The Wicked WOMBAT Wiki wombat

wombat:allfaqs

Anonymous (anonymous@undisclosed.example.com) — 2018-10-26T16:05:31+1000

FAQ sections * Error Messages * Standard errors * How to do ... ?? * Confusion * Miscellaneous * Windows specific problems

wombat:answerfaq1

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

* Q: When I run WOMBAT I sometimes get a message to the screen, saying either small, negative or invalid pivot. What does it mean and what should or can I do about it? * A: All the calculations in WOMBAT assume that the coefficient matrix in the mixed model equations for the model fitted is positive definite. In essence, the coefficient matrix is factored sequentially and the `pivot' is the current diagonal element, adjusting for (or absorbing) all rows and columns already processed. If this…

wombat:answerfaq2

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

* Q: WOMBAT crashes with a “Segmentation fault” with a heap of unintelligible numbers to follow -- this seems to happen quite early on, i.e. during the set-up phase before any likelihoods are printed to the screen. What is wrong? * A: A `segmentation fault' (or 'access violation') message is a run-time error message generated by the FORTRAN compiler. In contrast, the majority of error messages in WOMBAT are programmed in to catch mistakes made by the programs user

wombat:answerfaq3

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

???? FAQ: Polynomial regression ???? The default form of regression equation in WOMBAT is chosen to account for rank deficiencies in the fixed effects part of the coefficient matrix in the MME when estimating variance components. If your aim is to obtain `adjustment factors' for other analyses, it is best to

wombat:answerfaq4

Anonymous (anonymous@undisclosed.example.com) — 2018-10-11T17:01:57+1000

FAQ: Accuracy of breeding values I am using WOMBAT to obtain breeding values for animals. How can I get the corresponding accuracies? This depends on what exactly you are doing. WOMBAT does not provide approximations as needed for large models - however, if the inverse of the coefficient matrix can be calculated, there are several scenarios and ways to obtain the standard errors or sampling variances which you can then use to calculate the corresponding accuracies.

wombat:answerfaq5

Anonymous (anonymous@undisclosed.example.com) — 2018-08-29T17:03:09+1000

I am trying to run a multivariate analysis, but WOMBAT stops immediately with a message that that the Matrix of starting values is “invalid”. * What does this mean and what can I do about it? * And why can't WOMBAT fix this automatically?

wombat:clones

Anonymous (anonymous@undisclosed.example.com) — 2018-08-30T10:50:03+1000

Dealing with `clones' In some instances we have clones, i.e. subjects which are genetically identical. For instance, monozygotic twins are naturally occuring clones. If these individuals have different identity codes and the same parents, WOMBAT will simply treat them as ordinary full-sibs. Alternatively, if all members of the clone are given the same identity, records on all members of the clone are treated as if they were repeated observations for the same individual. That is not correct eit…

wombat:converged

Anonymous (anonymous@undisclosed.example.com) — 2018-08-31T12:41:13+1000

Checking convergence of REML analyses WOMBAT employs iterative schemes to locate the maximum of the (log) likelihood function. The program stops when a certain maximum number of iterates have been carried out or when it considers changes between iterates to be sufficiently small.

wombat:copyright

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

wombat:ex1page

Anonymous (anonymous@undisclosed.example.com) — 2018-10-30T11:17:28+1000

Example 1 for WOMBAT Download Example1 One of the simplest analysis in quantitative genetics is the case where we have one trait of interest which is recorded only once, and where we have no additional random effects. Assuming a general pedigree (i.e. information from various types of relatives), we then fit a simple animal model, with additive genetic effects due to the individual to estimate the additive genetic and residual variance components and calculate the heritability of the trait fro…

wombat:ex2page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 2 for WOMBAT Download example2.tar.gz This is Example 2 as previously distributed with DFREML. It illustrates a bivariate analysis for a model fitting an additional random effects. Records are the mouse data given in GSE 23:67-81 (1991), with both traits recorded for all animals. The model of analysis is the same for both traits and is comprised of 3 cross-classified fixed effects and genetic( animal or sire) and litter effects as random effects.

wombat:ex3page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 3 for WOMBAT Download example3.tar.gz This is Example 3 as previously distributed with DFREML. Data are mature cow weight records from the Wokalup selection experiment, recorded annually in January. Up to 6 records per cow are available. The only fixed effect considered is contemporary groups.

