### Table of Contents

## 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 – but I know that there are animals which do. Why is WOMBAT so confused ?**A:**WOMBAT requires the data file to be in a certain order to correctly identify that an individual has multiple records – please check the manual! Perhaps you have forgotten to**sort**the data file, or the sort did not work properly. Please sort the data file as required and try again – and double-check that`SumModel.out`

gives the correct numbers of individuals with records for each pair of traits before proceeding to the estimation step.

Another possibility is that you have specified starting values of zero for the residual covariances – this causes WOMBAT not to estimate these values and fix them at their starting values. However, in that case`SumModel.out`

should report numbers of individuals with pairs of records greater than zero.

#### Interaction for fixed effects

**Q:**I want to fit a model with an interaction between two fixed effects. How do I do that ? The manual says*Not Yet implemented*– surely, that can't be true ?**A:**The manual is slightly misleading here: Yes, of course you can fit a model with an interaction. What the manual means is that WOMBAT won't to the relevant coding for you. So what you have to do is:- Generate a code for the interaction from the two fixed effects codes and write this to a new column in your data file. For example, if fixed effect A has a maximum value of 8571 and you want to fit an interaction between fixed effects A and B, the new code could be 10000*code(B)+code(A). In doing so, ensure that your new code is still a valid integer variable, i.e. does not exceed
**2,147,483,647**. - Fit this new effect as if it were a cross-classified fixed effect.
- Check carefully for any dependencies among the fixed effects before running your analysis. If necessary, tell WOMBAT about them using the

option. This is particularly important, if you want to fit effects A (or B) in addition to the interaction - you then have the interaction nested in A (or B), i.e. if effect A has**ZEROUT***a*levels, you have*(a-1)*additional dependencies among the fixed effects. WOMBAT may find some of them, but you cannot rely on it.

## Polynomial regression

**Q:**I am fitting age as a quadratic covariable in the model, using the default polynomial regression. WOMBAT gives me estimates of regression coefficients in`FixSolutions.out`

, but: a) I can't find the intercept, and b) these estimates don't make sense, i.e. when I plug them into the regression equation, I don't get a curve which fits the data. What is wrong?**A:**Long answer on separate page – here

## Categorical traits

**Q:**What options does WOMBAT provide for the analysis of categorical traits – I cannot find anything about it in the manual.**A:**None – the manual clearly states that WOMBAT is geared towards the analysis of*continuous*traits (only!), assuming a multivariate normal distribution.