Contents


1 Introduction
2 Availability
3 Getting started
 3.1 Installation
  3.1.1 Installation for LINUX operating systems
  3.1.2 Installation under WINDOWS
  3.1.3 Running WOMBAT
  3.1.4 Examples and testing
  3.1.5 Compilation notes
  3.1.6 Updates
 3.2 Using the manual
 3.3 Troubleshooting
4 Parameter file
 4.1 Overview
 4.2 General rules
 4.3 Run options
 4.4 Comment line
 4.5 Analysis type
 4.6 Pedigree file
 4.7 Data file
  4.7.1 Simple
  4.7.2 Compact
 4.8 Model of analysis
  4.8.1 Effects fitted
  4.8.2 Traits analysed
 4.9 Covariance components
  4.9.1 Residual covariances
  4.9.2 Covariances for random effects
 4.10 Special information
  4.10.1 Dependencies among fixed effects
  4.10.2 Random effects to be treated as fixed
  4.10.3 Covariance components to be treated as fixed
  4.10.4 Additional functions of covariance components
  4.10.5 Pooling estimates of covariance components
  4.10.6 Miscellaneous
  4.10.7 Penalized estimation
5 Run options
 5.1 Overview
 5.2 Basic run options
  5.2.1 Continuation run
  5.2.2 Level of screen output
  5.2.3 Set-up steps
  5.2.4 Quality of starting values
  5.2.5 Numerical settings
  5.2.6 Intermediate results
  5.2.7 Prediction only
  5.2.8 Simulation only
  5.2.9 Sampling to approximate standard errors
  5.2.10 Matrix inversion only
  5.2.11 Quadratic approximation
  5.2.12 Analyses of subsets of traits
  5.2.13 Pooling estimates of covariance components from part analyses
  5.2.14 Miscellaneous
 5.3 Advanced run options
  5.3.1 Ordering strategies
  5.3.2 REML algorithms
  5.3.3 Parameterisation
  5.3.4 Matrix storage mode
  5.3.5 Sparse matrix factorisation, auto-differentiation and inversion
  5.3.6 Other
 5.4 Parameter file name
6 Input files
 6.1 Format
 6.2 Data File
 6.3 Pedigree File
 6.4 Parameter File
 6.5 Other Files
  6.5.1 General inverse
  6.5.2 Basis function
  6.5.3 GWAS: Allele counts
  6.5.4 Results from part analyses
  6.5.5 ‘Utility’ files
  6.5.6 File SubSetsList
  6.5.7 File(s) Pen*(.dat)
7 Output files
 7.1 Main results files
  7.1.1 File SumPedigrees.out
  7.1.2 File SumModel.out
  7.1.3 File SumEstimates.out
  7.1.4 File BestSoFar.out
  7.1.5 File FixSolutions.out
  7.1.6 File SumSampleAI.out
 7.2 Additional results
  7.2.1 File Residuals.dat
  7.2.2 File(s) RnSoln_rname.dat
  7.2.3 File(s) Curve_cvname(_trname).dat
  7.2.4 File(s) RanRegname.dat
  7.2.5 Files SimDatan.dat
  7.2.6 Files EstimSubSetn+...  +m.dat
  7.2.7 Files PDMatrix.dat and PDBestPoint
  7.2.8 Files PoolEstimates.out and PoolBestPoint
  7.2.9 Files MME*.dat
  7.2.10 File QTLSolutions.dat
  7.2.11 Files Pen*(.dat) and ValidateLogLike.dat
  7.2.12 File CovSamples_name  .dat
 7.3 ‘Utility’ files
  7.3.1 File ListOfCovs
  7.3.2 File RepeatedRecordsCounts
  7.3.3 File BestPoint
  7.3.4 File Iterates
  7.3.5 File OperationCounts
  7.3.6 Files AvInfoParms and AvinfoCovs
  7.3.7 Files Covariable.baf
  7.3.8 File LogL4Quapprox.dat
  7.3.9 File SubSetsList
 7.4 Miscellaneous
  7.4.1 File ReducedPedFile.dat
  7.4.2 Files PrunedPedFilen   .dat
  7.4.3 File WOMBAT.log
8 Work files
9 Examples
A Technical details
 A.1 Ordering strategies
 A.2 Convergence citeria
 A.3 Parameterisation
 A.4 Approximation of sampling errors
  A.4.1 Sampling covariances
  A.4.2 Sampling errors of genetic parameters
 A.5 Modification of the average information matrix
 A.6 Iterative summation