wombat:ex4page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 4 for WOMBAT this page will be constructed in the future Download Example4

wombat:ex5page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 5 for WOMBAT Download example5.tar.gz This example considers a simple animal model for 6 traits with contemporary groups as the only fixed effect. The same model is fitted for all traits. In addition to the “grouped” specification of the layout of the data file, it demonstrates a reduces and analysis and how to impose a factor-analytic structure on the genetic covariance matrix.

wombat:ex6page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 6 for WOMBAT Download Example6 this page to be written later

wombat:ex7page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 7 for WOMBAT Download Example7 later!

wombat:ex8page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 8 for WOMBAT Download Example8 later still!

wombat:ex9page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 9 for WOMBAT Download example9.tar.gz This example -- using monthly weight records on beef calves -- illustrates more complicated random regression analyses than Example 3, namely a model with an additional random effect, fitting quadratic B-splines (rather than Legendre polynomials) as basis functions, and how to obtain reduced rank estimates.

wombat:ex10page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 10 for WOMBAT Download Example10

wombat:ex11page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 11 for WOMBAT Download example11.tar.gz This example illustrates the use of a bivariate random regression analysis and shows how a multivariate RR analysis can be used to fit a standard multivariate model with a `tricky' residual covariance structure. The data are simulated records - obtained by simulating two (unrelated) samples for the data in Example 3 (see file

wombat:ex13page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 13 for WOMBAT Download example13.tar.gz This example illustrates multivariate analyses with repeated records per trait -- this can be tricky to model if same records for different traits are taken at the same time and others are not. New features have been implemented to assist with this:

wombat:ex14page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 14 for WOMBAT Download example14.tar.gz This example illustrates `automatic' GWAS analysis using WOMBAT for a toy example (simulated data). * A: Demonstrates run option ----snap. This invokes estimation of SNP effects and their standard errors for (co)variances assumed to be known. In addition to the data, pedigree and parameter file required for 'standard' analyses, it requires a file supplying counts for the number of copies of the reference allele; this has the de…

wombat:ex15page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 15 Download example15.tar.gz This example illustrates how to pool estimates of covariance components by (penalized) maximum likelihood using WOMBAT. The example is comprised of 14 traits, with 6 traits measured on few animals and the remaining records representing 4 traits with measures on males and females treated as different traits (Results from Meyer 2007; J. Anim. Breed. Genet, 124:50-64). There are results from 76 bivariate and one six-variate analysis to be combined. Due to t…

wombat:ex16page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 16 Download example16.tar.gz This example shows what options are available in WOMBAT to fit `social interaction' type models. * DirectoryA: This directory shows an example run for simulated data for a dilution factor of 0, treating direct and social genetic effects as uncorrelated.

wombat:ex17page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 17 Download example17.tar.gz

wombat:ex18page

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Example 18 Download example18.tar.gz This example demonstrates the use of the single step module, using tiny data sets from Examples 1 and 2 * Directory A: Univariate analysis, using a user-supplied inverse relationship matrix. Here, animal.gin is simply the inverse of the pedigree derived NRM; note the third column in animal.codes which specifies the type ofanimal.

wombat:ex19page

Anonymous (anonymous@undisclosed.example.com) — 2018-08-08T11:45:24+1000

Example 19 for WOMBAT Download Example19

wombat:ex20page

Anonymous (anonymous@undisclosed.example.com) — 2018-08-08T11:44:41+1000

Example 20 for WOMBAT Download Example20

wombat:ex21page

Anonymous (anonymous@undisclosed.example.com) — 2018-08-08T11:45:52+1000

Example 21 for WOMBAT Download Example21

wombat:examples

Anonymous (anonymous@undisclosed.example.com) — 2018-08-08T11:42:39+1000

Worked Examples Use of WOMBAT is illustrated by a suite of worked examples. The complete set of examples 1 to 16 (Linux version; gzipped tar ball) can be downloaded here. There are a total of 11 example data sets with a number of different analyses shown for most of them to illustrate different models and options available.

