These are large files, most likely subject to further processing by other programs. Thus they contain minimum or no text. They have extension .dat.
This files gives the residuals for all observations, for the model fitted and current estimates of covariance components. It has the same order as the data file, and contains 3 space separated columns :
The first line contains the column names. Note that this file is not produced for runs involving iterative solution of the mixed model equations.
Summary statistics about the distribution of residuals can be readily obtained using standard statistical packages. For example, the following R commands compute means, standard deviations and quartiles, and plot the two columns against each other as well as a distribution histogram for the residuals :
Solutions for each random effect are written to a separate file. These files have names RnSoln_rname.dat, with rname representing the name of the random effect. Columns in these files are :
For genetic random effects with covariance option NRM, WOMBAT calculates inbreeding coefficients from the list of pedigrees specified. For such effects, there may be an additional column containing these coefficients (in %). This should be the last column in the RnSoln_rname.dat file (NB: For multivariate analyses, this is only given once per individual, in the line corresponding to the first trait).
There may be up to 7 columns – ignore column 6 unless you recognize the numbers (calculations for column 6 are not fully debugged, but may be o.k. for simple models).
If you have carried out a reduced rank analysis, i.e. give the PC option for the analysis type, the solutions in RnSoln_rname.dat pertain to the principal components! You might then also be interested in the corresponding solutions on the original scale – WOMBAT endeavours to calculate these for you and writes them to the file RnSoln_rname-tr.dat. However, if you have carried out a run in which you have calculated standard errors for the effects fitted, these are ignored in the back-transformation and you will find that column 5 (in RnSoln_rname-tr.dat) consists entirely of zeros – this does not mean that these s.e. are zero, only that they have not been determined.
At convergence, curves for fixed covariables fitted are evaluated and written to separate files, one per covariable and trait. These have names Curve_cvname.dat for univariate analyses and Curve_cvname_ trname.dat for multivariate analyses, with cvname the name of the covariable as specified in the parameter file and, correspondingly, trname the name of the trait. Curves are only evaluated at points corresponding to nearest integer values of values found in the data. Each file has four columns :
HINT: To get most information from these files, it might be worth your while scaling your covariables prior to analysis!
For random regression analyses, WOMBAT evaluates variance components (file
RanRegVariances.dat), variance ratios (file
RanRegVarRatios.dat, not written if more than one control variable is used) and selected correlations (RanRegCorrels.dat) for values of the control variable(s) occurring in the data. If approximate sampling variances of parameters are available, it is attempted to approximate the corresponding sampling errors. The general layout of the files is as follows :
In addition, the files contain some rudimentary headings.
IF the special option RRCORR-ALL has been specified (see 4.16.13), a file RanRegCorrAll.dat is written out in addition. This contains the following columns:
Simulated records are written to files with the standard name
SimDatan.dat, where is a three-digit integer value (i.e. , , ). These files have the same number of columns as specified for the data file in the parameter file (i.e. any trailing variables in the original data file not listed are ignored), with the trait values replaced by simulated records. These variables are followed by the simulated values for individual random effects : The first of these values is the residual error term, the other values are the random effects as sampled (standard uni-/multivariate analyses) or as evaluated using the random regression coefficients sampled - in the same order as the corresponding covariance matrices are specified in the parameter file. Except for the trait number in multivariate analyses (first variable), all variables are written out as real values.
If an analysis considering a subset of traits is carried out, WOMBAT writes out a file EstimSubsetn+…+m.dat with the estimates of covariance matrices for this analysis. Writing of this file is ‘switched on’ when encountering the syntax “m”->n, specifying the trait number in the parameter file (see 4.9.7). The first two lines of EstimSubsetn++m.dat gives the following information :
This is followed by the covariance matrices estimated. The first matrix given is the matrix of residual covariances, the other covariance matrices are given in the same order as specified in the parameter file.
Finally, EstimSubsetn++m.dat gives some information on the data structure (not used subsequently) :
These files give the pooled covariance matrices, obtained running WOMBAT with option --itsum.
PDMatrix.dat is meant to be readily pasted (as starting values) into the parameter file for an analysis considering all traits simultaneously. It contains the following information for each covariance matrix :
PDBestPoint has the same form as BestPoint (see 7.3.3). It is meant to be copied (or renamed) to BestPoint, so that WOMBAT can be run with option --best to generate a ‘results’ file (BestSoFar) with correlations, variance ratios and eigenvalues of the pooled covariance matrices.
These files provided the results from a run with the option --pool:
The two files MMECoeffMatrix.dat and MMEEqNos+Solns.dat are written out when
the run option --mmeout is specified.
MMECoeffMatrix.dat contains the non-zero elements in the lower triangle of the coefficient matrix in the MME. There is one line per element, containing 3 space-separated variables:
HINT: This file is in the correct format to be inverted using run option --invert or --invrev.
This is the output file for a run using option --snap. It contains one line for each line found in the input file QTLAllels.dat containing
QTLCovariances.dat is generated only when multiple SNPs are considered simultaneously and the option COVOUT is specified (see 4.16.6). This causes the upper triangle of the matrix of sampling covariances to be written to this file ( elements for SNPs, space separated).
The following files are created in conjunction with penalized estimation. Some can be used by WOMBAT in additional steps.
This file gives a brief summary of estimates together with log likelihood values for all values of the tuning parameter given.
This file collects the BestPoint’s for all tuning parameters. The format for each is similar to that for BestPoint (see 7.3.3), except that the first line has 3 entries comprising the tuning factor, the maximum penalized likelihood and the corresponding unpenalized value. It is suitable as input for additional calculations aimed at comparing estimates, and used as input file for ‘validation’ runs (see run option --valid, 5.3.2).
Output to this file is cumulative, i.e. if it exists in the working directory it is not over-written but appended to.
Similarly, this file collects the values of the tuning factors and corresponding penalized and unpenalized log likelihood values. It has one line for each tuning factor. For a penalty on the canonical eigenvalues, estimates of the latter are written out as well (in descending order). Again, if this file exists in the working directory it is not over-written but appended to.
If the option PHENV (see 4.16.15) is specified, WOMBAT writes out this file with a suitable target matrix. For penalty COVARM a covariance matrix and for CORREL the corresponding correlation matrix is given. For a multivariate analysis fitting a simple animal model, this is the phenotypic covariance (correlation) matrix. For a random regression analysis, corresponding matrices are based on the sum of the covariance matrices among random regression coefficients due the two random effects fitted, assumed to represent individuals’ genetic and permanent environmental effects (which must be fitted using the same number of basis functions).
Written out is the upper triangle of the matrix.
This file is the output resulting from a run with the option --valid. It contains one line per tuning factor with he following entries:
If this file exists in the working directory it is not over-written but appended to.
This (potentially large) file contains the samples drawn from the multivariate normal distribution of estimates, either for all random effects in the analysis ( = ALL) or for single, selected effect. The file contains one line per replicate, with covariance matrices written in the same sequence as in the corresponding estimation run (for ALL), giving the upper triangle for each matrix.