can be overridden by a new 'special' option (see section 4.8 of the manual). In addition, WOMBAT now checks for duplicate identities in the pedigree file and stops if these give different parental identities. | ||
| + | |||
| + | == 11/7/2008 == | ||
| + | When writing out solutions for random effects for multivariate analyses using the "PC" option, WOMBAT now produces | ||
| + | additional files with corresponding solutions transformed `back' to the original scale. | ||
| + | |||
| + | == 1/7/2008 == | ||
| + | WOMBAT now checks for values of zero for covariables fitted. If the data contains such values, it expects | ||
| + | a 'special' option (see section 4.8 of the manual) telling it whether to ignore such records or treat them as valid values for the covariable. | ||
| + | |||
| + | == 16/5/2008 == | ||
| + | Added facilities to a) fix selected covariance matrices at their `input' values, b) replace the "1" in design matrices (standard uni- and multivariate analyses only) by a value (weight) obtained from the data file. | ||
| + | |||
| + | == 15/5/2008 == | ||
| + | Warren S. pointed out that WOMBAT would not allow correlated random effects in conjunction with a general | ||
| + | relationship matrix. Changed - WOMBAT now allows both NRM and GIN options for such effects. | ||
| + | |||
| + | |||
| + | == 24/4/2008 == | ||
| + | Added option ''−−mmeout'' — this is like ''−−solvit'' but writes out the complete mixed model equations to file, | ||
| + | including solutions and mapping of effects fitted to equation numbers. This is the option for folks who want to calculate linear contrasts, F-ratios etc. for fixed effects. | ||
| + | |||
| + | == 8/4/2008 == | ||
| + | Martin L. reported that WOMBAT would complain about an animal occurring as sire and dam for a sire model when a bull occurred as sire and MGS. Fixed. | ||
| + | |||
| + | == 1/4/2008 == | ||
| + | New run option: ''−−solvit'' provides a BLUP analysis solving the mixed model equations iteratively. | ||
| + | |||
| + | == 20/2/2008 == | ||
| + | Pia B. reported that WOMBAT had trouble coping with blank lines in the pedigree file. Fixed. | ||
| + | |||
| + | == 8/1/2008 == | ||
| + | Added option for `stand-alone' matrix inversion. | ||
| + | |||
| + | ==== 2007 ==== | ||
| + | |||
| + | == 20/11/2007 == | ||
| + | Have changed (made faster) computation of average information matrix in reduced rank analyses - Cholesky factor of numerator relationship matrix no longer required or written out (Files ''cholnrm*.bin''). | ||
| + | |||
| + | == 17/07/2007 == | ||
| + | David H. reported that the Windows versions failed for multivariate, reduced rank analyses while the Linux versions did not. This turned out to be due to a minor bug in the g95 compiler. Both compiler and Windows versions have been fixed. | ||
| + | |||
| + | |||
| + | == 29/06/2007 == | ||
| + | New features have been added : | ||
| + | |||
| + | - WOMBAT can now carry out analyses involving subsets of traits in multivariate analyses, without the need to extracts subsets of the data file or renumber traits. | ||
| + | - An option is provided to write out the parameter files for bivariate analyses of all pairs of traits, using the parameter file for the complete analysis as input | ||
| + | - When encountering such analyses of subsets, abbreviated files of partial results are written out automatically. These can be used as input files when pooling results. | ||
| + | - WOMBAT can now combine results from multiple analyses of subsets of traits into positive definite, pooled covariance matrices using a (weighted) iterative summation of expanded part matrices. | ||
| + | |||
| + | ===== Known problems ===== | ||
| + | |||
| + | * Andrew S. reported that the Windows versons of WOMBAT crash when attempting to write out a "Curve_" file for a nested covariable - this seems to be a problem associated with a '*' in the file name. | ||
| + | |||
| + | * Occasionally WOMBAT hangs up or crashes during the set-up phase. This occurs mainly for very large data sets or models with a dense coefficient matrix in the mixed model equations, and can be attributed to 'failure' of the routine used to re-order the mixed model equations.\\ WOMBAT employs three different public domain routines to carry out the ordering. Unfortunately, none of them is `bomb-proof'. In particular, the routine from the <nowiki>MeTiS</nowiki> package (which is used by default for large analyses) is prone to problems and does not provide the possibility of a graceful exit when this occurs. If this happens, please try one of the other ordering strategies or other <nowiki>MeTiS</nowiki> options. | ||
| + | |||
| + | * Operating system incompatibility? Steven M. reported a 'segmentation fault' for WOMBAT versions compiled with ifort when running under Fedora. This fault was not replicable for other Linux versions or executables compiled with a different compiler and thus has not be resolved. Beware! | ||