wombat:famodel

Anonymous (anonymous@undisclosed.example.com) — 2018-08-30T10:17:21+1000

Fitting a factor-analytic model COM Example par file for FA model ANAL MUV PC 6 PEDS ../carcped.dat DATA ../carcsix.dat GRP TRNOS 1 2 3 4 5 6 traitno 6 animal 0 bnimal 0 cg 299 NAMES cwt cema cimf crby cp8 crib END MODEL FIX cg RAN animal nrm RAN bnimal nrm tr cwt 1 tr cema 2 tr cimf 3 tr crby 4 tr cp8 5 tr crib 6 END MOD VAR animal 6 1 177 29 3.1 -11 15 8 9.8 0…

wombat:faqsconfusion

Anonymous (anonymous@undisclosed.example.com) — 2018-09-13T10:45:34+1000

Confusion Zero residual covariances * Q: My multivariate analysis gives `estimates' of residual covariances which are zero, and SumModel.out tells me that WOMBAT thinks that there are no animals which have records for the corresponding pairs of traits

wombat:faqserr

Anonymous (anonymous@undisclosed.example.com) — 2018-09-13T09:58:50+1000

FAQ: Error messages Crash "Segmentation fault" * Q: WOMBAT crashes with a “Segmentation fault” with a heap of unintelligible numbers to follow -- this seems to happen quite early on, i.e. during the set-up phase before any likelihoods are printed to the screen. What is wrong?

wombat:faqshow

Anonymous (anonymous@undisclosed.example.com) — 2018-09-13T10:58:36+1000

Missing covariables * Q I want to fit a covariable, but there are some records where this is not recorded. What should I do? WOMBAT doesn't seem to allow for a 'missing value' code there, so I have set them all to a value of zero. Is that o.k. * $\Phi_{i}$$a$$$b_{1i}\Phi_{1}(a) + b_{2i} \Phi_{2}(a)+ b_{3i} \Phi_{3}(a)$$$b_{ji}$$\Phi_{j}(a)$$a$

wombat:faqsmisc

Anonymous (anonymous@undisclosed.example.com) — 2018-10-30T10:01:28+1000

What is: Pruning and pedigree reduction * Q: What exactly does WOMBAT do to the pedigree information I supply? * A: WOMBAT tries to `condense' the pedigrees supplied as far as possible without loosing any information -- this makes computations more efficient. There are two separate processes:

wombat:faqwin

Anonymous (anonymous@undisclosed.example.com) — 2018-10-30T10:02:32+1000

Frequently Asked Question - Related to Windows Examples under Windows * Q: I have downloaded the examples and am trying to run them under Windows, but WOMBAT fails straightaway, even for the simplest case. What is wrong ? * A: The examples have been produced under Linux. Windows/DOS and Linux differ in the `end-of-line' characters used. DOS uses a CR/LF (CR=Carriage return, LF=line feed) while Linux uses a LF only. Hence, a Linux file under DOS will be interpreted as a file with a single…

wombat:gin4impf90

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Click tab to download !------------------------------------------------------------------------------ ! Program GIN4IMPRINT ! ! Auxiliary program for WOMBAT to set up inverse of gametic relationship matrix ! Files written out allow imprinting effects to be fitted with a GIN covariance ! structure: ! 1. The .gin file -> default name: imprint.gin ! 2. The corresponding .codes file -> default name: imprint.codes ! Gametes are coded as: animal ID * 10 + 1 (paternal)…

wombat:gin4imprinting.f90

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

!------------------------------------------------------------------------------ ! Program GIN4IMPRINT ! ! Auxiliary program for WOMBAT to set up inverse of gametic relationship matrix ! Files written out allow imprinting effects to be fitted with a GIN covariance ! structure: ! 1. The .gin file -> default name: imprint.gin ! 2. The corresponding .codes file -> default name: imprint.codes ! Gametes are coded as: animal ID * 10 + 1 (paternal) and ! …

wombat:gwas

Anonymous (anonymous@undisclosed.example.com) — 2018-08-30T11:12:50+1000

GWAS analyses Toy example @Article{km11c, author = {Meyer, K. and Tier, B.}, title = {"SNP Snappy": A strategy for fast genome wide association studies fitting a full mixed model}, year = 2011, journal = {Genetics}, volume = 00, pages = {000 (published on-line before print October 20, 2011)}, url = {http://www.dx.org/10.1534/genetics.111.134841} }

wombat:hypotheses

Anonymous (anonymous@undisclosed.example.com) — 2018-09-13T16:29:56+1000

Hypothesis testing for REML analyses Wikipedia links Likelihood ratio test Akaike Information Criterion Bayesian Information Criterion Score test Wald test With a maximum likelihood framework of estimation, tests based on the (log) likelihood are the obvious choice for hypothesis testing. Random effects REML, short for restricted or residual maximum likelihood, estimation involves maximising the likelihood of the residuals, i.e the observations adjusted for estimates of the fixe…

