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# GLPLOT procedure

Plots residuals from a `GLMM` analysis (R.W. Payne).

### Options

 `RMETHOD` = string token Which random terms to use when calculating the residuals (`final`, `all`); default `all` `BACKTRANSFORM` = string token Whether to plot residuals on the natural scale (calculated using back-transformed fitted values) or standardized residuals on the linear-predictor scale (`link, none`); default `none` `INDEX` = variate or factor X-variable for an index plot; default `!(1,2...)` `OFFSET` = scalar Value of offset to use when calculating the residuals; default 0 `GRAPHICS` = string token What type of graphics to use (`lineprinter`, `highresolution`); default `high` `TITLE` = text Overall title for the plots; the default is to form a title displaying the identifier of the y-variate and the type of residual `GLSAVE` = pointer Save structure from the `GLMM` analysis; default `*` uses the `GLSAVE` structure from the most recent `GLMM` analysis

### Parameters

 `METHOD` = string tokens Type of residual plot (`fittedvalues`, `normal`, `halfnormal`, `histogram`, `absresidual`, `index`); default `fitt`, `norm`, `half`, `hist` `PEN` = scalars, variates or factors Pen(s) to use for each plot

### Description

`GLPLOT` provides up to four types of residual plots from a `GLMM` analysis. These are selected using the `METHOD` parameter, with settings: `fitted` for residuals versus fitted values, `normal` for a Normal plot, `halfnormal` for a half-Normal plot, `histogram` for a histogram of residuals, `absresidual` for a plot of the absolute values of the residuals versus the fitted values, and `index` for a plot against an “index” variable (specified by the `INDEX` option). The `PEN` parameter can specify the graphics pen or pens to use for each plot.

The residuals and fitted values are accessed automatically from the analysis specified by the `GLSAVE` option. If the `GLSAVE` option has not been set, they are taken from the most recent `GLMM` analysis.

The `RMETHOD` option controls which random terms are used to calculate the residuals:

`all` all the random effects (default), and
`final` only the final random term.

Note that residuals based on the final random term will not be calculated when any of the variance components are negative, as the associated negative correlations can generate very misleading patterns. `GLPLOT` will then generate a warning that all the residuals are missing. You should then use `RMETHOD=all` instead.

The `BACKTRANSFORM` option specifies the scale of the residuals. The default is to plot standardized residuals on the linear-predictor scale. To avoid problems with 0 and 100% observations, these are formed as the difference between the adjusted dependent variate and the fitted values on the linear predictor scale (and then standardized). Alternatively, you can set `BACKTRANSFORM=link` to plot (unstandardized) residuals on the natural scale.

The `OFFSET` option specifies the offset value to use when calculating the residuals. The default is zero.

By default, high-resolution graphics are used. Line-printer graphics can be used instead, by setting option `GRAPHICS=lineprinter`.

The `TITLE` option can supply an overall title. If this is not set, a default title is formed displaying the identifier of the y-variate and the type of residual.

Options: `RMETHOD`, `BACKTRANSFORM`, `INDEX`, `OFFSET`, `GRAPHICS`, `TITLE`, `GLSAVE`.
Parameters: `METHOD`, `PEN`.

### Method

Residuals and fitted values effects are accessed, using `GLKEEP`. The plots are produced using the `DRESIDUALS` procedure.

### Action with `RESTRICT`

If the y-variate in the `GLMM` analysis was restricted, only units included by the restriction will be used in the graphs.

Procedures: `GLMM`, `GLDISPLAY`, `GLKEEP`, `GLPERMTEST`, `GLPREDICT`, `GLRTEST`, `GLTOBITPOISSON`.
Commands for: Regression analysis.

### Example

```CAPTION   'GLPLOT example',\
!t('Data from an experiment on Great Knott, Rothamsted;',\
'see West, J.S., Fitt, B.D.L., Leech, P.K., Biddulph, J.E.,',\
'Huang, Y.-J. &, Balesdent, M.-H. (2002).',\
'Effects of timing of ~italic{Leptosphaeria maculans}',\
'ascospore release and fungicide regime on phoma leaf spot',\
'and phoma stem canker development on winter oilseed rape',\
'(~italic{Brassica napus}) in southern England.',\
'Plant Pathology, 51, 454–463.'); STYLE=meta,plain