# plot.merMod

##### Diagnostic Plots for 'merMod' Fits

diagnostic plots for merMod fits

##### Usage

```
# S3 method for merMod
plot(x,
form = resid(., type = "pearson") ~ fitted(.), abline,
id = NULL, idLabels = NULL, grid, …)
# S3 method for merMod
qqmath(x, id = NULL, idLabels = NULL, …)
```

##### Arguments

- x
a fitted [ng]lmer 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 lattice display. Default is`resid(., type = "pearson") ~ fitted(.)`

, corresponding to a plot of the standardized residuals versus fitted values.- 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, or normalized residuals. Observations with absolute standardized (normalized) 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 and used to label the observations identified according to

`id`

. If given as a vector, it is converted to character 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 and used to label the identified observations. Default is the interaction of all the grouping variables in the data frame. The special formula`idLabels=~.obs`

will label the observations according to observation number.- grid
an optional logical value indicating whether a grid should be added to plot. Default depends on the type of lattice plot used: if

`xyplot`

defaults to`TRUE`

, else defaults to`FALSE`

.- …
optional arguments passed to the lattice plot function.

##### Details

Diagnostic plots for the linear mixed-effects 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
lattice 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
lattice 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 lattice 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 lattice function `bwplot`

is used).

`qqmath`

produces a Q-Q plot of the residuals
(see `qqmath.ranef.mer`

for Q-Q plots of the
conditional mode values).

##### Examples

```
# NOT RUN {
data(Orthodont,package="nlme")
fm1 <- lmer(distance ~ age + (age|Subject), data=Orthodont)
## standardized residuals versus fitted values by gender
plot(fm1, resid(., scaled=TRUE) ~ fitted(.) | Sex, abline = 0)
## box-plots of residuals by Subject
plot(fm1, Subject ~ resid(., scaled=TRUE))
## observed versus fitted values by Subject
plot(fm1, distance ~ fitted(.) | Subject, abline = c(0,1))
## residuals by age, separated by Subject
plot(fm1, resid(., scaled=TRUE) ~ age | Sex, abline = 0)
library(lattice) ## needed for qqmath
qqmath(fm1, id=0.05)
ggp.there <- "package:ggplot2" %in% search()
if (ggp.there || require("ggplot2")) {
## we can create the same plots using ggplot2 and the fortify() function
fm1F <- fortify.merMod(fm1)
ggplot(fm1F, aes(.fitted,.resid)) + geom_point(colour="blue") +
facet_grid(.~Sex) + geom_hline(yintercept=0)
## note: Subjects are ordered by mean distance
ggplot(fm1F, aes(Subject,.resid)) + geom_boxplot() + coord_flip()
ggplot(fm1F, aes(.fitted,distance)) + geom_point(colour="blue") +
facet_wrap(~Subject) +geom_abline(intercept=0,slope=1)
ggplot(fm1F, aes(age,.resid)) + geom_point(colour="blue") + facet_grid(.~Sex) +
geom_hline(yintercept=0)+ geom_line(aes(group=Subject),alpha=0.4) +
geom_smooth(method="loess")
## (warnings about loess are due to having only 4 unique x values)
if(!ggp.there) detach("package:ggplot2")
}
# }
```

*Documentation reproduced from package lme4, version 1.1-23, License: GPL (>= 2)*