wombat:imprinting

Anonymous (anonymous@undisclosed.example.com) — 2018-08-30T11:09:50+1000

Fitting imprinting effects !------------------------------------------------------------------------------ ! Program GIN4IMPRINT ! ! Auxiliary program for WOMBAT to set up inverse of gametic relationship matrix ! ! Files written out allow imprinting effects to be fitted with a GIN covariance ! structure: ! 1. The .gin file -> default name: imprint.gin ! 2. The corresponding .codes file -> default name: imprint.codes ! Gametes are coded as…

wombat:install

Anonymous (anonymous@undisclosed.example.com) — 2018-08-10T11:01:07+1000

Linux Installation * Download the appropriate, pre-compiled executable program for your computer. Unless you have an old or `unusual' machine, this should be * wombat64.tar.gz for a 64-bit machine * wombat32.tar.gz for a 32-bit machine - Update: 32-bit version no longer built

wombat:navigation

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

* Start Page * Help * Other links * Site map * WOMBAT Manual

wombat:prepost

Anonymous (anonymous@undisclosed.example.com) — 2018-11-10T12:01:19+1000

Supplementary pre- or post analysis steps WOMBAT has a (growing) number of features or pre- or post- mixed model analyses. These include facilities to * Invert a matrix * Pool results from analyses by parts * Carry out calculations involving genomic relationship matrices or

wombat:referrers

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

wombat:runtimeoptions

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Using `advanced' run time options WOMBAT offers a substantial number of so-called advanced run time options. While simple analyses tend to work well without them, using these options can greatly enhance reliability and efficiency for analyses involving more than a few traits (or RR coefficents) or multiple random effects. This is especially important for large data sets where each additional iterate or likelihood evaluation can require substantial time !

wombat:sexlinked

Anonymous (anonymous@undisclosed.example.com) — 2018-08-30T11:11:45+1000

Fitting X-linked genetic effects PED pedigree.dat +SEX DAT xldata.dat fixeff 2 animal xlink record end ANAL UNI MODEL RAN animal NRM RAN xlink SEX FIX fixeff TR record END VAR animal 1 16 VAR xlink 1 4 VAR error 1 20

wombat:sidebar

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

WOMBAT Home page WOMBAT online manual Site map

wombat:specialanalyses

Anonymous (anonymous@undisclosed.example.com) — 2025-11-12T16:45:38+1000

Specialized analyses with WOMBAT This page provides some hints for non-standard analyses. Fitting a factor-analytic model WOMBAT can accommodate a factor-analytic model for the structure of covariance matrices of random effects. While there is no explicit option for this structure, it is easily fitted indirectly. ${\bf H}^{-1} $$ {\bf G}^{-1} - {\bf A}_{22}^{-1}$

wombat:startingvalues

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

Starting values for covariance components To run WOMBAT, starting values for all matrices of covariance components are required. A common question is how best to derive these. * Often we have estimates for the same (or very similar) traits from previous analyses which can be used as guideline. For instance, estimates from different locations or breeds, including literature values.

wombat:sterrors

Anonymous (anonymous@undisclosed.example.com) — 2018-09-14T09:26:40+1000

Standard errors I am getting a value of -1.0 as standard error for some of my estimates of genetic parameters, together with a note that Negative values for s.e. indicate failed approximation!. What does is mean and what can I do about it? ? As it says in plain English: the approximation of standard errors failed.

wombat:updates

Anonymous (anonymous@undisclosed.example.com) — 2018-07-02T12:37:05+1000

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

wombat:wombatauxf90

Anonymous (anonymous@undisclosed.example.com) — 2018-09-13T10:55:56+1000

Auxiliary programs for WOMBAT This page collects a small number of simple, stand-alone programs to be used in conjunction with WOMBAT. Change the output statements as you please. NB: You need a FORTRAN 95 compiler to be able to generate `executables' from the source code given here; e.g. `gfortran' is free and available for most common operating systems.

wombat:wombatcites

Anonymous (anonymous@undisclosed.example.com) — 2021-04-22T15:03:15+1000

Some publications citing or using WOMBAT @Article{piper2007, author = {Piper, L.R. and Swan, A. A. and H. G. Brewer}, title = {Is increased fleece weight associated with reduced reproduction rate? Results from long term multi-trait selection flocks}, journal = {Proc. Assoc. Advmt. Anim. Breed. Genet.}, year = 2007, volume = 17, pages = {103--106}