# asreml-r, extracting results

One of the big differences between the console version and the R version of
asreml is the way output is dealt with. The console version generates several
text files with the same base name of the .as file containing the job, but
different extensions. For example, a `job.as`

file will generate `job.asr`

with a summary of the run, `job.sln`

with the fixed and random effect
solutions, `job.yht`

with predicted values, etc. In contrast, asreml-r follows
the ‘R way’, creating an object that contains all the output. This object has
to be queried, by using specific functions, to obtain particular parts of the
output.

Let’s assume that we have fitted a simple linear mixed model to explain plant
yield (`yield`

), based on overall mean (`1`

), Fertilizer dose (`Fert`

) and a
genetic effect (`ped(Tree)`

):

```
fm <- asreml(yield ~ 1 + Fertil, random =~ ped(Tree),
data = mytrial)
```

An asreml object for a linear mixed model will contain information on the
model fitted, Log likelihood, predicted values for fixed and random effects,
residuals, variance components, etc. A common way to obtain summary results in
R is to use the function summary on the fitted object as `summary(fm)`

.
Unfortunately, the summary function in asreml displays the whole contents of
the object, which will be many pages and not a summary at all. So, how do you
get a proper summary in asreml-r?

Part of the default output of running asreml-r is to display the log likelihood of the fitted model. Most likely, the next thing that we would like to know are the variance components, which we can obtain as:

```
summary(fm)$varcomp
```

Random and fixed effects are extracted using the `coef`

& `$random`

and
`coef`

& `fixed`

names for the fitted model. The outputs are matrices with 3
columns: solution, standard error and z ratio. The latter is simply the
solution divided by its standard error, an indication of significance.

```
# Extracting random effects
coef(fm)$random
# Extracting fixed effects
coef(fm)$fixed
```

R matrices can have associated row names and column names. The matrices
containing solutions have column names `solution`

, `std error`

and `z ratio`

,
while the row names correspond to the names of the factor, followed by
underscores with the levels of the factor.