Diagnostic plots for the linear model fit are obtained. The
`form`

argument gives considerable flexibility in the type of
plot specification. A conditioning expression (on the right side of a
`|`

operator) always implies that different panels are used for
each level of the conditioning factor, according to a Trellis
display. If `form`

is a one-sided formula, histograms of the
variable on the right hand side of the formula, before a `|`

operator, are displayed (the Trellis function `histogram`

is
used). If `form`

is two-sided and both its left and
right hand side variables are numeric, scatter plots are displayed
(the Trellis function `xyplot`

is used). Finally, if `form`

is two-sided and its left had side variable is a factor, box-plots of
the right hand side variable by the levels of the left hand side
variable are displayed (the Trellis function `bwplot`

is used).

```
# S3 method for gls
plot(x, form, abline, id, idLabels, idResType, grid, …)
```

x

an object inheriting from class `"gls"`

, representing
a generalized least squares fitted linear model.

form

an optional formula specifying the desired type of
plot. Any variable present in the original data frame used to obtain
`x`

can be referenced. In addition, `x`

itself
can be referenced in the formula using the symbol
`"."`

. Conditional expressions on the right of a `|`

operator can be used to define separate panels in a Trellis
display. Default is `resid(., type = "p") ~ fitted(.) `

,
corresponding to a plot of the standardized residuals versus fitted
values, both evaluated at the innermost level of nesting.

abline

an optional numeric value, or numeric vector of length two. If given as a single value, a horizontal line will be added to the plot at that coordinate; else, if given as a vector, its values are used as the intercept and slope for a line added to the plot. If missing, no lines are added to the plot.

id

an optional numeric value, or one-sided formula. If given as
a value, it is used as a significance level for a two-sided outlier
test for the standardized residuals. Observations with
absolute standardized residuals greater than the \(1 - value/2\)
quantile of the standard normal distribution are identified in the
plot using `idLabels`

. If given as a one-sided formula, its
right hand side must evaluate to a logical, integer, or character
vector which is used to identify observations in the plot. If
missing, no observations are identified.

idLabels

an optional vector, or one-sided formula. If given as a
vector, it is converted to character mode and used to label the
observations identified according to `id`

. If given as a
one-sided formula, its right hand side must evaluate to a vector
which is converted to character mode and used to label the identified
observations. Default is the innermost grouping factor.

idResType

an optional character string specifying the type of
residuals to be used in identifying outliers, when `id`

is a
numeric value. If `"pearson"`

, the standardized residuals (raw
residuals divided by the corresponding standard errors) are used;
else, if `"normalized"`

, the normalized residuals (standardized
residuals pre-multiplied by the inverse square-root factor of the
estimated error correlation matrix) are used. Partial matching of
arguments is used, so only the first character needs to be
provided. Defaults to `"pearson"`

.

grid

an optional logical value indicating whether a grid should
be added to plot. Default depends on the type of Trellis plot used:
if `xyplot`

defaults to `TRUE`

, else defaults to
`FALSE`

.

…

optional arguments passed to the Trellis plot function.

a diagnostic Trellis plot.

```
# NOT RUN {
fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
correlation = corAR1(form = ~ 1 | Mare))
# standardized residuals versus fitted values by Mare
plot(fm1, resid(., type = "p") ~ fitted(.) | Mare, abline = 0)
# box-plots of residuals by Mare
plot(fm1, Mare ~ resid(.))
# observed versus fitted values by Mare
plot(fm1, follicles ~ fitted(.) | Mare, abline = c(0,1))
# }
```

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