plot.gls {nlme} | R Documentation |

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 class '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.

Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates bates@stat.wisc.edu

`gls`

, `xyplot`

,
`bwplot`

,
`histogram`

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))

[Package *nlme* version 3.1-66 Index]